![\"](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/Picture3.png?ssl=1\")
The \"sea capital\" of Bulgaria, the city of Varna, hosted a very special occasion during the past week – an international conference marking the 20th anniversary of the LTER-BG network. Over the past two decades, its members have been dedicated to establishing roadmaps and infrastructures for generating, consolidating and sharing ecosystem research data across the Balkan country and beyond.
\n\n\n\nIn celebration of this milestone, members of the wider eLTER community, encompassing the whole of Europe, contributed to a three-day agenda packed with progress updates, innovative showcases and meaningful discussions on the past and future of long-term ecosystem, critical zone and socio-ecological research.
\n\n\n\nPensoft Publishers has served as the communication and dissemination partner for the eLTER Research Infrastructure for the past six years. Pensoft has also always supported the activities of LTER Bulgaria.
\n\n\n\nFor this 20th anniversary conference, all 55 abstracts for oral and poster presentations were organised and published in a special collection titled \"Long-Term Ecosystem Research: Contributions, Challenges and Future Perspectives\" on the ARPHA Conference Abstracts, and for less than a week it has already garnered over 6,000 views.
\n\n\n\n![\"ARPHA](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/Screenshot-2026-10-21-110541.png?ssl=1\")
Impressed by the statements of engagement made by young scientists within the eLTER community, the Pensoft team supported the organisers' idea to provide an Early Career Scientist Award, which granted its recipient a free publication in the One Ecosystem journal.
\n\n\n\nFollowing a unanimous vote by the dedicated jury members Svetla Doncheva, Vesela Evtimova, Elena Todorova and Alexandra Tzvetkova, early career researcher Sabica Naz from the Slovak Academy of Sciences was selected as the winner. She distinguished herself with the presentation \"Impacts of pre-season climatic and functional drivers on the spring onset of phenocam-derived GCC\".
\n\n\n\nAs the official communication partner of eLTER and its affiliated projects, Pensoft provided dissemination materials by eLTER RI at the dedicated booth where attendees also had the opportunity to familiarise themselves with the company's wider publishing and research project portfolio.
\n\n\n\nAt the booth, participants could get acquainted with Pensoft's wider scientific journal portfolio. With One Ecosystem and Nature Conservation covering ecosystem science and conservation practices, NeoBiota focuses on biological invasions and Advances in Pollinator Research dedicated to all things pollinator science. Individual-based Ecology publishes research on individual-level ecological processes while the Biodiversity Data Journal supports the publication of biodiversity data. Alongside these, Research Ideas and Outcomes offers a platform for sharing research across the whole project cycle, from proposals to final results.
\n\n\n\nBeyond these commitments, Pensoft was front and centre within the event's agenda as well.
\n\n\n\n![\"Alexandra](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/MVIMG_20261014_111007-scaled.jpg?ssl=1\")
During the opening panel, Alexandra Tzvetkova, part of the Pensoft team working for eLTER RI, welcomed the participants, reminded them to start sharing the special collection of abstracts with their networks and highlighted the innovative propositions from Pensoft that were about to be presented in the next days and could be very useful for the eLTER community in the future – Scientiana and ORPHO.
\n\n\n\nFurther, two Pensoft presentations were delivered as part of the thematic session \"Emerging Technologies in Ecosystem Research, Data Management and Open Science in LTER\", and brought the audience closer to the publisher's vision for the future:
\n\n\n\nSenior Communications Officer Peter Bozakov delved into the forthcoming science communication platform for research projects Scientiana. Launching in early 2027, it is set to be a portal for consolidating knowledge, mapping out collaborations and innovating outreach in the context of past, present and future scientific initiatives at all scales.
\n\n\n\n![\"Pensoft's](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/image-6.jpeg?ssl=1\")
While, Events and Marketing Coordinator Victoria Stoyanova explored the new frontiers that an AI-FAIR outlook unveils in the domain of academic publishing. Specifically, she showcased the evolution of the ARPHA platform and the newly launched ORPHO, Pensoft's next-gen collaborative writing tool, as examples of innovation placed directly in the hands of authors.
\n\n\n\nTogether, ARPHA and ORPHO support the entire manuscript workflow from submission to publication, with structuring, taxon tagging, classification, and data publication taking place as part of the publication process itself.
\n\n\n\n![\"A](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/image-7.jpeg?ssl=1\")
The presentations proved themselves a stepping stone to further discussions on potential collaborations with scientists, conversations that were bolstered by on-site demonstrations of the tools in question.
\n\n\n\nThe conference in Varna was enjoyable, fruitful and full of hope and esteem for the better future of long-term ecosystem research. And our Pensoft team left with many ideas and an affirmed ambition to keep working to provide better solutions and services for the development of European science. What we will always remember are the words of our host – the national coordinator of LTER Bulgaria in the past 20 years, Svetla Doncheva-Bratanova:
\n\n\n\n\n\n\n\n\nI would like to thank the Pensoft team for the wonderful participation in the conference. You are amazing and I am certain we could do wonders together!
\n
Many thanks to the Bulgarian LTER community and the wider eLTER community for bringing together so many passionate researchers and making these past few days special.
\n\n","doi":"https://doi.org/10.59350/qvd14-6tt55","guid":"https://blog.pensoft.net/?p=21294","image":"https://blog.pensoft.net/wp-content/uploads/2026/10/16_9-Journal-comms-1-1.png","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792713600,"rid":"0nc1r-sp482","summary":"Tweet The \"sea capital\" of Bulgaria, the city of Varna, hosted a very special occasion during the past week \u2013 an international conference marking the 20th anniversary of the LTER-BG network. Over the past two decades, its members have been dedicated to establishing roadmaps and infrastructures for generating, consolidating and sharing ecosystem research data across the Balkan country and beyond.","tags":["Advances In Pollinator Research","ARPHA Publishing Platform","Biodiversity Data Journal","ELTER","Individual-based Ecology"],"title":"Pensoft at the LTER-BG International Scientific Conference 2026","updated_at":1792743313,"url":"https://blog.pensoft.net/2026/10/23/pensoft-comes-together-with-the-elter-community-for-the-lter-bg-international-scientific-conference-2026/","version":"v1"}},{"document":{"authors":[{"affiliation":[{"id":"https://ror.org/0524sp257","name":"University of Bristol"}],"contributor_roles":[],"family":"Taylor","given":"Mike","url":"https://orcid.org/0000-0002-1003-5675"}],"blog":{"authors":[{"name":"Mike Taylor","url":"https://orcid.org/0000-0002-1003-5675"},{"name":"Matt Wedel","url":"https://orcid.org/0000-0001-6082-3103"}],"community_id":"0e13541f-417e-46c0-a859-65927249df72","created":1675209600,"current_feed_url":null,"description":"SV-POW! ... All sauropod vertebrae, except when we're talking about Open Access. ISSN 3033-3695","doi":"https://doi.org/10.59350/svpow","favicon":"https://rogue-scholar.org/api/communities/0e13541f-417e-46c0-a859-65927249df72/logo","feed_format":"application/atom+xml","feed_url":"https://svpow.com/feed/atom/","filter":null,"generator":"WordPress.com","home_page_url":"https://svpow.com","issn":"3033-3695","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"svpow","status":"active","subfield":"1911","title":"Sauropod Vertebra Picture of the Week","updated":1792660591,"use_api":true},"blog_name":"Sauropod Vertebra Picture of the Week","blog_slug":"svpow","content_html":"As you may know, SV-POW! uses the excellent Rogue Scholar service to archive all our posts and to allocate DOIs. There’s plenty more going on at Rogue Scholar, and one of the in-progress initiatives is an attempt to categorize scholarly blog posts. Martin Fenner, who created and maintains Rogue Scholar, has tentatively proposed a simple split into seven categories, and is seeking feedback.
\nHis seven proposed categories are (and here I quote directly):
\nI thought it might be useful to try to categorize the last 40 SV-POW! posts and see where there might be gaps. Here’s what I came up with (in reverse chronological order):
\n(5) — No AI comments. None. No exceptions.
\n(1ish) — Friday's impromptu tortoise rescue
\n(1ish) — Easty the box turtle: both osteophagous and coprophagous
\n(6ish) — BYU's fossil vending machine
\n(4) — Speculative sauropods
\n(6ish) — SV-POW! at 19, and trying to see what's not there
\n(1) — (When) will we find apatosaurines outside of North America?
\n(1ish) — The atlas/axis complex of Apatosaurus louisae CM 3018 in dorsal and lateral views
\n(7) — Horrible Megalosaurus larva tears its way out of Matt's stomach
\n(3) — Documenting Skeletal Mounts
\n(7) — Current status
\n(6ish) — A gentle rebuke, well taken
\n(3) — Wildlife on the Planet Furaha by Gert van Dijk
\n(3) — Andy Frazer's Aquilops, and DinoCon 2026
\n(1ish) — Dogs are experiments in applied genetics
\n(7ish) — My adventures with Tri-bear-atops
\n(1ish) — Genuinely, my all-time favourite image: Mamenchisaurus hochuanensis
\n(3) — Revisiting Aquilops and Pentaceratops at the Sam Noble Museum
\n(1ish) — Where did the One of our Dinosaurs is Missing dinosaur come from?
\n(3) — Curiousiday at the Sam Noble Museum: Sauroposeidon, Apatosaurus, Aquilops, and more
\n(3) — The \"Bizarre Headgear\" exhibit at the Sam Noble Museum is incredible
\n(1ish) — The mystery of the other rearing sauropod of the Egidio Feruglio museum
\n(1ish) — Looking for CC By photos of these rearing sauropod mounts
\n(1ish) — An even earlier life restoration of a sauropod (1885)
\n(1ish) — The Lego Natural History Museum, and the question of scale
\n(6) — Upcoming public talks about dinosaurs at the Sam Noble Oklahoma Museum of Natural History
\n(7ish) — On the evolution of the atlas-axis complex
\n(1ish) — In search of rearing mounted sauropod skeletons
\n(4ish) — The Nazi sauropod \u2014 Giraffatitan (= \"Brachiosaurus\") brancai in 1937
\n(1) — The checklist for new zoological genus and species names is published
\n(1) — Checklist for new zoological genus and species names
\n(1ish) — What was the first life restoration of a sauropod?
\n(1) — Belatedly \u2026 here's DRAFT v4 of the checklist for new zoological genus and species names
\n(2) — Never name a new species of an existing dinosaur genus
\n(1ish) — Stop it, birds, your necks are stupid
\n(1ish) — Yet more raptors with their heads on backwards
\n(2) — Three Four quotes about doing good work
\n(2) — Do it yourself.
\n(1ish) — More raptors with their heads on backwards
\n(3) — New paper: Hart et al. 2025 on neural canal ridges in crocs
Some of these categorizations could be quibbled with, and 40 posts is not a huge sample, but I think there are still two findings worth discussing.
\nFirst, category 1 (Research findings) significantly dominates, with 19 of the 40 posts falling more or less into this category. That’s followed by category 3 (Commentary and peer review) with 7 posts. All seven categories do appear, but there’s only one post in category 5 (Editorial) and only two posts in category 4 (Review).
\nSecond, it’s a bit shocking how many of our posts don’t really seem to fit neatly into any of Martin’s suggested categories. 21 of the 40 posts \u2014 more than half \u2014 I had to qualify with “ish”. For example, is A gentle rebuke, well taken really “Community news”? I put it in that category because Martin’s description includes conference reports in its brief: “The research community and working life: Conference reports, announcements, obituaries, interviews, career advice, lab news, job postings, reflections on teaching.”
\nMartin astutely comments on his tentative categorization:
\n\nIt is no coincidence that the list has seven categories: that is the level of differentiation I can understand, even if means some details are conflated. I hope this posts generates a discussion that refines the list. Not more categories, but potentially different labels or groupings. This starting list helps clarify some questions that I wondered about ever since I started Rogue Scholar.
I think that’s smart, and I don’t want to propose adding more categories. (It really doesn’t take long before such categorizations become too unwieldy to be much use.)
\nBut.
\nIt’s the 15 posts categorized as “1ish” that bother me. Fully 37% of our posts fall squarely into a not-really-research category that is not included among the seven, which I would characterize as “observation”. Calling Stop it, birds, your necks are stupid a research finding is obviously an overreach, yet it seems a less wrong categorization than any of the others.
\nWhat’s more, I think that observations are a great example of what scholarly blogs can be really useful for. You would never be able to get Easty the box turtle: both osteophagous and coprophagous published in a journal, and probably not even onto a preprint server, yet it contains a significant and AFAIK novel observation that is properly part of the scholarly record. I have more than once published blog-posts containing observations primarily so I can then go on to cite them in a more formal paper, e.g. Atlantal ribs of the Carnegie Diplodocus, Moscow and Vienna casts cited in Taylor et al.’s (2025) history of the Carnegie Diplodocus mount.
\nSo my humble suggestion to Martin is this: promote Observation to its own category, and merge two of the others to make space. (Maybe merge Review into Commentary and peer review, for example?)
\nLong live observations!
\n\n
Dear rOpenSci friends, it's time for our monthly news roundup!You can read this post on our blog.Now let's dive into the activity at and around rOpenSci!
Mark Padgham is leaving rOpenSci at the end of October, but his impact on rOpenSci will remain.
Mark joined rOpenSci as a staff member in December 2019 to help us expand software peer review to statistical topics.However, Mark's impact on rOpenSci has gone far beyond this one project.Mark has not only shaped how rOpenSci reviews statistical software, but has also built much of the tooling that supports the peer review processes, and R packages which not only support but also strengthen our community.If you have submitted a package to rOpenSci, reviewed or edited one, you have almost certainly used something Mark made!
Read more about his work in our blog post, and consider joining our farewell celebration on Wednesday, October 28th at 15h00 Europe Central.
Our current 2026-2027 cohort is working on their projects around package development and package peer-review.We celebrated our first cohort meeting (across two different gatherings to accommodate time zones) where participants shared their progress and got feedback from other Champions.
Outreach activities are also under way: Linda Cabrera, assisted by her mentor Luis Verde, conducted her outreach activity by leading a workshop on R Projects with RStudio and GitHub for the Ecuadorian Statistical Society, where she had the opportunity to share information about rOpenSci and our programs with the attendees.
The 2025\u20132026 cohort wrapped up their journey with a closing community call, M\u00e1s All\u00e1 del C\u00f3digo: muestra abierta de los proyectos de nuestros campeon(a|e)s (Beyond the Code: an open showcase of our Champions' Projects).At the call, the Champions presented their final projects, from creating, improving, and reviewing R packages to the outreach work that brought those projects to their communities.They also shared what their projects led to, including scholarships, new collaborations, and professional growth.The recording and subtitles, all in Spanish, have been published.
Several Champions and mentors will join LatinR 2026 in Medell\u00edn, Colombia, to present their work during the program and participate in HackeaR, the hackathon event where we will work on issues, translations, and Pull Requests on base R and on rOpenSci packages and resources.
If you are around, come and join us!
\ud83e\uddec We have made good progress on the migration of Bioconductor to R-Universe infrastructure, see also this presentation by Sean Davis.Among other things, packages from the Bioconductor \"experiment\", \"workflows\" and \"books\" repositories have been added to bioc.r-universe.dev and bioc-release.r-universe.dev.To support this, R-Universe now has a special category of \"data\" packages, which get a higher size limit but are only built and checked on Linux.
\ud83d\ude80 With about 3000 packages, Bioconductor is by far the largest universe, so along the way we made dozens of performance improvements to the frontend and server, making pages and repositories load faster for every universe.Stay tuned for a dedicated blog post on the state of the Bioconductor transition before the end of the year!
We continue to uncover the stories of the people behind rOpenSci.This month, Mauro Lepore tells us about his journey with rOpenSci and shares lessons learned that can be applied beyond our community.
We're also sharing a recap of the synchronous events we held, where we discussed the past, present, and future of rOpenSci with the people who joined us to celebrate these 15 years.
Stay tuned for more rOpenSci's stories.
Read all about coworking!
And remember, you can always cowork independently on work related to R, work on packages that tend to be neglected, or work on what ever you need to get done!
The following three packages recently became a part of our software suite:
ibger, developed by Andr\u00e9 Leite together with Marcos Wasiliew, Hugo Vasconcelos, Carlos Amorim, and Diogo Bezerra: Tidyverse-friendly interface to the Brazilian Institute of Geography and Statistics (IBGE) aggregate data API https://servicodados.ibge.gov.br/api/docs/agregados?versao=3.Query aggregates, variables, localities, periods, and metadata from surveys and censuses conducted by IBGE.It has been reviewed by Allan Quadros and Diana Garc\u00eda-Cort\u00e9s.
rcrisp, developed by Claudiu Forgaci together with Francesco Nattino: Provides tools to automate the morphological delineation of riverside urban areas based on a method introduced in Forgaci (2018) https://doi.org/10.7480/abe.2018.31.Delineation entails the identification of corridor boundaries, segmentation of the corridor, and delineation of the river space using two-dimensional spatial information from street network data and digital elevation data in a projected CRS.The resulting delineation can be used to characterise spatial phenomena that can be related to the river as a central element.It has been reviewed by Mark Padgham and Anatolii Tsyplenkov.
coevolve, developed by Scott Claessens together with Erik Ringen: Fit Bayesian generalized dynamic phylogenetic models using Stan or JAX.The package allows an arbitrary number of variables with different response distributions to coevolve on a phylogenetic tree via an Ornstein-Uhlenbeck evolutionary process, allowing users to assess directionality between coevolving variables.The optional JAX backend enables high-performance sampling with NumPyro and potential GPU acceleration via reticulate.It has been reviewed by Rob Moss and Krzysztof Bartoszek.
Discover more packages, read more about Software Peer Review.
The following sixteen packages have had an update since the last newsletter: coevolve (v1.2.1), ruODK (v1.6.3), pkgcheck (v0.3.4), rcrisp (v1.0.0), pkgstats (v0.2.5), openalexR (v3.1.2), webchem (v2.0.0), ReLTER (V3.1.2), rerddap (v1.3.1), ibger (v0.2.1), rgbif (v3.9.0), rglobi (v0.3.5), lakefetch (v0.1.14), visdat (v0.6.1), weatherOz (v3.0.1), and nlrx (v0.4.6).
There are seventeen recently closed and active submissions and 4 submissions on hold.Issues are at different stages:
Three at '6/approved':
ibger, Access the IBGE Aggregate Data API from R.Submitted by Andre Leite Wanderley.
rcrisp, Automate the Delineation of Urban River Spaces.Submitted by Claudiu Forgaci.(Stats).
coevolve, Fit Bayesian Generalized Dynamic Phylogenetic Models using Stan.Submitted by Scott Claessens.(Stats).
One at '5/awaiting-reviewer(s)-response':
Two at '4/review(s)-in-awaiting-changes':
camtrapReport, Camera-Trap Report Generator.Submitted by Elham Ebrahimi.
nert, Curated Access to TERN Environmental Raster Data.Submitted by Max Moldovan.
Two at '3/reviewer(s)-assigned':
tezr, Access Thesis Metadata from Turkiye's National Thesis Center.Submitted by Emrah Er.
rfastlowess, High-Performance LOWESS Smoothing for R.Submitted by Amir Valizadeh.(Stats).
Two at '2/seeking-reviewer(s)':
corila, Sparse modelling with grouped and correlated features allowing for privileged information.Submitted by Armin Rauschenberger.(Stats).
grumpy, Read NumPy .npy and .npz Files.Submitted by Hugo Gruson.
Seven at '1/editor-checks':
ocean3d, Three-Dimensional Marine Spatial Analysis.Submitted by Jay Matsushiba.
emodnet.wcs, Access EMODnet Web Coverage Service data through R.Submitted by Ma\u00eblle Salmon.
qualtdict, Generate Variable Dictionaries and Labelled Survey Data for.Submitted by lyh970817.
tarpolyglot, Run Python, Julia, Rust, and C++ Inside targets Pipeline Steps.Submitted by Pierre9344.
seasight, Tools for Seasonal Adjustment Diagnostics and Reporting.Submitted by Philipp Wegmueller.(Stats).
OptSurvCutR, Optimal Survival Cut-Point Discovery for Time-to-Event Analysis with OptSurvCutR.Submitted by Payton Yau.(Stats).
HydraR, Stateful Agentic Orchestration for Scientific Reproducibility.Submitted by Ignatius Pang.
Find out more about Software Peer Review and how to get involved.
Celebrating the rOpenSci Community by Mauro Lepore.rOpenSci turns 15 and I've been a part of this community for a good chunk of that time.Here I share some memories and the lessons I learned.Other languages: Celebrando a la comunidad de rOpenSci (es).
Celebrating 15 Years of rOpenSci: Then, Now & Next by Yanina Bellini Saibene, Steffi LaZerte, and Noam Ross.Reflections and ideas shared by participants across the two special gatherings named \"rOpenSci Community Celebration: Then, Now & Next\".
Mark Padgham: Building the Machinery of Software Peer Review by The rOpenSci Team.Mark Padgham is leaving rOpenSci at the end of October, and we want to take this moment to recognize his impact and say thank you for helping to shape rOpenSci.
If you're interested in maintaining any of the R packages below, you might enjoy reading our blog post What Does It Mean to Maintain a Package?.
suppdata, Grabbing SUPPlementary DATA in R.Issue for volunteering.
ghql, GraphQL R client.Issue for volunteering.
Refer to our help wanted page \u2013 before opening a PR, we recommend asking in the issue whether help is still needed.
Some useful information for R package developers.\ud83d\udc40
Jonathan Carroll created and wrote about a package repository that is open to PRs by newbies.It's a playground for learning how to create pull requests.It's also an inspiration for package maintainers who want to encourage new contributors!
\"My target audience for this repository is people who wish they had somewhere to send a real pull request because they don't yet feel comfortable participating in open source software.\"
Did you know about testthat::set_state_inspector()?If you use it by registering some things you don't want to change (environment variables for instance), it is run before and after each test, and reports whether there's any discrepancy in the global state.Here's how it's used in vcr:
![\"ORPHO](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/IMG_7412-1-1-scaled.jpg?resize=840%2C1120\")
![\"Metabarcoding](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/IMG_7414-3-scaled.jpg?resize=840%2C1120\")
![\"Frontiers](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/IMG_7410-3-scaled.jpg?resize=840%2C1120\")
![\"Advances](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/IMG_7409-3-scaled.jpg?resize=840%2C1120\")
![\"Individual-based](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/IMG_7407-3-scaled.jpg?resize=840%2C1120\")
![\"One](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/IMG_7405-3-scaled.jpg?resize=840%2C1120\")
![\"NeoBiota](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/IMG_7404-4-scaled.jpg?resize=840%2C1120\")
testthat::set_state_inspector(\\() { temp_files <- dir(tempdir()) temp_files <- temp_files[!grepl(\"^callr\", temp_files)] temp_files <- temp_files[!grepl(\"^webfakes\", temp_files)] list( temp_files = temp_files, wd_files = dir(), vcr_config = the$config )})Steffi LaZerte noticed the function in Hadley Wickham's and Jenny Bryan's workshop materials that Mauro Lepore shared in our Slack workspace.
just to run a subset of testsSpeaking of tests\u2026 Did you know that testthat's test function have a filter argument to only run tests that match a given string?Etienne Bacher wrote a nice little post about using the just command-line tool to generate aliases for easily running a subset of tests using this filter.
The post also mentions other use cases of just, e.g.\u00a0defining just lint to run Jarl on the current directory.
Are you aware that Git plans to change its content hashing algorithm?Here's a good post by Scott Chacon, the author of the Pro Git book, on why it is important and might be problematic.
Thanks for reading!If you want to get involved with rOpenSci, check out our Contributing Guide.This guide will help direct you to the right place, whether you want to make code contributions, non-code contributions, or contribute in other ways such as through sharing use cases.You can also support our work through donations.
If you haven't subscribed to our newsletter yet, you can do so though our signup form.Until it's time for our next newsletter, you can keep in touch with us through our website, Mastodon, or LinkedIn.See you soon!
","doi":"https://doi.org/10.59350/mq5hp-ema25","guid":"https://doi.org/10.59350/mq5hp-ema25","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792627200,"rid":"y05yf-jyw67","summary":"Dear rOpenSci friends, it's time for our monthly news roundup!You can read this post on our blog.Now let's dive into the activity at and around rOpenSci! \ud83d\udd17rOpenSci HQ \ud83d\udd17Team update: thank you Mark Padgham! Mark Padgham is leaving rOpenSci at the end of October, but his impact on rOpenSci will remain.","tags":["Newsletter"],"title":"rOpenSci News Digest, October 2026","updated_at":1792740610,"url":"https://ropensci.org/blog/2026/10/22/news-october-2026/","version":"v1"}},{"document":{"authors":[{"contributor_roles":[],"family":"Baroncini","given":"Sofia"}],"blog":{"authors":null,"community_id":"be4c775e-c004-4189-8322-25abe1cc96c9","created":1737676800,"current_feed_url":null,"description":"Leibniz Institute of European History (IEG)","doi":null,"favicon":"https://rogue-scholar.org/api/communities/be4c775e-c004-4189-8322-25abe1cc96c9/logo","feed_format":"application/atom+xml","feed_url":"https://dhlab.hypotheses.org/feed/atom/","filter":null,"generator":"WordPress","home_page_url":"https://dhlab.hypotheses.org","issn":null,"language":"deu","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":null,"relative_url":null,"secure":true,"slug":"dhlab","status":"active","subfield":"1202","title":"DH Lab","updated":1792684487,"use_api":true},"blog_name":"DH Lab","blog_slug":"dhlab","content_html":"Everything we can do on a computer is encoded; namely, a sequence of 0-1 bits is associated with symbolic content. This is the core fundamental principle allowing us to do a range of different operations on a computer, from writing a document in Word to viewing an image.
\nIf everything can be encoded through this kind of association, then machines can compute meanings as well. Since the 1950s, the branch of symbolic AI has researched the possibility of doing a detailed description of the world, in the form of concepts and relations, and associating them with logical rules. In this way, a computer could do sophisticated operations, such as inferring knowledge not directly stated in the data. For example, if the data states that Sonia is the sister of Juliette and Alice, and the relation is declared as being transitive, then the system could infer that Juliette and Alice are sisters, too.
\nOne application of this approach is ontologies, in other words, a structured way, processable by computers, of describing a particular domain of knowledge. It identifies the main concepts in that domain and, most importantly, the relationships between them. For example, in a project about works of art, an ontology might define concepts such as Person, Artwork, the Creation Event, Institutions holding the artwork, the Iconography depicted, and so on. In this sense, an ontology does more than provide a list of terms. It provides a shared conceptual framework that helps both humans and computers understand how different pieces of information are connected.
\nFurthermore, an ontology can also state logical rules allowing the system to infer further information, or to check that data is described correctly. For example, in Figure 1, the ontology states that the concept \"Artist\" is a subclass of \"Person\". If, in the dataset, \"Monet\" is described as \"Artist\", the computer, through a reasoner (i.e., a software tool that automatically checks the logical consistency of the ontology and derives new facts from it), can infer that Monet is not only an artist, but also a person. This means that in a dataset in which all people are described according to their profession, and all the professions are stated as a subclass of \"Person\", we can easily retrieve all the people in the dataset although none of them is explicitly described as a person.
\n![\"Figure](\"https://dhlab.hypotheses.org/files/2026/09/Fig1_new-scaled.png\")
A key concept is the distinction between the ontology itself, defining classes or concepts, and data described according to that ontology, representing individuals or instances (see Figure 2). Whereas the first describes how the types of entities relate to each other and represents the domain in abstract terms (e.g., \"Artist\" is a subclass of \"Person\"), the latter contains the actual content (\"Monet\"). In other words, it is similar to the difference between an Excel sheet showing only the column names and the same sheet filled with actual data: the columns give us information about how the data is organized (\"People\"), whereas the rows are the actual individuals (\"Monet\", \"Picasso\", etc.). In ontology development, these are also called \"T-BOX\" and \"A-BOX\". The actual content needs to follow the structure defined in the ontology, as shown in Figure 2.
\nFrom a technical point of view, ontologies are commonly formalized in a specific language, OWL 2 (Web Ontology Language 2), which defines the logical relations among entities, and in the RDF Schema, a light and less expressive vocabulary to define classes, subclasses, and relations. Ontologies can be easily created with Prot\u00e9g\u00e9, an open-source program with a user-friendly interface to create entities and relations and options for saving them in OWL.
\n![\"Figure](\"https://dhlab.hypotheses.org/files/2026/09/Fig2_new.jpg\")
Several languages and applications exist. One of the most common areas of application in the DH sector is in the Semantic Web. Semantic Web is an extension of the hypertext web in which not only web pages, but also concepts are related to each other. URIs are used not only to identify web pages, but also to identify concepts, entities, and relationships. For example, this URI on Wikidata identifies the Mona Lisa painting, and it also states, through the URI indicating the relationship of \"creator\", that it was painted by Leonardo da Vinci, associated with another URI.
\nThe benefits of the Semantic Web and ontologies in general are multiple. They help algorithms to clearly identify concepts and differentiate among them, even if they have the same name (e.g., \"Venus\" as a planet is different from \"Venus\" indicating the deity of love in Greek mythology). As computers can process this information, computational operations are done with semantic data. An example is protein prediction in the field of biology, done through ontologies and Machine Learning.
\nIn the humanities area, ontologies are mainly used as standards to guarantee interoperability between datasets maintained by different institutions in the GLAM (Galleries, Libraries, Archives, Museums) sector. If structured data is described according to the same ontology, data can be integrated and queried together, even though separate datasets are created and maintained by different institutions. In this way, a global, interconnected knowledge graph can be created in a decentralized way. The use of ontologies to describe data is an important component of the creation of Linked (Open) Data, i.e., a network of integrated data described using common, open ontologies. The linked data cloud describes the massive, growing amount of LOD datasets and their interconnections (Figure 3).
\nFollowing these principles, portals offering access to massive amounts of data were created, such as Europeana, the European portal for Cultural Heritage, or Artresearch.net, a knowledge graph integrating data from the art photographic archives of the PHAROS association.
\n![\"Figure](\"https://dhlab.hypotheses.org/files/2026/09/Figure3.png\")
But how to create an ontology? In this blog post, we will take you through an overview of the steps to create an ontology through the concrete example of the development of the Cultural Heritage Interactions Ontology (CHint) (Baroncini & Heuvel, 2026). The aim of the ontology is to represent various types of interactions between material and immaterial cultural heritage (CH) that occur over time and space. In other words, it relates a CH object with 1) ideas and values that are relevant in the context(s) in which the object is located (i.e., a belief system), 2) the function(s) that such objects acquire in different contexts, 3) the evolution of these features over time, 4) their interaction with contextual ephemeral events and immaterial cultural heritage practices, and 5) different aspects of uncertainty related to the reconstruction of past state-of-affairs of the object.
\nBefore getting into details, it is important to underline that there's never a single way to model knowledge. Every model reduces infinite reality by selecting specific features. For example, the floor plan of a building does not render the 3D appearance of the building, nor does a 3D accurate scan record the temperature inside the rooms. Every model follows a specific purpose or research question, and discards a certain amount of information.
\nThe same happens with data modeling. Whereas \"data\" \u2013 literally, something \"given\" from the Latin word datum – is perceived as being something neutral, it always reflects a particular point of view on reality. This is particularly evident when we deal with humanities data. Not only do the branches of study reflect a worldview or way of thinking, but also the information modeled relies on often uncertain, approximate, and incomplete sources, which raise a range of subjective interpretations about the past state of affairs.
\nSeveral methodologies can be used to develop an ontology. Among them, agile and iterative approaches, such as NeOn (Su\u00e1rez-Figueroa et al., 2015), eXtreme Design (Presutti et al., 2009), and SAMOD, are particularly relevant. Instead of modeling the whole ontology at once, the developer divides the domain into smaller areas and adds them iteratively to the main ontology. During the development of CHint, we adopted the SAMOD method (Peroni, 2016) for modular development, with the aid of the Ontology Requirements Specification Document for the initial definition of the characteristics of the overall ontology (Su\u00e1rez-Figueroa et al., 2009). For this reason, we will focus on them in the illustration of the development process.
\nIn the first place, the scope and aim of the project should be defined: what's the aim of the modeling? In which domain? For whom? What questions should the model be able to answer? If a domain expert and a developer are involved, these aspects should be defined together. It is a fundamental phase, as the decisions that are taken in this step shape all the following process.
\nThe set of needs that the model should fulfill to be considered finished is called \"requirements\". Documents such as the Ontology Requirements Specification Document (Su\u00e1rez-Figueroa et al., 2009) are useful for clarifying these characteristics. In SAMOD, however, these requirements are progressively defined and refined through a series of concrete motivating scenarios. Rather than trying to specify the whole ontology from the beginning, each iteration focuses on a specific part of the domain. Following the SAMOD method, domain experts describe a specific motivating scenario, i.e., a small, concrete description of a problem in the domain that needs to be modeled, accompanied by examples. From this scenario, the developing team formulates informal competency questions, namely, questions that the ontology should eventually be able to answer (for example, \"which subjects are represented in Botticelli's Primavera\"?).
\nFor the development of the Cultural Heritage Interactions Ontology, it was set that the ontology aimed to narrow the gap between records about physical cultural heritage objects (e.g., paintings, altarpieces) and manifestations of immaterial culture (e.g., a certain belief, religious events) that regard them over time and space. Such interaction can indeed deeply change the object, resulting in new functions or iconography \u2013 take into account, for example, the religious objects often musealized, appreciated more for their aesthetic value than for their religious function after their decontextualization. The scope of application is the CH sector, and it is intended to be used by digital cultural historians and/or computer scientists interested in developing applications concerning cross-cultural understanding of CH objects. The intended use of the ontology is to \"express in a machine-readable format the complex interactions between contemporary culture and immaterial events, and thoughts that eventually influenced CH objects themselves, their function and/or meaning\" (Baroncini & Heuvel, 2026, p. 14). The technical requirements were an extensive reuse of available ontologies and the formalization in OWL 2. Whereas the document was initially used to set the aim, scope, and use of the ontology, further sections were filled during the following development steps. For example, the definition of the glossary of terms, i.e., keywords relevant to the domain, depended on the theories taken into account for the definition of the domain, illustrated in the following section. Another example is the definition of competency questions, defined in the SAMOD iterations during the development. Furthermore, at this initial stage, we identified a set of requirements the ontology should address, developed in specific scenarios during\u00a0the development steps.
\n\n
![\"Figure](\"https://dhlab.hypotheses.org/files/2026/09/Fig4_new-scaled-e1790177672417.jpg\")
The first important step to take is to think deeply about the domain. Depending on the cases and theories available, two main approaches (or a mix of them) are possible. The first one, top-down, consists of searching for pre-existing domain theories that model the domain and implementing them in the modeling. In this case, the developer adopts a deductive approach, and they move from the theory to the implementation. The second, opposite approach is to induce a general structure from multiple real cases, called bottom-up. For example, if there is a dataset about artworks sold in auctions, we can infer how artworks interact with the auction events and buyers from the data itself, and base the ontology on that rich example.
\nIn the DH domain, ontologies often rely on preexisting theories or modeling patterns to represent the domain at hand. Indeed, domain theories are already a conceptualization of the world proposed by historians, philosophers, and humanists who are or were experts in their fields. For this reason, domain theories can be an invaluable source when formalizing information. Nevertheless, theories may have their limits, as they were not at first created to be a computational model, and they reflect a socioculturally situated worldview, which may be outdated, biased, or limited to a certain culture (e.g., the Western world).
\nOnce the best approach has been identified, according to the available theories or data, it is a good idea to start sketching on a whiteboard or piece of paper how concepts relate to each other. Figure 4 shows the results of a first brainstorming session we had to create the CHint ontology, in which we thought about how the chosen theories could relate to each other. For the development, we have adopted a top-down approach, as we identified relevant theories concerning the evolution of time and space, frames, and the relation of works of art with a belief system.
\nIt is good practice to reuse existing models if they are in line with the aims of the ontology. As one of the main goals of the Semantic Web and Linked Open Data is the integration of different datasets described with a common structure, it is fundamental to identify which standards and existing ontologies can be reused for the task. Usually, standards for each domain exist, providing a backbone of how the concepts are organized in the domain. For the CH domain, the main standard is CIDOC-CRM, a conceptual framework developed and maintained by the International Council of Museums (ICOM), which serves as a structure to model museum data in different areas, from art to maritime CH. It is a good practice to reuse the standards and existing ontologies as much as possible, as they have already solved core modeling issues, making the work of the ontology developer easier and guaranteeing interoperability.
\nIn the CHint development, this means that existing models such as CIDOC-CRM can provide concepts that are relevant to the domain. Reusing these solutions improves interoperability and makes the resulting ontology easier to connect with other datasets.
\nOnce there is an idea of the domain, scope, data, and theories available, the actual modeling can start. As cited above, many methodologies focus on the development of small portions of the ontology. Each iteration should include at least two types of testing: 1) testing the logical consistency of the ontology through a reasoner, and 2) testing the model against real data (A-BOX). This ensures that there are no logical inconsistencies and that the ontology can actually address the real-world scenario taken into account.
\n\n
![\"Figure](\"https://dhlab.hypotheses.org/files/2026/09/Fig5_Samod_new.png\")
As introduced above, the SAMOD method1 divides the ontology into small motivating scenarios to allow agile development and focus on simpler aspects (Figure 5). Each scenario is a textual description of the area of the domain, and it is accompanied by a glossary of terms describing the core terminology of the scenario.
\nFor the development, we've taken into account a specific case study, chosen for its richness, as a concrete example on which the model should be tested, constituting the A-BOX of the ontology. The case concerns the relics of\u00a0 St. Servatius preserved in Maastricht, the Netherlands, which are regularly brought in procession from the 14th century to the present day. For the richness of documentation, the strong relation with the Catholic community, and the frequency with which it interacts with an immaterial cultural manifestation, it was considered a prime example for the development.
\n\n
The module Historical Frame of the CHint ontology was developed in one iteration and had one motivating scenario.
\nWe quote here, as a way of example, one part of the motivating scenario:
\n\nA CH object has one or multiple contexts that are related to it. A context expresses the historical, socio-cultural situation in which an artwork exists. By definition, its delimitation is fuzzy, as it corresponds to a certain culture. It includes several traits of various natures, such as religion, social practice, taste, style, etc. Humans, and experts in art history, history, and so on, identify sets of salient traits for each context. In doing so, they frame reality in the sense of Nelson's theory to abstract such traits. In other words, they create observation frames that isolate from the reality contexts that present unifying traits. In doing so, they create a Historical Frame, which is a portion of the spacetime continuum created to better observe a context that already presents traits of unity. The traits are then collected in Reference Frames, defined according to Minsky's theory, that work as the domain pre-knowledge which is necessary for relating CH objects to their contexts (e.g., placing Raffaello's work in the Italian Renaissance).
\nAn object participates in one or more cultural frames, corresponding to 1) the context of artwork creation, and 2) further contexts the object traverses.
The scenario, indeed, describes the interaction of CH objects with the socio-cultural, immaterial contexts in which they existed \u2013 either at the time of their creation, or in following situations. The glossary included key terms such as historical frame, time, event, etc.
\nFor this scenario, we defined Competency Questions (CQs), questions that data described with the ontology should be able to answer. For this reason, the CQs explicitly refer to the case study:
\nOn the basis of the motivating scenario, glossary, and CQs, the ontology engineer drafts a modelet representing how the concepts relate to each other. The design is first a sketch, which is then rendered in an OWL 2 ontology through programs for ontology editing such as Prot\u00e9g\u00e9. In this stage, the design should take into account existing standards and available modeling patterns, but without explicitly importing them. Figure 6 illustrates the modelet of the Historical Frame motivating scenario illustrated with the Graffoo representation through the program draw.io. Whereas not explicitly introduced in the modelet to lower the complexity of the task at this step, classes and relations of existing ontologies, mainly standards, were taken into account. For example, the class E92 Spacetime-Volume of CIDOC-CRM was already identified as being in line with the concept of historical frame, as it describes a portion of space and time, or the Cultural Phenomenon class of the ICON ontology, representing deep socio-cultural phenomena recognized in artworks.
\n\n
![\"Figure](\"https://dhlab.hypotheses.org/files/2026/09/Fig6_new.png\")
After the creation of the modelet, its logical consistency should be tested through a reasoner, an operation that can be done in Prot\u00e9g\u00e9. If the test doesn't raise any error, then a small dataset of real examples described according to the model (A-BOX) needs to be created, and the logical test repeated. If no errors are raised, the Competency Questions should be translated into real SPARQL queries and performed over the dataset. If the queries give the expected result, we can merge the modelet with the main ontology developed in the previous phases.
\nThe last phase of each iteration is the refactoring, namely, the alignment of the current ontology with existing ones, or replacing classes and relations with equivalent or more appropriate terms from existing models. For example, during the modeling of the modelet, we previously identified the class E92 Spacetime-Volume of CIDOC-CRM as suitable to express the concept of Historical Frame, of which it could be a specification. At this stage, we make this alignment explicit, and we declare the class Historical Frame as a subclass of crm:E92. All the tests should be performed again.
\n\n
![\"Figure](\"https://dhlab.hypotheses.org/files/2026/09/Picture7.png\")
\n
The process should be iterated on all the scenarios until there are no more scenarios to be modeled. At that point, the ontology is ready to be published.
\n\n
After the ontology is developed, it is still important to make it FAIR (Findable, Accessible, Interoperable, Reusable). It is good practice to assign it a permanent URI, publish documentation, and include it in the main indexes of LOD vocabularies.
\nA permanent URI can be assigned through w3id.org, whereas various tools, such as PyLode, can be used to automatically generate the documentation of the ontology from the OWL 2 file.
\nIn the case of CHint, a permanent ID was assigned to the ontology OWL file,\u00a0 the development and documentation, which was\u00a0created through PyLode.
\nFinally, it is highly recommended to use tools such as the Ontology Pitfalls Scanner (OOPS!) and FAIR Ontology Pitfalls Scanner (FOOPS!) to detect errors or missing descriptions (e.g., labels, inverse relations) and fix the ontology accordingly before publishing it.
\nFollowing these steps, it is possible to create a robust ontology, which can address specific domain aspects and be aligned with standards.
\nBaroncini, S., & van den Heuvel, C. (2026). The Historical Framing Problem: Temporal Modeling of Interactions between Tangible and Intangible Cultural Heritage. Semantic Web, 17(4), 1\u201343. https://doi.org/10.1177/22104968261454485
\nPeroni, S. (2016). SAMOD: An agile methodology for the development of ontologies. Proceedings of the 13th OWL: Experiences and Directions Workshop and 5th OWL Reasoner Evaluation Workshop (OWLED-ORE 2016). https://doi.org/10.6084/M9.FIGSHARE.3189769
\nPresutti, V., Daga, E., Gangemi, A., & Blomqvist, E. (2009). eXtreme Design with Content Ontology Design Patterns. Proceedings of the 2009 International Conference on Ontology Patterns, 516, 83\u201397. https://ceur-ws.org/Vol-516/pap21.pdf
\nSu\u00e1rez-Figueroa, M. C., G\u00f3mez-P\u00e9rez, A., & Fern\u00e1ndez-L\u00f3pez, M. (2015). The NeOn Methodology framework: A scenario-based methodology for ontology development. Applied Ontology, 10(2), 107\u2013145. https://doi.org/10.3233/AO-150145
\nSu\u00e1rez-Figueroa, M., Gomez-Perez, A., & Villazon Terrazas, B. (2009). How to Write and Use the Ontology Requirements Specification Document. On the Move to Meaningful Internet Systems: OTM 2009: Confederated International Conferences, CoopIS, DOA, IS, and ODBASE 2009, Vilamoura, Portugal, November 1-6, 2009, Proceedings, 2, 966\u2013982. https://doi.org/10.1007/978-3-642-05151-7_16
\nFeatured image: Sketches by Sofia Baroncini and Charles van den Heuvel to grasp the interaction between artworks and immaterial culture over time and space at the beginning of the development of the CHint Ontology. Copyright of the authors.
\nThe Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Moaaz Khokhar, a PhD Candidate at Ko\u00e7 University, was awarded an OBF Event Fellowship to attend the European Conference on Computational Biology (ECCB 2026).\n![\"Moaaz](\"https://www.open-bio.org/img/2026/2026-10-03-moaaz-presenting-deepalloweb-eccb-2026.jpeg\"/)
I attended the 25th European Conference on Computational Biology in Geneva, held from 31 August to 4 September 2026. I work on predicting allosteric sites in proteins: regions where binding can influence activity elsewhere in the molecule. This makes the relationship between sequence, structure and function a practical problem in my research.
\nI presented a poster on DeepAlloWeb, which builds on DeepAllo by making allosteric pocket prediction accessible through an interactive web server. The method combines a fine-tuned protein language model, ProtBERT-BFD, with structural pocket features extracted using FPocket. The underlying DeepAllo code is available as open-source software under the GPL-3.0 licence, allowing other researchers to inspect, reuse, and extend the method. Sharing the code alongside an accessible web interface supports the open-science values promoted by OBF and helps researchers build on our work. Presenting this work gave me an opportunity to introduce fellow researchers to a tool that could help them prioritise candidate allosteric pockets for further investigation. I also sought constructive feedback to guide the next version of DeepAlloWeb. Developing the tool has led me towards a broader question that shaped my interests at the conference: how much biological meaning can we assign to a model's predictions and the residues it highlights?
\nThe conference programme included Ivet Bahar's Rhapsody-2 talk, which was interested me because it used protein dynamics to help explain mutation effects. For DeepAllo, I could test whether adding those dynamics features improves the ranking of allosteric pockets. Samuele Firmani's RIBEX work gave me another idea. They changed short stretches of protein sequences and checked how the RNA-binding prediction changed. I want to try something similar with DeepAllo: change regions highlighted in its attention maps, then compare the effect on pocket scores with changes in control regions. That would help me check whether the regions we show users actually matter to the prediction.
\nThe ELIXIR programme at ECCB included FAIR data, interoperable resources and research software. For a machine learning project, practical reproducibility involves recording the source structures, label evidence, preprocessing steps, model versions and evaluation splits. Those details determine whether another group can reproduce a result or understand why a method fails on a new protein. Developing DeepAlloWeb has made accessibility a concrete part of my work. A researcher should be able to inspect predicted pockets and residue-level outputs without first reconstructing the entire software environment. I want future work to make the assumptions behind those outputs equally accessible, including the limits of the training data and the meaning of the scores. The source code is available on GitHub.
\nAs a Pakistani researcher based in Turkey, I value support that makes participation in an international research community more accessible. Sharing methods, documentation and practical examples also matters after the conference, particularly for students entering computational biology from a computer science background.
\nMy priority is to develop open-source allosteric prediction methods that can be examined critically at both the model and biological levels. That means evaluating uncertain labels and testing the sensitivity of explanations.
\nI thank the Open Bioinformatics Foundation for awarding me the fellowship in support of my participation and research presentation at ECCB 2026.
\nMoaaz Ur Rehman Azhar Khokhar
\nPhD researcher and KUIS AI Fellow at Ko\u00e7 University
A few weeks ago I was moaning about there being no OpenBanking API for personal use. Thankfully, I was wrong!
\n\nAs pointed out by Dave a company called Nordigen was set up to provide a free Open Banking service. It was quickly bought by GoCardless who said:
\n\n\n\nWe believe access to open banking data should be free. We can now offer it at scale to anyone - developers, partners and Fintechs - looking to solve customer problems.
And, I'm delighted to report, it works! As a solo developer you can get access to your own data for free via the GoCardless APIs.
\n\n![\"Screenshot](\"https://shkspr.mobi/blog/wp-content/uploads/2023/10/gocardless-fs8.png\")
\n\nYou'll get back a JSON file from each of your banks and credit cards with information like this in it:
\n\n{\n \"bookingDate\": \"2023-07-11\",\n \"bookingDateTime\": \"2023-07-11T20:52:05Z\",\n \"transactionAmount\": {\n \"amount\": \"-2.35\",\n \"currency\": \"GBP\"\n },\n \"creditorName\": \"GREGGS PLC\",\n \"remittanceInformationUnstructured\": \"Greggs PLC, London se1\",\n \"merchantCategoryCode\": \"5812\",\n \"internalTransactionId\": \"123456789\"\n}\nFor foreign exchange, transactions look like this:
\n\n{\n \"bookingDate\": \"2023-10-01\",\n \"bookingDateTime\": \"2023-10-01T21:41:40Z\",\n \"transactionAmount\": {\n \"amount\": \"-0.82\",\n \"currency\": \"GBP\"\n },\n \"currencyExchange\": {\n \"instructedAmount\": {\n \"amount\": \"1.00\",\n \"currency\": \"USD\"\n },\n \"sourceCurrency\": \"USD\",\n \"exchangeRate\": \"1.2195\",\n \"targetCurrency\": \"GBP\"\n },\n \"creditorName\": \"KICKSTARTER.COM\",\n \"remittanceInformationUnstructured\": \"Kickstarter.com, Httpswww.kick, 1.0 U.S. DOLLAR USA\",\n \"merchantCategoryCode\": \"5815\",\n \"internalTransactionId\": \"987654321\"\n}\nDepending on your card and the transaction type, you might also get a few more bits of metadata.
\n\nGet started at https://gocardless.com/bank-account-data/. From there, it's a case of following the quickstart guide.
\n\nThere's a bit of bouncing around. You've got to get an API key, get the institution ID, sign in, get redirected, get an ID from the callback, then get the bank account details. And then you can get the transactions!
\n\nOh, and the access token only lasts a short while, so you'll need to either re-auth or use a refresh token.
\n\nBank authorisation only lasts 90 days, so you'll have to refresh your details every 3 months. That's standard across all opening banking, but a bit of a pain.
\n\nGoCardless have pretty comprehensive bank coverage but they are missing a few which you might find useful.
\n\nBecause there are so many financial institution in there, you might find it difficult to work out which one you need to log in to. For example, if you have a Barclays Credit Card, which of these is the right one for you?
\n\n{\n \"id\": \"BARCLAYCARD_COMMERCIAL_BUKBGB22\",\n \"name\": \"Barclaycard Commercial Payments\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYCARD_COMMERCIAL_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYCARD_BUKBGB22\",\n \"name\": \"Barclaycard UK\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYCARD_COMMERCIAL_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYS_BUSINESS_BUKBGB22\",\n \"name\": \"Barclays Business\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYS_WEALTH_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYS_CORPORATE_BUKBGB22\",\n \"name\": \"Barclays Corporate\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYS_WEALTH_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYS_BUKBGB22\",\n \"name\": \"Barclays Personal\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYS_WEALTH_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYS_WEALTH_BUKBGB22\",\n \"name\": \"Barclays Wealth\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYS_WEALTH_BUKBGB22.png\"\n },\nBut, overall, it's an excellent service. Now I just need to find / write something to ingest the data and do something with it!
![](\"https://shkspr.mobi/blog/wp-content/themes/edent-wordpress-theme/info/okgo.php?ID=48443&HTTP_REFERER=DOI\"){kind=small}
","doi":"https://doi.org/10.59350/06y2r-g1f54","guid":"https://shkspr.mobi/blog/?p=48443","image":"https://shkspr.mobi/blog/wp-content/uploads/2023/10/gocardless-fs8.png","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1697932800,"rid":"qs1hr-jfg18","summary":"A few weeks ago I was moaning about there being no OpenBanking API for personal use. Thankfully, I was wrong! As pointed out by Dave a company called Nordigen was set up to provide a free Open Banking service. It was quickly bought by GoCardless who said: We believe access to open banking data should be free.","tags":["/etc/","API","Data","Finance","Money"],"title":"Free Open Banking API using Nordigen / GoCardless","updated_at":1792694538,"url":"https://shkspr.mobi/blog/2023/10/free-open-banking-api-using-nordigen-gocardless/","version":"v1"}},{"document":{"authors":[{"contributor_roles":[],"family":"Friederichs","given":"Hendrik"}],"blog":{"authors":null,"community_id":"304adf51-cbb7-4ff1-a505-1dc06082fbad","created":1776988800,"current_feed_url":null,"description":"Aktuelle Einblicke aus der medizinischen Bildungsforschung \u2014 evidenzbasiert, verst\u00e4ndlich, mit gelegentlichem Augenzwinkern.","doi":"https://doi.org/10.59350/medical_education","favicon":"https://rogue-scholar.org/api/communities/304adf51-cbb7-4ff1-a505-1dc06082fbad/logo","feed_format":"application/rss+xml","feed_url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/blog.xml","filter":null,"generator":"Quarto","home_page_url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/blog.html","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"medical_education","status":"active","subfield":"2739","title":"Entscheiden(d) lernen","updated":1792620000,"use_api":null},"blog_name":"Entscheiden(d) lernen","blog_slug":"medical_education","content_html":"![](\"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-10-22-forschendes-lernen/FriederichsH_forschendes-lernen.png\"/)
Warum offenes Forschen allein wenig bringt, mit kluger Anleitung aber zu den st\u00e4rkeren Lehrformaten geh\u00f6rt. Ein Blick auf die Metaanalysen \u2013 und auf die Frage, wie viel F\u00fchrung gutes Forschen vertr\u00e4gt.
\nMit dem Ruf nach mehr Wissenschaftlichkeit im Medizinstudium r\u00fcckt das Forschende Lernen st\u00e4rker in den Blick. In gewisser Form ist es in der Medizin l\u00e4ngst Alltag, denn viele Studierende beginnen ihre Doktorarbeit schon w\u00e4hrend des Studiums. Ebenso lange steht die studienbegleitende Promotion in der Kritik. Die Reformvorschl\u00e4ge reichen von der Abschaffung des Dr.\u00a0med. bis zur verpflichtenden Forschungsarbeit f\u00fcr alle Studierenden. Unabh\u00e4ngig davon, wie man den wissenschaftlichen Wert solcher Arbeiten einsch\u00e4tzt, lohnt sich die Frage, was das Forschen den Studierenden selbst f\u00fcr ihr Lernen bringt.
\nDie Antwort der Lernforschung wirkt auf den ersten Blick widerspr\u00fcchlich. L\u00e4sst man Lernende v\u00f6llig frei entdecken, schneiden sie schlechter ab als mit klassischer Instruktion (Effektst\u00e4rke d = \u22120,38). Unterst\u00fctzt man sie beim Entdecken gezielt, kehrt sich das Bild um (d = 0,30) [1]. Wer Forschendes Lernen in ein Curriculum bringt, steht also vor einer genaueren Frage als \"daf\u00fcr oder dagegen\", n\u00e4mlich wie viel F\u00fchrung offenes Forschen braucht, damit daraus wirksames Lernen wird.
\nForschendes Lernen hat einen prominenten Gegenspieler. Kirschner, Sweller und Clark argumentierten 2006, minimal angeleitetes Lernen \u00fcberfordere das Arbeitsged\u00e4chtnis \u2013 besonders bei Anf\u00e4ngerinnen und Anf\u00e4ngern [2]. Der Einwand sitzt. Aus meiner Sicht trifft er aber vor allem eine bestimmte Variante, n\u00e4mlich das ungef\u00fchrte Entdecken.
\nDenn die Daten zeigen ein differenzierteres Bild. Die Metaanalyse von Lazonder und Harmsen (72 Studien) belegt, dass Anleitung beim Forschenden Lernen die Lernergebnisse deutlich verbessert (d = 0,50) und die Erfolgsquote bei den Forschungsaufgaben selbst noch st\u00e4rker (d = 0,71) [3]. Entscheidend ist also die Dosierung.
\nF\u00fcr diese Dosierungsfrage gibt es seit ziemlich genau f\u00fcnfzig Jahren einen Begriff. Wood, Bruner und Ross beobachteten beim Tutoring, wie erfolgreiche Lehrende ein \"Bauger\u00fcst\" um eine Aufgabe errichten. Sie dosieren die Komplexit\u00e4t, halten die Aufmerksamkeit auf dem Ziel, markieren das Wesentliche und fangen Frustration ab [4].
\nEntscheidend ist, was Scaffolding von blo\u00dfer Dauerhilfe unterscheidet. Ein Review von van de Pol, Volman und Beishuizen destilliert drei Merkmale:
\nDie Unterst\u00fctzung passt sich diagnostisch dem aktuellen Stand an (Kontingenz),
sie wird systematisch zur\u00fcckgenommen (Fading),
und die Verantwortung geht Schritt f\u00fcr Schritt auf die Lernenden \u00fcber [5].
Ein Ger\u00fcst, das stehen bleibt, ist kein Ger\u00fcst mehr, sondern eine Art Kr\u00fccke \u2013 es erzeugt eher Abh\u00e4ngigkeit als Kompetenz.
\nWie viel Ger\u00fcst Studierende brauchen, h\u00e4ngt vor allem an ihrem Vorwissen. Novizen fehlen die mentalen Schemata \u2013 die geordneten Wissensstrukturen im Langzeitged\u00e4chtnis \u2013, mit denen sich ein offenes Problem gliedern l\u00e4sst. Sie lernen zun\u00e4chst mehr aus durchgearbeiteten L\u00f6sungsbeispielen als aus eigenem Herumprobieren. Mit wachsender Expertise kehrt sich das um. Der \"expertise reversal effect\" zeigt, dass Unterst\u00fctzung, die Anf\u00e4ngern hilft, f\u00fcr Fortgeschrittene \u00fcberfl\u00fcssig oder sogar hinderlich wird [6].
\nUnd dann gibt es noch den scheinbaren Gegenbeweis: Productive Failure. Eine Metaanalyse von Sinha und Kapur (53 Studien) fand, dass Probleml\u00f6sen vor der Instruktion dem umgekehrten Ablauf im Schnitt \u00fcberlegen ist (g = 0,36) [7]. Ein Widerspruch? Eher nicht. Auch Productive Failure ist im Endeffekt hochgradig designt. Die Probleme sind sorgf\u00e4ltig konstruiert, und die anschlie\u00dfende Konsolidierung ist Pflicht. Beides folgt derselben Logik \u2013 die F\u00fchrung wird an das angepasst, was Lernende schon mitbringen.
\nVerglichen mit klassischen Lerntechniken wirkt Forschendes Lernen auf den ersten Blick unspektakul\u00e4r. So erreicht das aktive Abrufen aus dem Ged\u00e4chtnis (Retrieval Practice) in einer gro\u00dfen Metaanalyse mittlere Effektst\u00e4rken um g = 0,5 bis 0,6 [8].
\nNur hinkt dieser Vergleich. Retrieval Practice ist eine Mikrotechnik, Forschendes Lernen ein Makroformat \u2013 die beiden konkurrieren nicht, sie operieren auf verschiedenen Ebenen. Die produktive Lesart ist, die Mikrotechniken in das Format einzubauen. Methodenwissen l\u00e4sst sich quizbasiert konsolidieren, bevor es im Projekt gebraucht wird. Nach meiner Einsch\u00e4tzung macht genau diese Kombination aus einem moderaten ein starkes Format.
\nF\u00fcr Medizinstudierende kommt ein Effekt hinzu, den keine Lerntechnik liefert. Ein systematisches Review mit Metaanalyse zeigt, dass Medizinstudierende mit Forschungserfahrung eine rund dreieinhalbfache Chance haben (Odds Ratio 3,55), sich f\u00fcr Forschung in ihrer sp\u00e4teren Laufbahn zu interessieren. Die Autorinnen und Autoren betonen allerdings, dass Forschungserfahrung ein vorhandenes Interesse eher verst\u00e4rkt, als es neu zu wecken [9]. Zugleich zeigen Daten des deutschen Studierendensurveys aus dem Wintersemester 2009/10 eine L\u00fccke, denn 45 Prozent der Humanmedizin-Studierenden arbeiteten in Forschungsprojekten mit, aber nur 25 Prozent f\u00fchlten sich in ihrer Forschungskompetenz gef\u00f6rdert [10]. Mitmachen allein reicht offenbar nicht \u2013 es braucht das Ger\u00fcst drumherum.
\nPraktisch hei\u00dft das, Forschendes Lernen als Stufenweg zu denken. Plant man ein solches Curriculum, sollte man mit gef\u00fchrten Formaten hoher Struktur beginnen, etwa der angeleiteten Kritik publizierter Studien. Sp\u00e4ter folgt die eigene Methodenwahl bei vorgegebener Frage, am Ende die offene, eigene Forschungsfrage \u2013 mit Betreuung, die sich planvoll zur\u00fcckzieht. Auch bei der eingangs erw\u00e4hnten Promotion w\u00e4re dann weniger zu fragen, ob sie ins Studium geh\u00f6rt, als wie das Ger\u00fcst um sie herum aussieht.
\nTransparenzhinweis:
\n@misc{friederichs2026,\n author = {Friederichs, Hendrik},\n title = {Forschendes Lernen \u2013 bringt das etwas?},\n date = {2026-10-22},\n url = {https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-10-22-forschendes-lernen/},\n langid = {de}\n}\nThis week we've added 'agency pulse' pages for EPA, CDC, and SAMHSA.\nThese visualizations are created from USAspending data using the same methods as our NOAA agency pulse page.
","doi":"https://doi.org/10.59350/b3jgk-skq14","guid":"https://doi.org/10.59350/b3jgk-skq14","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792627200,"rid":"d8303-fad75","summary":"This week we've added 'agency pulse' pages for EPA , CDC , and SAMHSA . These visualizations are created from USAspending data using the same methods as our NOAA agency pulse page.","title":"Now Tracking Grantmaking for EPA, CDC, and SAMHSA","updated_at":1792687505,"url":"https://grantwitness.org/updates/2026-10-22-added-funding-curves","version":"v1"}},{"document":{"authors":[{"contributor_roles":[],"name":"Pensoft Editorial Team"}],"blog":{"authors":null,"community_id":"1e54953c-587a-4743-89af-ebd2cb45660c","created":1789516800,"current_feed_url":null,"description":null,"doi":"https://doi.org/10.59350/pensoft","favicon":"https://rogue-scholar.org/api/communities/1e54953c-587a-4743-89af-ebd2cb45660c/logo","feed_format":"application/atom+xml","feed_url":"https://blog.pensoft.net/feed/atom/","filter":null,"generator":"WordPress","home_page_url":"https://blog.pensoft.net/","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"pensoft","status":"active","subfield":"2303","title":"Pensoft Blog","updated":1792742974,"use_api":true},"blog_name":"Pensoft Blog","blog_slug":"pensoft","content_html":"\n\nFor millennia, people have gathered data and knowledge \u2013 about where to hunt, eat, trade, and live \u2013 and shared it through experiences, stories and songs. Today, we continue to do so by creating and sharing knowledge in order to \"advance human understanding and the common good.\"
\n\n\n\nThis year's International Open Access Week theme, \"The Cost of Knowledge,\" reminds us that sharing knowledge has a price: subscription fees and article processing charges, the time and expertise of authors, reviewers and editors, and the investment and know-how behind user-friendly digital infrastructures.
\n\n\nThe themes echo the ones we looked at during Peer Review Week 2026, where we gave our Editors-in-Chief the chance to share the challenges they face in sustaining the peer review process, from the influx of papers and data to the shortage of researchers willing to review \u2013 you can read what they told us here: https://blog.pensoft.net/2026/09/11/peer-review-week-2026-building-capacity-for-the-long-run/
\n\n\n\n![\"ZooKeys](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/image-3.png?ssl=1\")
At Pensoft, open access has never been an add-on. Founded in 1992 by scientists for scientists, we launched our first journal, ZooKeys, as fully open access in 2008, and it has been open from its very first issue. After all, it has always been our thinking that research can only serve the common good when everyone can read it, use it and build on it. This is why from the very start, we wanted ZooKeys to speed up research and free the exchange of information in taxonomy.
\n\n\n\nThat principle has shaped every journal we have incepted since from PhytoKeys and MycoKeys to Biodiversity Data Journal to more recently launched Natural History Collections and Museomics and Individual-Based Ecology.
\n\n\n\n![\"Research](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/image-2.png?ssl=1\")
In 2025, together with long-term collaborators from the open-science community, we founded the quite revolutionary and unique journal Research Ideas and Outcomes (RIO) with the aim to catalyse the culture change in research communication by publishing ideas, project proposals, data/software management plans and various other outcomes that would typically be lost for the scientific community. The recognition for RIO's approach to scholarly communication came only half a year later when SPARC went on to name an Open Science Innovator.
\n\n\n\n![\"ARPHA](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/Copy-of-International-Open-Access-Week.png?ssl=1\")
Throughout our existence as a publisher all of our journals have been 100% open access. Hosted on our own ARPHA Publishing Platform and operating under CC BY license, all scholarly titles in our portfolio make sure that every article can be read, shared and reused freely while authors retain the copyright to their work.
\n\n\n\nYet, open should also mean fair. Our article processing charges are among the most competitive in the field, and we are transparent about what they cover: we were among the first publishers to share our pricing and services through Plan S's Journal Comparison Service, and publicly provide our Open Access and APC Policies in full compliance with the Plan S requirements. We also work with international consortia to further reduce financial frictions and administrative burden for researchers and their institutions. As of this year, for instance, we've partnered up with Bibsam Consortium to advance open scholarly publishing across Sweden.
\n\n\n\n![\"ARPHA](\"https://i0.wp.com/blog.pensoft.net/wp-content/uploads/2026/10/ARPHA-services-.png?ssl=1\")
Our proprietary ARPHA Publishing Platform offers a full-featured, end-to-end open access publishing and hosting solution, with a suite of connected services built around it.
\n\n\n\nApart from about 100 open-access scholarly journals, ARPHA powers the ARPHA Preprints platform, which seamlessly integrates with journals to let authors make their manuscripts publicly available upon submission; the platform also provides high-quality and technologically advanced open-access publication for conference outputs through ARPHA Proceedings and ARPHA Conference Abstracts. Through Advanced Books, authors and researchers can bring whole open access books to readers in semantically enhanced HTML and PDF formats.
\n\n\n\nMost recently, we launched ORPHO, our next-generation collaborative workspace for scientific writing. Within ORPHO, researchers and authors can enrich their manuscripts semantically, so that their research, as well as underlying data remains FAIR (Findable, Accessible, Interoperable, and Reusable) and AI-ready.
\n\n\n\nTogether, these tools streamline the publication of text and semantically rich data, making openness a natural part of the research workflow rather than an extra step.
\n\n\n\nAlso, along with Plazi, we run the Biodiversity Literature Repository on Zenodo, which gives articles, figures and taxonomic treatments their own DOIs and releases them under CC0, so the data inside publications can be found, cited and reused by platforms such as GBIF.
\n\n\n\nThis is what a publisher built by scientists can offer: a model that treats knowledge as something to be shared, prices that stay open and transparent, and infrastructure that makes research easier to find, reuse and trust.
\n\n\n\n\n\n\n\n\nThroughout our existence as a scholarly publisher and technology provider, Pensoft has always considered it our responsibility to ensure that valuable research outputs are shared efficiently with the world. This gives everyone, everywhere, the opportunity to make sense of and use this knowledge, while giving full credit to the scientists behind it. This is how, in our vision, scientific work and knowledge can achieve optimal impact on society and future research.
\ncomments Iva Boyadzhieva, Head of Journal development and PR at Pensoft.
As this year's Open Access Week puts it:
\n\n\n\n\"Momentum is growing for approaches to treat knowledge as a common good and not a commodity to be mined.\" \u2013 Open Access Week 2026
\n\n\n\nWe believe that momentum is real, and we have seen it grow ever since the first issue of ZooKeys. At Pensoft we are proud to say that we have championed open access in publishing, building the tools, workflows and partnerships that make it work in practice, and we will keep doing so alongside the institutions, funders, editors and researchers who share this commitment.
\n\n\n\nExplore our journals and services at pensoft.net
\n\n","doi":"https://doi.org/10.59350/7xeg8-c9z23","guid":"https://blog.pensoft.net/?p=21383","image":"https://blog.pensoft.net/wp-content/uploads/2026/10/Copy-of-International-Open-Access-Week-1.png","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792540800,"rid":"0jm9r-aaj40","summary":"Tweet For millennia, people have gathered data and knowledge \u2013 about where to hunt, eat, trade, and live \u2013 and shared it through experiences, stories and songs.","tags":["Advanced Books","ARPHA Preprints","ARPHA Publishing Platform","Biodiversity Data Journal","Individual-based Ecology"],"title":"Open Access Week 2026: Why Pensoft Chose Open from the Start","updated_at":1792654210,"url":"https://blog.pensoft.net/2026/10/21/open-access-week-2026-why-pensoft-chose-open-from-the-start/","version":"v1"}},{"document":{"authors":[{"contributor_roles":[],"name":"The rOpenSci Team"}],"blog":{"authors":[{"name":"The rOpenSci Team"}],"community_id":"19c501a7-647b-4a11-9f5e-cf400817cce3","created":1780876800,"current_feed_url":null,"description":"Open Tools and R Packages for Open Science","doi":"https://doi.org/10.59350/ropensci","favicon":"https://rogue-scholar.org/api/communities/19c501a7-647b-4a11-9f5e-cf400817cce3/logo","feed_format":"application/feed+json","feed_url":"https://ropensci.org/blog/index.json","filter":null,"generator":"Hugo","home_page_url":"https://ropensci.org/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"ropensci","status":"active","subfield":"1710","title":"rOpenSci - open tools for open science","updated":1792656480,"use_api":null},"blog_name":"rOpenSci - open tools for open science","blog_slug":"ropensci","content_html":"Mark Padgham is leaving rOpenSci at the end of October, and we want to take this moment to recognize his impact and say thank you for helping to shape rOpenSci.
Mark joined rOpenSci as a staff member in December 2019 to help us expand software peer review to statistical topics.However, Mark's impact on rOpenSci has gone far beyond this one project.Mark has not only shaped how rOpenSci reviews statistical software, but has also built much of the tooling that supports the peer review processes, and R packages which not only support but also strengthen our community.If you have submitted a package to rOpenSci, reviewed or edited one, you have almost certainly used something Mark made!
Mark's most visible contribution is to statistical software peer review.Reviewing a package that implements statistical methods is a different job from reviewing a package that accesses an API.Mark tackled the task of translating what \"good\" means in a statistical package and how a reviewer can assess it.He recruited a new set of editors with the expertise to tackel this work and turned insights into a concrete set of statistical software standards and the guide that accompanies them (rOpenSci Statistical Software Testing and Peer Review Community Call).Mark also built the machinery to go with this new type of review: pkgstats gathers information about a package's structure, helps authors and editors see what a submission contains and how it is organised; srr allows package authors to document their adherence to statistical software standards.
The result of all this work was our first peer-reviewed statistical packages, published in November 2022, and to date we've had over 26 statistical packages go through this review!Anyone who has gone through statistical software review has benefited from the groundwork Mark laid.
Peer review at rOpenSci is a human process, but it runs on a lot of automation, and a good part of that automation is Mark's work.
Mark built and maintained pkgcheck, which runs automated checks on submitted packages, and the GitHub Action that allows anyone to run the same checks on their own repository.pkgcheck uses goodpractice, another package maintained by Mark, that recently rolled out a host of updates and extension.Mark maintained Buffy, the bot behind our chat review system on GitHub, which lets editors assign reviewers, track deadlines and move submissions along with simple comments, and many other pieces of infrastructure that make the whole system work.
In early 2025, Mark became our new Software Review Lead.In this role he was in charge of editorial management, curating the current editorial board and planning its future.Mark helped guide peer-review through new challenges, such as how review should handle AI-assisted contributions, resulting in rOpenSci's first AI policy; or how to deal with large software submissions, resulting in our first group peer review.
Mark's care for rOpenSci goes beyond software.He researched alternatives to GitHub, sharing the results in Beyond GitHub, a thoughtful look at what it would mean for a community like ours to depend less on a single platform.
He has also served on our Code of Conduct committee, work that helps ensure rOpenSci remains a welcoming and safe community.
Mark also builds tools that help the wider R community.The allcontributors package, inspired by the allcontributors project, makes it easy to recognise everyone who contributes to a project, not just those who write code.His work on repometrics explores how to understand the health and activity of software repositories, and his work on deposits looks at how research data and software can be deposited in trusted repositories.
Mark's work has shaped how we review software, support contributors, and build a more reliable and sustainable open science ecosystem.Thank you, Mark, for building so much of the infrastructure and process that we rely on, and for leaving it in a much better shape than you found it.
If you have benefited from Mark's work, reach out to Mark and let him know!You can keep following his work through his website and social media.
","doi":"https://doi.org/10.59350/hbr59-wee08","guid":"https://doi.org/10.59350/hbr59-wee08","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792540800,"rid":"pph7s-cc368","summary":"Mark Padgham is leaving rOpenSci at the end of October, and we want to take this moment to recognize his impact and say thank you for helping to shape rOpenSci.","tags":["Staff","Statistical-software","Software Peer Review"],"title":"Mark Padgham: Building the Machinery of Software Peer Review","updated_at":1792654210,"url":"https://ropensci.org/blog/2026/10/21/mark-building-machinery-software-review/","version":"v1"}}],"items":[{"authors":[{"contributor_roles":[],"name":"Pensoft Editorial Team"}],"blog":{"authors":null,"community_id":"1e54953c-587a-4743-89af-ebd2cb45660c","created":1789516800,"current_feed_url":null,"description":null,"doi":"https://doi.org/10.59350/pensoft","favicon":"https://rogue-scholar.org/api/communities/1e54953c-587a-4743-89af-ebd2cb45660c/logo","feed_format":"application/atom+xml","feed_url":"https://blog.pensoft.net/feed/atom/","filter":null,"generator":"WordPress","home_page_url":"https://blog.pensoft.net/","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"pensoft","status":"active","subfield":"2303","title":"Pensoft Blog","updated":1792742974,"use_api":true},"blog_name":"Pensoft Blog","blog_slug":"pensoft","content_html":"\n\nThe \"sea capital\" of Bulgaria, the city of Varna, hosted a very special occasion during the past week – an international conference marking the 20th anniversary of the LTER-BG network. Over the past two decades, its members have been dedicated to establishing roadmaps and infrastructures for generating, consolidating and sharing ecosystem research data across the Balkan country and beyond.
\n\n\n\nIn celebration of this milestone, members of the wider eLTER community, encompassing the whole of Europe, contributed to a three-day agenda packed with progress updates, innovative showcases and meaningful discussions on the past and future of long-term ecosystem, critical zone and socio-ecological research.
\n\n\n\nPensoft Publishers has served as the communication and dissemination partner for the eLTER Research Infrastructure for the past six years. Pensoft has also always supported the activities of LTER Bulgaria.
\n\n\n\nFor this 20th anniversary conference, all 55 abstracts for oral and poster presentations were organised and published in a special collection titled \"Long-Term Ecosystem Research: Contributions, Challenges and Future Perspectives\" on the ARPHA Conference Abstracts, and for less than a week it has already garnered over 6,000 views.
\n\n\n\nImpressed by the statements of engagement made by young scientists within the eLTER community, the Pensoft team supported the organisers' idea to provide an Early Career Scientist Award, which granted its recipient a free publication in the One Ecosystem journal.
\n\n\n\nFollowing a unanimous vote by the dedicated jury members Svetla Doncheva, Vesela Evtimova, Elena Todorova and Alexandra Tzvetkova, early career researcher Sabica Naz from the Slovak Academy of Sciences was selected as the winner. She distinguished herself with the presentation \"Impacts of pre-season climatic and functional drivers on the spring onset of phenocam-derived GCC\".
\n\n\n\nAs the official communication partner of eLTER and its affiliated projects, Pensoft provided dissemination materials by eLTER RI at the dedicated booth where attendees also had the opportunity to familiarise themselves with the company's wider publishing and research project portfolio.
\n\n\n\nAt the booth, participants could get acquainted with Pensoft's wider scientific journal portfolio. With One Ecosystem and Nature Conservation covering ecosystem science and conservation practices, NeoBiota focuses on biological invasions and Advances in Pollinator Research dedicated to all things pollinator science. Individual-based Ecology publishes research on individual-level ecological processes while the Biodiversity Data Journal supports the publication of biodiversity data. Alongside these, Research Ideas and Outcomes offers a platform for sharing research across the whole project cycle, from proposals to final results.
\n\n\n\nBeyond these commitments, Pensoft was front and centre within the event's agenda as well.
\n\n\n\nDuring the opening panel, Alexandra Tzvetkova, part of the Pensoft team working for eLTER RI, welcomed the participants, reminded them to start sharing the special collection of abstracts with their networks and highlighted the innovative propositions from Pensoft that were about to be presented in the next days and could be very useful for the eLTER community in the future – Scientiana and ORPHO.
\n\n\n\nFurther, two Pensoft presentations were delivered as part of the thematic session \"Emerging Technologies in Ecosystem Research, Data Management and Open Science in LTER\", and brought the audience closer to the publisher's vision for the future:
\n\n\n\nSenior Communications Officer Peter Bozakov delved into the forthcoming science communication platform for research projects Scientiana. Launching in early 2027, it is set to be a portal for consolidating knowledge, mapping out collaborations and innovating outreach in the context of past, present and future scientific initiatives at all scales.
\n\n\n\nWhile, Events and Marketing Coordinator Victoria Stoyanova explored the new frontiers that an AI-FAIR outlook unveils in the domain of academic publishing. Specifically, she showcased the evolution of the ARPHA platform and the newly launched ORPHO, Pensoft's next-gen collaborative writing tool, as examples of innovation placed directly in the hands of authors.
\n\n\n\nTogether, ARPHA and ORPHO support the entire manuscript workflow from submission to publication, with structuring, taxon tagging, classification, and data publication taking place as part of the publication process itself.
\n\n\n\nThe presentations proved themselves a stepping stone to further discussions on potential collaborations with scientists, conversations that were bolstered by on-site demonstrations of the tools in question.
\n\n\n\nThe conference in Varna was enjoyable, fruitful and full of hope and esteem for the better future of long-term ecosystem research. And our Pensoft team left with many ideas and an affirmed ambition to keep working to provide better solutions and services for the development of European science. What we will always remember are the words of our host – the national coordinator of LTER Bulgaria in the past 20 years, Svetla Doncheva-Bratanova:
\n\n\n\n\n\n\n\n\nI would like to thank the Pensoft team for the wonderful participation in the conference. You are amazing and I am certain we could do wonders together!
\n
Many thanks to the Bulgarian LTER community and the wider eLTER community for bringing together so many passionate researchers and making these past few days special.
\n\n","doi":"https://doi.org/10.59350/qvd14-6tt55","guid":"https://blog.pensoft.net/?p=21294","image":"https://blog.pensoft.net/wp-content/uploads/2026/10/16_9-Journal-comms-1-1.png","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792713600,"rid":"0nc1r-sp482","summary":"Tweet The \"sea capital\" of Bulgaria, the city of Varna, hosted a very special occasion during the past week \u2013 an international conference marking the 20th anniversary of the LTER-BG network. Over the past two decades, its members have been dedicated to establishing roadmaps and infrastructures for generating, consolidating and sharing ecosystem research data across the Balkan country and beyond.","tags":["Advances In Pollinator Research","ARPHA Publishing Platform","Biodiversity Data Journal","ELTER","Individual-based Ecology"],"title":"Pensoft at the LTER-BG International Scientific Conference 2026","updated_at":1792743313,"url":"https://blog.pensoft.net/2026/10/23/pensoft-comes-together-with-the-elter-community-for-the-lter-bg-international-scientific-conference-2026/","version":"v1"},{"authors":[{"affiliation":[{"id":"https://ror.org/0524sp257","name":"University of Bristol"}],"contributor_roles":[],"family":"Taylor","given":"Mike","url":"https://orcid.org/0000-0002-1003-5675"}],"blog":{"authors":[{"name":"Mike Taylor","url":"https://orcid.org/0000-0002-1003-5675"},{"name":"Matt Wedel","url":"https://orcid.org/0000-0001-6082-3103"}],"community_id":"0e13541f-417e-46c0-a859-65927249df72","created":1675209600,"current_feed_url":null,"description":"SV-POW! ... All sauropod vertebrae, except when we're talking about Open Access. ISSN 3033-3695","doi":"https://doi.org/10.59350/svpow","favicon":"https://rogue-scholar.org/api/communities/0e13541f-417e-46c0-a859-65927249df72/logo","feed_format":"application/atom+xml","feed_url":"https://svpow.com/feed/atom/","filter":null,"generator":"WordPress.com","home_page_url":"https://svpow.com","issn":"3033-3695","language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"svpow","status":"active","subfield":"1911","title":"Sauropod Vertebra Picture of the Week","updated":1792660591,"use_api":true},"blog_name":"Sauropod Vertebra Picture of the Week","blog_slug":"svpow","content_html":"As you may know, SV-POW! uses the excellent Rogue Scholar service to archive all our posts and to allocate DOIs. There’s plenty more going on at Rogue Scholar, and one of the in-progress initiatives is an attempt to categorize scholarly blog posts. Martin Fenner, who created and maintains Rogue Scholar, has tentatively proposed a simple split into seven categories, and is seeking feedback.
\nHis seven proposed categories are (and here I quote directly):
\nI thought it might be useful to try to categorize the last 40 SV-POW! posts and see where there might be gaps. Here’s what I came up with (in reverse chronological order):
\n(5) — No AI comments. None. No exceptions.
\n(1ish) — Friday's impromptu tortoise rescue
\n(1ish) — Easty the box turtle: both osteophagous and coprophagous
\n(6ish) — BYU's fossil vending machine
\n(4) — Speculative sauropods
\n(6ish) — SV-POW! at 19, and trying to see what's not there
\n(1) — (When) will we find apatosaurines outside of North America?
\n(1ish) — The atlas/axis complex of Apatosaurus louisae CM 3018 in dorsal and lateral views
\n(7) — Horrible Megalosaurus larva tears its way out of Matt's stomach
\n(3) — Documenting Skeletal Mounts
\n(7) — Current status
\n(6ish) — A gentle rebuke, well taken
\n(3) — Wildlife on the Planet Furaha by Gert van Dijk
\n(3) — Andy Frazer's Aquilops, and DinoCon 2026
\n(1ish) — Dogs are experiments in applied genetics
\n(7ish) — My adventures with Tri-bear-atops
\n(1ish) — Genuinely, my all-time favourite image: Mamenchisaurus hochuanensis
\n(3) — Revisiting Aquilops and Pentaceratops at the Sam Noble Museum
\n(1ish) — Where did the One of our Dinosaurs is Missing dinosaur come from?
\n(3) — Curiousiday at the Sam Noble Museum: Sauroposeidon, Apatosaurus, Aquilops, and more
\n(3) — The \"Bizarre Headgear\" exhibit at the Sam Noble Museum is incredible
\n(1ish) — The mystery of the other rearing sauropod of the Egidio Feruglio museum
\n(1ish) — Looking for CC By photos of these rearing sauropod mounts
\n(1ish) — An even earlier life restoration of a sauropod (1885)
\n(1ish) — The Lego Natural History Museum, and the question of scale
\n(6) — Upcoming public talks about dinosaurs at the Sam Noble Oklahoma Museum of Natural History
\n(7ish) — On the evolution of the atlas-axis complex
\n(1ish) — In search of rearing mounted sauropod skeletons
\n(4ish) — The Nazi sauropod \u2014 Giraffatitan (= \"Brachiosaurus\") brancai in 1937
\n(1) — The checklist for new zoological genus and species names is published
\n(1) — Checklist for new zoological genus and species names
\n(1ish) — What was the first life restoration of a sauropod?
\n(1) — Belatedly \u2026 here's DRAFT v4 of the checklist for new zoological genus and species names
\n(2) — Never name a new species of an existing dinosaur genus
\n(1ish) — Stop it, birds, your necks are stupid
\n(1ish) — Yet more raptors with their heads on backwards
\n(2) — Three Four quotes about doing good work
\n(2) — Do it yourself.
\n(1ish) — More raptors with their heads on backwards
\n(3) — New paper: Hart et al. 2025 on neural canal ridges in crocs
Some of these categorizations could be quibbled with, and 40 posts is not a huge sample, but I think there are still two findings worth discussing.
\nFirst, category 1 (Research findings) significantly dominates, with 19 of the 40 posts falling more or less into this category. That’s followed by category 3 (Commentary and peer review) with 7 posts. All seven categories do appear, but there’s only one post in category 5 (Editorial) and only two posts in category 4 (Review).
\nSecond, it’s a bit shocking how many of our posts don’t really seem to fit neatly into any of Martin’s suggested categories. 21 of the 40 posts \u2014 more than half \u2014 I had to qualify with “ish”. For example, is A gentle rebuke, well taken really “Community news”? I put it in that category because Martin’s description includes conference reports in its brief: “The research community and working life: Conference reports, announcements, obituaries, interviews, career advice, lab news, job postings, reflections on teaching.”
\nMartin astutely comments on his tentative categorization:
\n\nIt is no coincidence that the list has seven categories: that is the level of differentiation I can understand, even if means some details are conflated. I hope this posts generates a discussion that refines the list. Not more categories, but potentially different labels or groupings. This starting list helps clarify some questions that I wondered about ever since I started Rogue Scholar.
I think that’s smart, and I don’t want to propose adding more categories. (It really doesn’t take long before such categorizations become too unwieldy to be much use.)
\nBut.
\nIt’s the 15 posts categorized as “1ish” that bother me. Fully 37% of our posts fall squarely into a not-really-research category that is not included among the seven, which I would characterize as “observation”. Calling Stop it, birds, your necks are stupid a research finding is obviously an overreach, yet it seems a less wrong categorization than any of the others.
\nWhat’s more, I think that observations are a great example of what scholarly blogs can be really useful for. You would never be able to get Easty the box turtle: both osteophagous and coprophagous published in a journal, and probably not even onto a preprint server, yet it contains a significant and AFAIK novel observation that is properly part of the scholarly record. I have more than once published blog-posts containing observations primarily so I can then go on to cite them in a more formal paper, e.g. Atlantal ribs of the Carnegie Diplodocus, Moscow and Vienna casts cited in Taylor et al.’s (2025) history of the Carnegie Diplodocus mount.
\nSo my humble suggestion to Martin is this: promote Observation to its own category, and merge two of the others to make space. (Maybe merge Review into Commentary and peer review, for example?)
\nLong live observations!
\n\n
Dear rOpenSci friends, it's time for our monthly news roundup!You can read this post on our blog.Now let's dive into the activity at and around rOpenSci!
Mark Padgham is leaving rOpenSci at the end of October, but his impact on rOpenSci will remain.
Mark joined rOpenSci as a staff member in December 2019 to help us expand software peer review to statistical topics.However, Mark's impact on rOpenSci has gone far beyond this one project.Mark has not only shaped how rOpenSci reviews statistical software, but has also built much of the tooling that supports the peer review processes, and R packages which not only support but also strengthen our community.If you have submitted a package to rOpenSci, reviewed or edited one, you have almost certainly used something Mark made!
Read more about his work in our blog post, and consider joining our farewell celebration on Wednesday, October 28th at 15h00 Europe Central.
Our current 2026-2027 cohort is working on their projects around package development and package peer-review.We celebrated our first cohort meeting (across two different gatherings to accommodate time zones) where participants shared their progress and got feedback from other Champions.
Outreach activities are also under way: Linda Cabrera, assisted by her mentor Luis Verde, conducted her outreach activity by leading a workshop on R Projects with RStudio and GitHub for the Ecuadorian Statistical Society, where she had the opportunity to share information about rOpenSci and our programs with the attendees.
The 2025\u20132026 cohort wrapped up their journey with a closing community call, M\u00e1s All\u00e1 del C\u00f3digo: muestra abierta de los proyectos de nuestros campeon(a|e)s (Beyond the Code: an open showcase of our Champions' Projects).At the call, the Champions presented their final projects, from creating, improving, and reviewing R packages to the outreach work that brought those projects to their communities.They also shared what their projects led to, including scholarships, new collaborations, and professional growth.The recording and subtitles, all in Spanish, have been published.
Several Champions and mentors will join LatinR 2026 in Medell\u00edn, Colombia, to present their work during the program and participate in HackeaR, the hackathon event where we will work on issues, translations, and Pull Requests on base R and on rOpenSci packages and resources.
If you are around, come and join us!
\ud83e\uddec We have made good progress on the migration of Bioconductor to R-Universe infrastructure, see also this presentation by Sean Davis.Among other things, packages from the Bioconductor \"experiment\", \"workflows\" and \"books\" repositories have been added to bioc.r-universe.dev and bioc-release.r-universe.dev.To support this, R-Universe now has a special category of \"data\" packages, which get a higher size limit but are only built and checked on Linux.
\ud83d\ude80 With about 3000 packages, Bioconductor is by far the largest universe, so along the way we made dozens of performance improvements to the frontend and server, making pages and repositories load faster for every universe.Stay tuned for a dedicated blog post on the state of the Bioconductor transition before the end of the year!
We continue to uncover the stories of the people behind rOpenSci.This month, Mauro Lepore tells us about his journey with rOpenSci and shares lessons learned that can be applied beyond our community.
We're also sharing a recap of the synchronous events we held, where we discussed the past, present, and future of rOpenSci with the people who joined us to celebrate these 15 years.
Stay tuned for more rOpenSci's stories.
Read all about coworking!
And remember, you can always cowork independently on work related to R, work on packages that tend to be neglected, or work on what ever you need to get done!
The following three packages recently became a part of our software suite:
ibger, developed by Andr\u00e9 Leite together with Marcos Wasiliew, Hugo Vasconcelos, Carlos Amorim, and Diogo Bezerra: Tidyverse-friendly interface to the Brazilian Institute of Geography and Statistics (IBGE) aggregate data API https://servicodados.ibge.gov.br/api/docs/agregados?versao=3.Query aggregates, variables, localities, periods, and metadata from surveys and censuses conducted by IBGE.It has been reviewed by Allan Quadros and Diana Garc\u00eda-Cort\u00e9s.
rcrisp, developed by Claudiu Forgaci together with Francesco Nattino: Provides tools to automate the morphological delineation of riverside urban areas based on a method introduced in Forgaci (2018) https://doi.org/10.7480/abe.2018.31.Delineation entails the identification of corridor boundaries, segmentation of the corridor, and delineation of the river space using two-dimensional spatial information from street network data and digital elevation data in a projected CRS.The resulting delineation can be used to characterise spatial phenomena that can be related to the river as a central element.It has been reviewed by Mark Padgham and Anatolii Tsyplenkov.
coevolve, developed by Scott Claessens together with Erik Ringen: Fit Bayesian generalized dynamic phylogenetic models using Stan or JAX.The package allows an arbitrary number of variables with different response distributions to coevolve on a phylogenetic tree via an Ornstein-Uhlenbeck evolutionary process, allowing users to assess directionality between coevolving variables.The optional JAX backend enables high-performance sampling with NumPyro and potential GPU acceleration via reticulate.It has been reviewed by Rob Moss and Krzysztof Bartoszek.
Discover more packages, read more about Software Peer Review.
The following sixteen packages have had an update since the last newsletter: coevolve (v1.2.1), ruODK (v1.6.3), pkgcheck (v0.3.4), rcrisp (v1.0.0), pkgstats (v0.2.5), openalexR (v3.1.2), webchem (v2.0.0), ReLTER (V3.1.2), rerddap (v1.3.1), ibger (v0.2.1), rgbif (v3.9.0), rglobi (v0.3.5), lakefetch (v0.1.14), visdat (v0.6.1), weatherOz (v3.0.1), and nlrx (v0.4.6).
There are seventeen recently closed and active submissions and 4 submissions on hold.Issues are at different stages:
Three at '6/approved':
ibger, Access the IBGE Aggregate Data API from R.Submitted by Andre Leite Wanderley.
rcrisp, Automate the Delineation of Urban River Spaces.Submitted by Claudiu Forgaci.(Stats).
coevolve, Fit Bayesian Generalized Dynamic Phylogenetic Models using Stan.Submitted by Scott Claessens.(Stats).
One at '5/awaiting-reviewer(s)-response':
Two at '4/review(s)-in-awaiting-changes':
camtrapReport, Camera-Trap Report Generator.Submitted by Elham Ebrahimi.
nert, Curated Access to TERN Environmental Raster Data.Submitted by Max Moldovan.
Two at '3/reviewer(s)-assigned':
tezr, Access Thesis Metadata from Turkiye's National Thesis Center.Submitted by Emrah Er.
rfastlowess, High-Performance LOWESS Smoothing for R.Submitted by Amir Valizadeh.(Stats).
Two at '2/seeking-reviewer(s)':
corila, Sparse modelling with grouped and correlated features allowing for privileged information.Submitted by Armin Rauschenberger.(Stats).
grumpy, Read NumPy .npy and .npz Files.Submitted by Hugo Gruson.
Seven at '1/editor-checks':
ocean3d, Three-Dimensional Marine Spatial Analysis.Submitted by Jay Matsushiba.
emodnet.wcs, Access EMODnet Web Coverage Service data through R.Submitted by Ma\u00eblle Salmon.
qualtdict, Generate Variable Dictionaries and Labelled Survey Data for.Submitted by lyh970817.
tarpolyglot, Run Python, Julia, Rust, and C++ Inside targets Pipeline Steps.Submitted by Pierre9344.
seasight, Tools for Seasonal Adjustment Diagnostics and Reporting.Submitted by Philipp Wegmueller.(Stats).
OptSurvCutR, Optimal Survival Cut-Point Discovery for Time-to-Event Analysis with OptSurvCutR.Submitted by Payton Yau.(Stats).
HydraR, Stateful Agentic Orchestration for Scientific Reproducibility.Submitted by Ignatius Pang.
Find out more about Software Peer Review and how to get involved.
Celebrating the rOpenSci Community by Mauro Lepore.rOpenSci turns 15 and I've been a part of this community for a good chunk of that time.Here I share some memories and the lessons I learned.Other languages: Celebrando a la comunidad de rOpenSci (es).
Celebrating 15 Years of rOpenSci: Then, Now & Next by Yanina Bellini Saibene, Steffi LaZerte, and Noam Ross.Reflections and ideas shared by participants across the two special gatherings named \"rOpenSci Community Celebration: Then, Now & Next\".
Mark Padgham: Building the Machinery of Software Peer Review by The rOpenSci Team.Mark Padgham is leaving rOpenSci at the end of October, and we want to take this moment to recognize his impact and say thank you for helping to shape rOpenSci.
If you're interested in maintaining any of the R packages below, you might enjoy reading our blog post What Does It Mean to Maintain a Package?.
suppdata, Grabbing SUPPlementary DATA in R.Issue for volunteering.
ghql, GraphQL R client.Issue for volunteering.
Refer to our help wanted page \u2013 before opening a PR, we recommend asking in the issue whether help is still needed.
Some useful information for R package developers.\ud83d\udc40
Jonathan Carroll created and wrote about a package repository that is open to PRs by newbies.It's a playground for learning how to create pull requests.It's also an inspiration for package maintainers who want to encourage new contributors!
\"My target audience for this repository is people who wish they had somewhere to send a real pull request because they don't yet feel comfortable participating in open source software.\"
Did you know about testthat::set_state_inspector()?If you use it by registering some things you don't want to change (environment variables for instance), it is run before and after each test, and reports whether there's any discrepancy in the global state.Here's how it's used in vcr:
testthat::set_state_inspector(\\() { temp_files <- dir(tempdir()) temp_files <- temp_files[!grepl(\"^callr\", temp_files)] temp_files <- temp_files[!grepl(\"^webfakes\", temp_files)] list( temp_files = temp_files, wd_files = dir(), vcr_config = the$config )})Steffi LaZerte noticed the function in Hadley Wickham's and Jenny Bryan's workshop materials that Mauro Lepore shared in our Slack workspace.
just to run a subset of testsSpeaking of tests\u2026 Did you know that testthat's test function have a filter argument to only run tests that match a given string?Etienne Bacher wrote a nice little post about using the just command-line tool to generate aliases for easily running a subset of tests using this filter.
The post also mentions other use cases of just, e.g.\u00a0defining just lint to run Jarl on the current directory.
Are you aware that Git plans to change its content hashing algorithm?Here's a good post by Scott Chacon, the author of the Pro Git book, on why it is important and might be problematic.
Thanks for reading!If you want to get involved with rOpenSci, check out our Contributing Guide.This guide will help direct you to the right place, whether you want to make code contributions, non-code contributions, or contribute in other ways such as through sharing use cases.You can also support our work through donations.
If you haven't subscribed to our newsletter yet, you can do so though our signup form.Until it's time for our next newsletter, you can keep in touch with us through our website, Mastodon, or LinkedIn.See you soon!
","doi":"https://doi.org/10.59350/mq5hp-ema25","guid":"https://doi.org/10.59350/mq5hp-ema25","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792627200,"rid":"y05yf-jyw67","summary":"Dear rOpenSci friends, it's time for our monthly news roundup!You can read this post on our blog.Now let's dive into the activity at and around rOpenSci! \ud83d\udd17rOpenSci HQ \ud83d\udd17Team update: thank you Mark Padgham! Mark Padgham is leaving rOpenSci at the end of October, but his impact on rOpenSci will remain.","tags":["Newsletter"],"title":"rOpenSci News Digest, October 2026","updated_at":1792740610,"url":"https://ropensci.org/blog/2026/10/22/news-october-2026/","version":"v1"},{"authors":[{"contributor_roles":[],"family":"Baroncini","given":"Sofia"}],"blog":{"authors":null,"community_id":"be4c775e-c004-4189-8322-25abe1cc96c9","created":1737676800,"current_feed_url":null,"description":"Leibniz Institute of European History (IEG)","doi":null,"favicon":"https://rogue-scholar.org/api/communities/be4c775e-c004-4189-8322-25abe1cc96c9/logo","feed_format":"application/atom+xml","feed_url":"https://dhlab.hypotheses.org/feed/atom/","filter":null,"generator":"WordPress","home_page_url":"https://dhlab.hypotheses.org","issn":null,"language":"deu","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":null,"relative_url":null,"secure":true,"slug":"dhlab","status":"active","subfield":"1202","title":"DH Lab","updated":1792684487,"use_api":true},"blog_name":"DH Lab","blog_slug":"dhlab","content_html":"Everything we can do on a computer is encoded; namely, a sequence of 0-1 bits is associated with symbolic content. This is the core fundamental principle allowing us to do a range of different operations on a computer, from writing a document in Word to viewing an image.
\nIf everything can be encoded through this kind of association, then machines can compute meanings as well. Since the 1950s, the branch of symbolic AI has researched the possibility of doing a detailed description of the world, in the form of concepts and relations, and associating them with logical rules. In this way, a computer could do sophisticated operations, such as inferring knowledge not directly stated in the data. For example, if the data states that Sonia is the sister of Juliette and Alice, and the relation is declared as being transitive, then the system could infer that Juliette and Alice are sisters, too.
\nOne application of this approach is ontologies, in other words, a structured way, processable by computers, of describing a particular domain of knowledge. It identifies the main concepts in that domain and, most importantly, the relationships between them. For example, in a project about works of art, an ontology might define concepts such as Person, Artwork, the Creation Event, Institutions holding the artwork, the Iconography depicted, and so on. In this sense, an ontology does more than provide a list of terms. It provides a shared conceptual framework that helps both humans and computers understand how different pieces of information are connected.
\nFurthermore, an ontology can also state logical rules allowing the system to infer further information, or to check that data is described correctly. For example, in Figure 1, the ontology states that the concept \"Artist\" is a subclass of \"Person\". If, in the dataset, \"Monet\" is described as \"Artist\", the computer, through a reasoner (i.e., a software tool that automatically checks the logical consistency of the ontology and derives new facts from it), can infer that Monet is not only an artist, but also a person. This means that in a dataset in which all people are described according to their profession, and all the professions are stated as a subclass of \"Person\", we can easily retrieve all the people in the dataset although none of them is explicitly described as a person.
\nA key concept is the distinction between the ontology itself, defining classes or concepts, and data described according to that ontology, representing individuals or instances (see Figure 2). Whereas the first describes how the types of entities relate to each other and represents the domain in abstract terms (e.g., \"Artist\" is a subclass of \"Person\"), the latter contains the actual content (\"Monet\"). In other words, it is similar to the difference between an Excel sheet showing only the column names and the same sheet filled with actual data: the columns give us information about how the data is organized (\"People\"), whereas the rows are the actual individuals (\"Monet\", \"Picasso\", etc.). In ontology development, these are also called \"T-BOX\" and \"A-BOX\". The actual content needs to follow the structure defined in the ontology, as shown in Figure 2.
\nFrom a technical point of view, ontologies are commonly formalized in a specific language, OWL 2 (Web Ontology Language 2), which defines the logical relations among entities, and in the RDF Schema, a light and less expressive vocabulary to define classes, subclasses, and relations. Ontologies can be easily created with Prot\u00e9g\u00e9, an open-source program with a user-friendly interface to create entities and relations and options for saving them in OWL.
\nSeveral languages and applications exist. One of the most common areas of application in the DH sector is in the Semantic Web. Semantic Web is an extension of the hypertext web in which not only web pages, but also concepts are related to each other. URIs are used not only to identify web pages, but also to identify concepts, entities, and relationships. For example, this URI on Wikidata identifies the Mona Lisa painting, and it also states, through the URI indicating the relationship of \"creator\", that it was painted by Leonardo da Vinci, associated with another URI.
\nThe benefits of the Semantic Web and ontologies in general are multiple. They help algorithms to clearly identify concepts and differentiate among them, even if they have the same name (e.g., \"Venus\" as a planet is different from \"Venus\" indicating the deity of love in Greek mythology). As computers can process this information, computational operations are done with semantic data. An example is protein prediction in the field of biology, done through ontologies and Machine Learning.
\nIn the humanities area, ontologies are mainly used as standards to guarantee interoperability between datasets maintained by different institutions in the GLAM (Galleries, Libraries, Archives, Museums) sector. If structured data is described according to the same ontology, data can be integrated and queried together, even though separate datasets are created and maintained by different institutions. In this way, a global, interconnected knowledge graph can be created in a decentralized way. The use of ontologies to describe data is an important component of the creation of Linked (Open) Data, i.e., a network of integrated data described using common, open ontologies. The linked data cloud describes the massive, growing amount of LOD datasets and their interconnections (Figure 3).
\nFollowing these principles, portals offering access to massive amounts of data were created, such as Europeana, the European portal for Cultural Heritage, or Artresearch.net, a knowledge graph integrating data from the art photographic archives of the PHAROS association.
\nBut how to create an ontology? In this blog post, we will take you through an overview of the steps to create an ontology through the concrete example of the development of the Cultural Heritage Interactions Ontology (CHint) (Baroncini & Heuvel, 2026). The aim of the ontology is to represent various types of interactions between material and immaterial cultural heritage (CH) that occur over time and space. In other words, it relates a CH object with 1) ideas and values that are relevant in the context(s) in which the object is located (i.e., a belief system), 2) the function(s) that such objects acquire in different contexts, 3) the evolution of these features over time, 4) their interaction with contextual ephemeral events and immaterial cultural heritage practices, and 5) different aspects of uncertainty related to the reconstruction of past state-of-affairs of the object.
\nBefore getting into details, it is important to underline that there's never a single way to model knowledge. Every model reduces infinite reality by selecting specific features. For example, the floor plan of a building does not render the 3D appearance of the building, nor does a 3D accurate scan record the temperature inside the rooms. Every model follows a specific purpose or research question, and discards a certain amount of information.
\nThe same happens with data modeling. Whereas \"data\" \u2013 literally, something \"given\" from the Latin word datum – is perceived as being something neutral, it always reflects a particular point of view on reality. This is particularly evident when we deal with humanities data. Not only do the branches of study reflect a worldview or way of thinking, but also the information modeled relies on often uncertain, approximate, and incomplete sources, which raise a range of subjective interpretations about the past state of affairs.
\nSeveral methodologies can be used to develop an ontology. Among them, agile and iterative approaches, such as NeOn (Su\u00e1rez-Figueroa et al., 2015), eXtreme Design (Presutti et al., 2009), and SAMOD, are particularly relevant. Instead of modeling the whole ontology at once, the developer divides the domain into smaller areas and adds them iteratively to the main ontology. During the development of CHint, we adopted the SAMOD method (Peroni, 2016) for modular development, with the aid of the Ontology Requirements Specification Document for the initial definition of the characteristics of the overall ontology (Su\u00e1rez-Figueroa et al., 2009). For this reason, we will focus on them in the illustration of the development process.
\nIn the first place, the scope and aim of the project should be defined: what's the aim of the modeling? In which domain? For whom? What questions should the model be able to answer? If a domain expert and a developer are involved, these aspects should be defined together. It is a fundamental phase, as the decisions that are taken in this step shape all the following process.
\nThe set of needs that the model should fulfill to be considered finished is called \"requirements\". Documents such as the Ontology Requirements Specification Document (Su\u00e1rez-Figueroa et al., 2009) are useful for clarifying these characteristics. In SAMOD, however, these requirements are progressively defined and refined through a series of concrete motivating scenarios. Rather than trying to specify the whole ontology from the beginning, each iteration focuses on a specific part of the domain. Following the SAMOD method, domain experts describe a specific motivating scenario, i.e., a small, concrete description of a problem in the domain that needs to be modeled, accompanied by examples. From this scenario, the developing team formulates informal competency questions, namely, questions that the ontology should eventually be able to answer (for example, \"which subjects are represented in Botticelli's Primavera\"?).
\nFor the development of the Cultural Heritage Interactions Ontology, it was set that the ontology aimed to narrow the gap between records about physical cultural heritage objects (e.g., paintings, altarpieces) and manifestations of immaterial culture (e.g., a certain belief, religious events) that regard them over time and space. Such interaction can indeed deeply change the object, resulting in new functions or iconography \u2013 take into account, for example, the religious objects often musealized, appreciated more for their aesthetic value than for their religious function after their decontextualization. The scope of application is the CH sector, and it is intended to be used by digital cultural historians and/or computer scientists interested in developing applications concerning cross-cultural understanding of CH objects. The intended use of the ontology is to \"express in a machine-readable format the complex interactions between contemporary culture and immaterial events, and thoughts that eventually influenced CH objects themselves, their function and/or meaning\" (Baroncini & Heuvel, 2026, p. 14). The technical requirements were an extensive reuse of available ontologies and the formalization in OWL 2. Whereas the document was initially used to set the aim, scope, and use of the ontology, further sections were filled during the following development steps. For example, the definition of the glossary of terms, i.e., keywords relevant to the domain, depended on the theories taken into account for the definition of the domain, illustrated in the following section. Another example is the definition of competency questions, defined in the SAMOD iterations during the development. Furthermore, at this initial stage, we identified a set of requirements the ontology should address, developed in specific scenarios during\u00a0the development steps.
\n\n
The first important step to take is to think deeply about the domain. Depending on the cases and theories available, two main approaches (or a mix of them) are possible. The first one, top-down, consists of searching for pre-existing domain theories that model the domain and implementing them in the modeling. In this case, the developer adopts a deductive approach, and they move from the theory to the implementation. The second, opposite approach is to induce a general structure from multiple real cases, called bottom-up. For example, if there is a dataset about artworks sold in auctions, we can infer how artworks interact with the auction events and buyers from the data itself, and base the ontology on that rich example.
\nIn the DH domain, ontologies often rely on preexisting theories or modeling patterns to represent the domain at hand. Indeed, domain theories are already a conceptualization of the world proposed by historians, philosophers, and humanists who are or were experts in their fields. For this reason, domain theories can be an invaluable source when formalizing information. Nevertheless, theories may have their limits, as they were not at first created to be a computational model, and they reflect a socioculturally situated worldview, which may be outdated, biased, or limited to a certain culture (e.g., the Western world).
\nOnce the best approach has been identified, according to the available theories or data, it is a good idea to start sketching on a whiteboard or piece of paper how concepts relate to each other. Figure 4 shows the results of a first brainstorming session we had to create the CHint ontology, in which we thought about how the chosen theories could relate to each other. For the development, we have adopted a top-down approach, as we identified relevant theories concerning the evolution of time and space, frames, and the relation of works of art with a belief system.
\nIt is good practice to reuse existing models if they are in line with the aims of the ontology. As one of the main goals of the Semantic Web and Linked Open Data is the integration of different datasets described with a common structure, it is fundamental to identify which standards and existing ontologies can be reused for the task. Usually, standards for each domain exist, providing a backbone of how the concepts are organized in the domain. For the CH domain, the main standard is CIDOC-CRM, a conceptual framework developed and maintained by the International Council of Museums (ICOM), which serves as a structure to model museum data in different areas, from art to maritime CH. It is a good practice to reuse the standards and existing ontologies as much as possible, as they have already solved core modeling issues, making the work of the ontology developer easier and guaranteeing interoperability.
\nIn the CHint development, this means that existing models such as CIDOC-CRM can provide concepts that are relevant to the domain. Reusing these solutions improves interoperability and makes the resulting ontology easier to connect with other datasets.
\nOnce there is an idea of the domain, scope, data, and theories available, the actual modeling can start. As cited above, many methodologies focus on the development of small portions of the ontology. Each iteration should include at least two types of testing: 1) testing the logical consistency of the ontology through a reasoner, and 2) testing the model against real data (A-BOX). This ensures that there are no logical inconsistencies and that the ontology can actually address the real-world scenario taken into account.
\n\n
As introduced above, the SAMOD method1 divides the ontology into small motivating scenarios to allow agile development and focus on simpler aspects (Figure 5). Each scenario is a textual description of the area of the domain, and it is accompanied by a glossary of terms describing the core terminology of the scenario.
\nFor the development, we've taken into account a specific case study, chosen for its richness, as a concrete example on which the model should be tested, constituting the A-BOX of the ontology. The case concerns the relics of\u00a0 St. Servatius preserved in Maastricht, the Netherlands, which are regularly brought in procession from the 14th century to the present day. For the richness of documentation, the strong relation with the Catholic community, and the frequency with which it interacts with an immaterial cultural manifestation, it was considered a prime example for the development.
\n\n
The module Historical Frame of the CHint ontology was developed in one iteration and had one motivating scenario.
\nWe quote here, as a way of example, one part of the motivating scenario:
\n\nA CH object has one or multiple contexts that are related to it. A context expresses the historical, socio-cultural situation in which an artwork exists. By definition, its delimitation is fuzzy, as it corresponds to a certain culture. It includes several traits of various natures, such as religion, social practice, taste, style, etc. Humans, and experts in art history, history, and so on, identify sets of salient traits for each context. In doing so, they frame reality in the sense of Nelson's theory to abstract such traits. In other words, they create observation frames that isolate from the reality contexts that present unifying traits. In doing so, they create a Historical Frame, which is a portion of the spacetime continuum created to better observe a context that already presents traits of unity. The traits are then collected in Reference Frames, defined according to Minsky's theory, that work as the domain pre-knowledge which is necessary for relating CH objects to their contexts (e.g., placing Raffaello's work in the Italian Renaissance).
\nAn object participates in one or more cultural frames, corresponding to 1) the context of artwork creation, and 2) further contexts the object traverses.
The scenario, indeed, describes the interaction of CH objects with the socio-cultural, immaterial contexts in which they existed \u2013 either at the time of their creation, or in following situations. The glossary included key terms such as historical frame, time, event, etc.
\nFor this scenario, we defined Competency Questions (CQs), questions that data described with the ontology should be able to answer. For this reason, the CQs explicitly refer to the case study:
\nOn the basis of the motivating scenario, glossary, and CQs, the ontology engineer drafts a modelet representing how the concepts relate to each other. The design is first a sketch, which is then rendered in an OWL 2 ontology through programs for ontology editing such as Prot\u00e9g\u00e9. In this stage, the design should take into account existing standards and available modeling patterns, but without explicitly importing them. Figure 6 illustrates the modelet of the Historical Frame motivating scenario illustrated with the Graffoo representation through the program draw.io. Whereas not explicitly introduced in the modelet to lower the complexity of the task at this step, classes and relations of existing ontologies, mainly standards, were taken into account. For example, the class E92 Spacetime-Volume of CIDOC-CRM was already identified as being in line with the concept of historical frame, as it describes a portion of space and time, or the Cultural Phenomenon class of the ICON ontology, representing deep socio-cultural phenomena recognized in artworks.
\n\n
After the creation of the modelet, its logical consistency should be tested through a reasoner, an operation that can be done in Prot\u00e9g\u00e9. If the test doesn't raise any error, then a small dataset of real examples described according to the model (A-BOX) needs to be created, and the logical test repeated. If no errors are raised, the Competency Questions should be translated into real SPARQL queries and performed over the dataset. If the queries give the expected result, we can merge the modelet with the main ontology developed in the previous phases.
\nThe last phase of each iteration is the refactoring, namely, the alignment of the current ontology with existing ones, or replacing classes and relations with equivalent or more appropriate terms from existing models. For example, during the modeling of the modelet, we previously identified the class E92 Spacetime-Volume of CIDOC-CRM as suitable to express the concept of Historical Frame, of which it could be a specification. At this stage, we make this alignment explicit, and we declare the class Historical Frame as a subclass of crm:E92. All the tests should be performed again.
\n\n
\n
The process should be iterated on all the scenarios until there are no more scenarios to be modeled. At that point, the ontology is ready to be published.
\n\n
After the ontology is developed, it is still important to make it FAIR (Findable, Accessible, Interoperable, Reusable). It is good practice to assign it a permanent URI, publish documentation, and include it in the main indexes of LOD vocabularies.
\nA permanent URI can be assigned through w3id.org, whereas various tools, such as PyLode, can be used to automatically generate the documentation of the ontology from the OWL 2 file.
\nIn the case of CHint, a permanent ID was assigned to the ontology OWL file,\u00a0 the development and documentation, which was\u00a0created through PyLode.
\nFinally, it is highly recommended to use tools such as the Ontology Pitfalls Scanner (OOPS!) and FAIR Ontology Pitfalls Scanner (FOOPS!) to detect errors or missing descriptions (e.g., labels, inverse relations) and fix the ontology accordingly before publishing it.
\nFollowing these steps, it is possible to create a robust ontology, which can address specific domain aspects and be aligned with standards.
\nBaroncini, S., & van den Heuvel, C. (2026). The Historical Framing Problem: Temporal Modeling of Interactions between Tangible and Intangible Cultural Heritage. Semantic Web, 17(4), 1\u201343. https://doi.org/10.1177/22104968261454485
\nPeroni, S. (2016). SAMOD: An agile methodology for the development of ontologies. Proceedings of the 13th OWL: Experiences and Directions Workshop and 5th OWL Reasoner Evaluation Workshop (OWLED-ORE 2016). https://doi.org/10.6084/M9.FIGSHARE.3189769
\nPresutti, V., Daga, E., Gangemi, A., & Blomqvist, E. (2009). eXtreme Design with Content Ontology Design Patterns. Proceedings of the 2009 International Conference on Ontology Patterns, 516, 83\u201397. https://ceur-ws.org/Vol-516/pap21.pdf
\nSu\u00e1rez-Figueroa, M. C., G\u00f3mez-P\u00e9rez, A., & Fern\u00e1ndez-L\u00f3pez, M. (2015). The NeOn Methodology framework: A scenario-based methodology for ontology development. Applied Ontology, 10(2), 107\u2013145. https://doi.org/10.3233/AO-150145
\nSu\u00e1rez-Figueroa, M., Gomez-Perez, A., & Villazon Terrazas, B. (2009). How to Write and Use the Ontology Requirements Specification Document. On the Move to Meaningful Internet Systems: OTM 2009: Confederated International Conferences, CoopIS, DOA, IS, and ODBASE 2009, Vilamoura, Portugal, November 1-6, 2009, Proceedings, 2, 966\u2013982. https://doi.org/10.1007/978-3-642-05151-7_16
\nFeatured image: Sketches by Sofia Baroncini and Charles van den Heuvel to grasp the interaction between artworks and immaterial culture over time and space at the beginning of the development of the CHint Ontology. Copyright of the authors.
\nThe Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Moaaz Khokhar, a PhD Candidate at Ko\u00e7 University, was awarded an OBF Event Fellowship to attend the European Conference on Computational Biology (ECCB 2026).\n
I attended the 25th European Conference on Computational Biology in Geneva, held from 31 August to 4 September 2026. I work on predicting allosteric sites in proteins: regions where binding can influence activity elsewhere in the molecule. This makes the relationship between sequence, structure and function a practical problem in my research.
\nI presented a poster on DeepAlloWeb, which builds on DeepAllo by making allosteric pocket prediction accessible through an interactive web server. The method combines a fine-tuned protein language model, ProtBERT-BFD, with structural pocket features extracted using FPocket. The underlying DeepAllo code is available as open-source software under the GPL-3.0 licence, allowing other researchers to inspect, reuse, and extend the method. Sharing the code alongside an accessible web interface supports the open-science values promoted by OBF and helps researchers build on our work. Presenting this work gave me an opportunity to introduce fellow researchers to a tool that could help them prioritise candidate allosteric pockets for further investigation. I also sought constructive feedback to guide the next version of DeepAlloWeb. Developing the tool has led me towards a broader question that shaped my interests at the conference: how much biological meaning can we assign to a model's predictions and the residues it highlights?
\nThe conference programme included Ivet Bahar's Rhapsody-2 talk, which was interested me because it used protein dynamics to help explain mutation effects. For DeepAllo, I could test whether adding those dynamics features improves the ranking of allosteric pockets. Samuele Firmani's RIBEX work gave me another idea. They changed short stretches of protein sequences and checked how the RNA-binding prediction changed. I want to try something similar with DeepAllo: change regions highlighted in its attention maps, then compare the effect on pocket scores with changes in control regions. That would help me check whether the regions we show users actually matter to the prediction.
\nThe ELIXIR programme at ECCB included FAIR data, interoperable resources and research software. For a machine learning project, practical reproducibility involves recording the source structures, label evidence, preprocessing steps, model versions and evaluation splits. Those details determine whether another group can reproduce a result or understand why a method fails on a new protein. Developing DeepAlloWeb has made accessibility a concrete part of my work. A researcher should be able to inspect predicted pockets and residue-level outputs without first reconstructing the entire software environment. I want future work to make the assumptions behind those outputs equally accessible, including the limits of the training data and the meaning of the scores. The source code is available on GitHub.
\nAs a Pakistani researcher based in Turkey, I value support that makes participation in an international research community more accessible. Sharing methods, documentation and practical examples also matters after the conference, particularly for students entering computational biology from a computer science background.
\nMy priority is to develop open-source allosteric prediction methods that can be examined critically at both the model and biological levels. That means evaluating uncertain labels and testing the sensitivity of explanations.
\nI thank the Open Bioinformatics Foundation for awarding me the fellowship in support of my participation and research presentation at ECCB 2026.
\nMoaaz Ur Rehman Azhar Khokhar
\nPhD researcher and KUIS AI Fellow at Ko\u00e7 University
A few weeks ago I was moaning about there being no OpenBanking API for personal use. Thankfully, I was wrong!
\n\nAs pointed out by Dave a company called Nordigen was set up to provide a free Open Banking service. It was quickly bought by GoCardless who said:
\n\n\n\nWe believe access to open banking data should be free. We can now offer it at scale to anyone - developers, partners and Fintechs - looking to solve customer problems.
And, I'm delighted to report, it works! As a solo developer you can get access to your own data for free via the GoCardless APIs.
\n\n\n\nYou'll get back a JSON file from each of your banks and credit cards with information like this in it:
\n\n{\n \"bookingDate\": \"2023-07-11\",\n \"bookingDateTime\": \"2023-07-11T20:52:05Z\",\n \"transactionAmount\": {\n \"amount\": \"-2.35\",\n \"currency\": \"GBP\"\n },\n \"creditorName\": \"GREGGS PLC\",\n \"remittanceInformationUnstructured\": \"Greggs PLC, London se1\",\n \"merchantCategoryCode\": \"5812\",\n \"internalTransactionId\": \"123456789\"\n}\nFor foreign exchange, transactions look like this:
\n\n{\n \"bookingDate\": \"2023-10-01\",\n \"bookingDateTime\": \"2023-10-01T21:41:40Z\",\n \"transactionAmount\": {\n \"amount\": \"-0.82\",\n \"currency\": \"GBP\"\n },\n \"currencyExchange\": {\n \"instructedAmount\": {\n \"amount\": \"1.00\",\n \"currency\": \"USD\"\n },\n \"sourceCurrency\": \"USD\",\n \"exchangeRate\": \"1.2195\",\n \"targetCurrency\": \"GBP\"\n },\n \"creditorName\": \"KICKSTARTER.COM\",\n \"remittanceInformationUnstructured\": \"Kickstarter.com, Httpswww.kick, 1.0 U.S. DOLLAR USA\",\n \"merchantCategoryCode\": \"5815\",\n \"internalTransactionId\": \"987654321\"\n}\nDepending on your card and the transaction type, you might also get a few more bits of metadata.
\n\nGet started at https://gocardless.com/bank-account-data/. From there, it's a case of following the quickstart guide.
\n\nThere's a bit of bouncing around. You've got to get an API key, get the institution ID, sign in, get redirected, get an ID from the callback, then get the bank account details. And then you can get the transactions!
\n\nOh, and the access token only lasts a short while, so you'll need to either re-auth or use a refresh token.
\n\nBank authorisation only lasts 90 days, so you'll have to refresh your details every 3 months. That's standard across all opening banking, but a bit of a pain.
\n\nGoCardless have pretty comprehensive bank coverage but they are missing a few which you might find useful.
\n\nBecause there are so many financial institution in there, you might find it difficult to work out which one you need to log in to. For example, if you have a Barclays Credit Card, which of these is the right one for you?
\n\n{\n \"id\": \"BARCLAYCARD_COMMERCIAL_BUKBGB22\",\n \"name\": \"Barclaycard Commercial Payments\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYCARD_COMMERCIAL_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYCARD_BUKBGB22\",\n \"name\": \"Barclaycard UK\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYCARD_COMMERCIAL_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYS_BUSINESS_BUKBGB22\",\n \"name\": \"Barclays Business\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYS_WEALTH_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYS_CORPORATE_BUKBGB22\",\n \"name\": \"Barclays Corporate\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYS_WEALTH_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYS_BUKBGB22\",\n \"name\": \"Barclays Personal\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYS_WEALTH_BUKBGB22.png\"\n },\n {\n \"id\": \"BARCLAYS_WEALTH_BUKBGB22\",\n \"name\": \"Barclays Wealth\",\n \"bic\": \"BUKBGB22\",\n \"transaction_total_days\": \"730\",\n \"countries\": [\n \"GB\"\n ],\n \"logo\": \"https://cdn.nordigen.com/ais/BARCLAYS_WEALTH_BUKBGB22.png\"\n },\nBut, overall, it's an excellent service. Now I just need to find / write something to ingest the data and do something with it!
","doi":"https://doi.org/10.59350/06y2r-g1f54","guid":"https://shkspr.mobi/blog/?p=48443","image":"https://shkspr.mobi/blog/wp-content/uploads/2023/10/gocardless-fs8.png","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1697932800,"rid":"qs1hr-jfg18","summary":"A few weeks ago I was moaning about there being no OpenBanking API for personal use. Thankfully, I was wrong! As pointed out by Dave a company called Nordigen was set up to provide a free Open Banking service. It was quickly bought by GoCardless who said: We believe access to open banking data should be free.","tags":["/etc/","API","Data","Finance","Money"],"title":"Free Open Banking API using Nordigen / GoCardless","updated_at":1792694538,"url":"https://shkspr.mobi/blog/2023/10/free-open-banking-api-using-nordigen-gocardless/","version":"v1"},{"authors":[{"contributor_roles":[],"family":"Friederichs","given":"Hendrik"}],"blog":{"authors":null,"community_id":"304adf51-cbb7-4ff1-a505-1dc06082fbad","created":1776988800,"current_feed_url":null,"description":"Aktuelle Einblicke aus der medizinischen Bildungsforschung \u2014 evidenzbasiert, verst\u00e4ndlich, mit gelegentlichem Augenzwinkern.","doi":"https://doi.org/10.59350/medical_education","favicon":"https://rogue-scholar.org/api/communities/304adf51-cbb7-4ff1-a505-1dc06082fbad/logo","feed_format":"application/rss+xml","feed_url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/blog.xml","filter":null,"generator":"Quarto","home_page_url":"https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/blog.html","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"medical_education","status":"active","subfield":"2739","title":"Entscheiden(d) lernen","updated":1792620000,"use_api":null},"blog_name":"Entscheiden(d) lernen","blog_slug":"medical_education","content_html":"
Warum offenes Forschen allein wenig bringt, mit kluger Anleitung aber zu den st\u00e4rkeren Lehrformaten geh\u00f6rt. Ein Blick auf die Metaanalysen \u2013 und auf die Frage, wie viel F\u00fchrung gutes Forschen vertr\u00e4gt.
\nMit dem Ruf nach mehr Wissenschaftlichkeit im Medizinstudium r\u00fcckt das Forschende Lernen st\u00e4rker in den Blick. In gewisser Form ist es in der Medizin l\u00e4ngst Alltag, denn viele Studierende beginnen ihre Doktorarbeit schon w\u00e4hrend des Studiums. Ebenso lange steht die studienbegleitende Promotion in der Kritik. Die Reformvorschl\u00e4ge reichen von der Abschaffung des Dr.\u00a0med. bis zur verpflichtenden Forschungsarbeit f\u00fcr alle Studierenden. Unabh\u00e4ngig davon, wie man den wissenschaftlichen Wert solcher Arbeiten einsch\u00e4tzt, lohnt sich die Frage, was das Forschen den Studierenden selbst f\u00fcr ihr Lernen bringt.
\nDie Antwort der Lernforschung wirkt auf den ersten Blick widerspr\u00fcchlich. L\u00e4sst man Lernende v\u00f6llig frei entdecken, schneiden sie schlechter ab als mit klassischer Instruktion (Effektst\u00e4rke d = \u22120,38). Unterst\u00fctzt man sie beim Entdecken gezielt, kehrt sich das Bild um (d = 0,30) [1]. Wer Forschendes Lernen in ein Curriculum bringt, steht also vor einer genaueren Frage als \"daf\u00fcr oder dagegen\", n\u00e4mlich wie viel F\u00fchrung offenes Forschen braucht, damit daraus wirksames Lernen wird.
\nForschendes Lernen hat einen prominenten Gegenspieler. Kirschner, Sweller und Clark argumentierten 2006, minimal angeleitetes Lernen \u00fcberfordere das Arbeitsged\u00e4chtnis \u2013 besonders bei Anf\u00e4ngerinnen und Anf\u00e4ngern [2]. Der Einwand sitzt. Aus meiner Sicht trifft er aber vor allem eine bestimmte Variante, n\u00e4mlich das ungef\u00fchrte Entdecken.
\nDenn die Daten zeigen ein differenzierteres Bild. Die Metaanalyse von Lazonder und Harmsen (72 Studien) belegt, dass Anleitung beim Forschenden Lernen die Lernergebnisse deutlich verbessert (d = 0,50) und die Erfolgsquote bei den Forschungsaufgaben selbst noch st\u00e4rker (d = 0,71) [3]. Entscheidend ist also die Dosierung.
\nF\u00fcr diese Dosierungsfrage gibt es seit ziemlich genau f\u00fcnfzig Jahren einen Begriff. Wood, Bruner und Ross beobachteten beim Tutoring, wie erfolgreiche Lehrende ein \"Bauger\u00fcst\" um eine Aufgabe errichten. Sie dosieren die Komplexit\u00e4t, halten die Aufmerksamkeit auf dem Ziel, markieren das Wesentliche und fangen Frustration ab [4].
\nEntscheidend ist, was Scaffolding von blo\u00dfer Dauerhilfe unterscheidet. Ein Review von van de Pol, Volman und Beishuizen destilliert drei Merkmale:
\nDie Unterst\u00fctzung passt sich diagnostisch dem aktuellen Stand an (Kontingenz),
sie wird systematisch zur\u00fcckgenommen (Fading),
und die Verantwortung geht Schritt f\u00fcr Schritt auf die Lernenden \u00fcber [5].
Ein Ger\u00fcst, das stehen bleibt, ist kein Ger\u00fcst mehr, sondern eine Art Kr\u00fccke \u2013 es erzeugt eher Abh\u00e4ngigkeit als Kompetenz.
\nWie viel Ger\u00fcst Studierende brauchen, h\u00e4ngt vor allem an ihrem Vorwissen. Novizen fehlen die mentalen Schemata \u2013 die geordneten Wissensstrukturen im Langzeitged\u00e4chtnis \u2013, mit denen sich ein offenes Problem gliedern l\u00e4sst. Sie lernen zun\u00e4chst mehr aus durchgearbeiteten L\u00f6sungsbeispielen als aus eigenem Herumprobieren. Mit wachsender Expertise kehrt sich das um. Der \"expertise reversal effect\" zeigt, dass Unterst\u00fctzung, die Anf\u00e4ngern hilft, f\u00fcr Fortgeschrittene \u00fcberfl\u00fcssig oder sogar hinderlich wird [6].
\nUnd dann gibt es noch den scheinbaren Gegenbeweis: Productive Failure. Eine Metaanalyse von Sinha und Kapur (53 Studien) fand, dass Probleml\u00f6sen vor der Instruktion dem umgekehrten Ablauf im Schnitt \u00fcberlegen ist (g = 0,36) [7]. Ein Widerspruch? Eher nicht. Auch Productive Failure ist im Endeffekt hochgradig designt. Die Probleme sind sorgf\u00e4ltig konstruiert, und die anschlie\u00dfende Konsolidierung ist Pflicht. Beides folgt derselben Logik \u2013 die F\u00fchrung wird an das angepasst, was Lernende schon mitbringen.
\nVerglichen mit klassischen Lerntechniken wirkt Forschendes Lernen auf den ersten Blick unspektakul\u00e4r. So erreicht das aktive Abrufen aus dem Ged\u00e4chtnis (Retrieval Practice) in einer gro\u00dfen Metaanalyse mittlere Effektst\u00e4rken um g = 0,5 bis 0,6 [8].
\nNur hinkt dieser Vergleich. Retrieval Practice ist eine Mikrotechnik, Forschendes Lernen ein Makroformat \u2013 die beiden konkurrieren nicht, sie operieren auf verschiedenen Ebenen. Die produktive Lesart ist, die Mikrotechniken in das Format einzubauen. Methodenwissen l\u00e4sst sich quizbasiert konsolidieren, bevor es im Projekt gebraucht wird. Nach meiner Einsch\u00e4tzung macht genau diese Kombination aus einem moderaten ein starkes Format.
\nF\u00fcr Medizinstudierende kommt ein Effekt hinzu, den keine Lerntechnik liefert. Ein systematisches Review mit Metaanalyse zeigt, dass Medizinstudierende mit Forschungserfahrung eine rund dreieinhalbfache Chance haben (Odds Ratio 3,55), sich f\u00fcr Forschung in ihrer sp\u00e4teren Laufbahn zu interessieren. Die Autorinnen und Autoren betonen allerdings, dass Forschungserfahrung ein vorhandenes Interesse eher verst\u00e4rkt, als es neu zu wecken [9]. Zugleich zeigen Daten des deutschen Studierendensurveys aus dem Wintersemester 2009/10 eine L\u00fccke, denn 45 Prozent der Humanmedizin-Studierenden arbeiteten in Forschungsprojekten mit, aber nur 25 Prozent f\u00fchlten sich in ihrer Forschungskompetenz gef\u00f6rdert [10]. Mitmachen allein reicht offenbar nicht \u2013 es braucht das Ger\u00fcst drumherum.
\nPraktisch hei\u00dft das, Forschendes Lernen als Stufenweg zu denken. Plant man ein solches Curriculum, sollte man mit gef\u00fchrten Formaten hoher Struktur beginnen, etwa der angeleiteten Kritik publizierter Studien. Sp\u00e4ter folgt die eigene Methodenwahl bei vorgegebener Frage, am Ende die offene, eigene Forschungsfrage \u2013 mit Betreuung, die sich planvoll zur\u00fcckzieht. Auch bei der eingangs erw\u00e4hnten Promotion w\u00e4re dann weniger zu fragen, ob sie ins Studium geh\u00f6rt, als wie das Ger\u00fcst um sie herum aussieht.
\nTransparenzhinweis:
\n@misc{friederichs2026,\n author = {Friederichs, Hendrik},\n title = {Forschendes Lernen \u2013 bringt das etwas?},\n date = {2026-10-22},\n url = {https://medical-education.pages.ub.uni-bielefeld.de/research/mes-blog/posts/2026-10-22-forschendes-lernen/},\n langid = {de}\n}\nThis week we've added 'agency pulse' pages for EPA, CDC, and SAMHSA.\nThese visualizations are created from USAspending data using the same methods as our NOAA agency pulse page.
","doi":"https://doi.org/10.59350/b3jgk-skq14","guid":"https://doi.org/10.59350/b3jgk-skq14","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792627200,"rid":"d8303-fad75","summary":"This week we've added 'agency pulse' pages for EPA , CDC , and SAMHSA . These visualizations are created from USAspending data using the same methods as our NOAA agency pulse page.","title":"Now Tracking Grantmaking for EPA, CDC, and SAMHSA","updated_at":1792687505,"url":"https://grantwitness.org/updates/2026-10-22-added-funding-curves","version":"v1"},{"authors":[{"contributor_roles":[],"name":"Pensoft Editorial Team"}],"blog":{"authors":null,"community_id":"1e54953c-587a-4743-89af-ebd2cb45660c","created":1789516800,"current_feed_url":null,"description":null,"doi":"https://doi.org/10.59350/pensoft","favicon":"https://rogue-scholar.org/api/communities/1e54953c-587a-4743-89af-ebd2cb45660c/logo","feed_format":"application/atom+xml","feed_url":"https://blog.pensoft.net/feed/atom/","filter":null,"generator":"WordPress","home_page_url":"https://blog.pensoft.net/","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"pensoft","status":"active","subfield":"2303","title":"Pensoft Blog","updated":1792742974,"use_api":true},"blog_name":"Pensoft Blog","blog_slug":"pensoft","content_html":"\n\nFor millennia, people have gathered data and knowledge \u2013 about where to hunt, eat, trade, and live \u2013 and shared it through experiences, stories and songs. Today, we continue to do so by creating and sharing knowledge in order to \"advance human understanding and the common good.\"
\n\n\n\nThis year's International Open Access Week theme, \"The Cost of Knowledge,\" reminds us that sharing knowledge has a price: subscription fees and article processing charges, the time and expertise of authors, reviewers and editors, and the investment and know-how behind user-friendly digital infrastructures.
\n\n\nThe themes echo the ones we looked at during Peer Review Week 2026, where we gave our Editors-in-Chief the chance to share the challenges they face in sustaining the peer review process, from the influx of papers and data to the shortage of researchers willing to review \u2013 you can read what they told us here: https://blog.pensoft.net/2026/09/11/peer-review-week-2026-building-capacity-for-the-long-run/
\n\n\n\nAt Pensoft, open access has never been an add-on. Founded in 1992 by scientists for scientists, we launched our first journal, ZooKeys, as fully open access in 2008, and it has been open from its very first issue. After all, it has always been our thinking that research can only serve the common good when everyone can read it, use it and build on it. This is why from the very start, we wanted ZooKeys to speed up research and free the exchange of information in taxonomy.
\n\n\n\nThat principle has shaped every journal we have incepted since from PhytoKeys and MycoKeys to Biodiversity Data Journal to more recently launched Natural History Collections and Museomics and Individual-Based Ecology.
\n\n\n\nIn 2025, together with long-term collaborators from the open-science community, we founded the quite revolutionary and unique journal Research Ideas and Outcomes (RIO) with the aim to catalyse the culture change in research communication by publishing ideas, project proposals, data/software management plans and various other outcomes that would typically be lost for the scientific community. The recognition for RIO's approach to scholarly communication came only half a year later when SPARC went on to name an Open Science Innovator.
\n\n\n\nThroughout our existence as a publisher all of our journals have been 100% open access. Hosted on our own ARPHA Publishing Platform and operating under CC BY license, all scholarly titles in our portfolio make sure that every article can be read, shared and reused freely while authors retain the copyright to their work.
\n\n\n\nYet, open should also mean fair. Our article processing charges are among the most competitive in the field, and we are transparent about what they cover: we were among the first publishers to share our pricing and services through Plan S's Journal Comparison Service, and publicly provide our Open Access and APC Policies in full compliance with the Plan S requirements. We also work with international consortia to further reduce financial frictions and administrative burden for researchers and their institutions. As of this year, for instance, we've partnered up with Bibsam Consortium to advance open scholarly publishing across Sweden.
\n\n\n\nOur proprietary ARPHA Publishing Platform offers a full-featured, end-to-end open access publishing and hosting solution, with a suite of connected services built around it.
\n\n\n\nApart from about 100 open-access scholarly journals, ARPHA powers the ARPHA Preprints platform, which seamlessly integrates with journals to let authors make their manuscripts publicly available upon submission; the platform also provides high-quality and technologically advanced open-access publication for conference outputs through ARPHA Proceedings and ARPHA Conference Abstracts. Through Advanced Books, authors and researchers can bring whole open access books to readers in semantically enhanced HTML and PDF formats.
\n\n\n\nMost recently, we launched ORPHO, our next-generation collaborative workspace for scientific writing. Within ORPHO, researchers and authors can enrich their manuscripts semantically, so that their research, as well as underlying data remains FAIR (Findable, Accessible, Interoperable, and Reusable) and AI-ready.
\n\n\n\nTogether, these tools streamline the publication of text and semantically rich data, making openness a natural part of the research workflow rather than an extra step.
\n\n\n\nAlso, along with Plazi, we run the Biodiversity Literature Repository on Zenodo, which gives articles, figures and taxonomic treatments their own DOIs and releases them under CC0, so the data inside publications can be found, cited and reused by platforms such as GBIF.
\n\n\n\nThis is what a publisher built by scientists can offer: a model that treats knowledge as something to be shared, prices that stay open and transparent, and infrastructure that makes research easier to find, reuse and trust.
\n\n\n\n\n\n\n\n\nThroughout our existence as a scholarly publisher and technology provider, Pensoft has always considered it our responsibility to ensure that valuable research outputs are shared efficiently with the world. This gives everyone, everywhere, the opportunity to make sense of and use this knowledge, while giving full credit to the scientists behind it. This is how, in our vision, scientific work and knowledge can achieve optimal impact on society and future research.
\ncomments Iva Boyadzhieva, Head of Journal development and PR at Pensoft.
As this year's Open Access Week puts it:
\n\n\n\n\"Momentum is growing for approaches to treat knowledge as a common good and not a commodity to be mined.\" \u2013 Open Access Week 2026
\n\n\n\nWe believe that momentum is real, and we have seen it grow ever since the first issue of ZooKeys. At Pensoft we are proud to say that we have championed open access in publishing, building the tools, workflows and partnerships that make it work in practice, and we will keep doing so alongside the institutions, funders, editors and researchers who share this commitment.
\n\n\n\nExplore our journals and services at pensoft.net
\n\n","doi":"https://doi.org/10.59350/7xeg8-c9z23","guid":"https://blog.pensoft.net/?p=21383","image":"https://blog.pensoft.net/wp-content/uploads/2026/10/Copy-of-International-Open-Access-Week-1.png","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792540800,"rid":"0jm9r-aaj40","summary":"Tweet For millennia, people have gathered data and knowledge \u2013 about where to hunt, eat, trade, and live \u2013 and shared it through experiences, stories and songs.","tags":["Advanced Books","ARPHA Preprints","ARPHA Publishing Platform","Biodiversity Data Journal","Individual-based Ecology"],"title":"Open Access Week 2026: Why Pensoft Chose Open from the Start","updated_at":1792654210,"url":"https://blog.pensoft.net/2026/10/21/open-access-week-2026-why-pensoft-chose-open-from-the-start/","version":"v1"},{"authors":[{"contributor_roles":[],"name":"The rOpenSci Team"}],"blog":{"authors":[{"name":"The rOpenSci Team"}],"community_id":"19c501a7-647b-4a11-9f5e-cf400817cce3","created":1780876800,"current_feed_url":null,"description":"Open Tools and R Packages for Open Science","doi":"https://doi.org/10.59350/ropensci","favicon":"https://rogue-scholar.org/api/communities/19c501a7-647b-4a11-9f5e-cf400817cce3/logo","feed_format":"application/feed+json","feed_url":"https://ropensci.org/blog/index.json","filter":null,"generator":"Hugo","home_page_url":"https://ropensci.org/blog","issn":null,"language":"eng","license":"https://creativecommons.org/licenses/by/4.0/legalcode","prefix":"10.59350","relative_url":null,"secure":true,"slug":"ropensci","status":"active","subfield":"1710","title":"rOpenSci - open tools for open science","updated":1792656480,"use_api":null},"blog_name":"rOpenSci - open tools for open science","blog_slug":"ropensci","content_html":"Mark Padgham is leaving rOpenSci at the end of October, and we want to take this moment to recognize his impact and say thank you for helping to shape rOpenSci.
Mark joined rOpenSci as a staff member in December 2019 to help us expand software peer review to statistical topics.However, Mark's impact on rOpenSci has gone far beyond this one project.Mark has not only shaped how rOpenSci reviews statistical software, but has also built much of the tooling that supports the peer review processes, and R packages which not only support but also strengthen our community.If you have submitted a package to rOpenSci, reviewed or edited one, you have almost certainly used something Mark made!
Mark's most visible contribution is to statistical software peer review.Reviewing a package that implements statistical methods is a different job from reviewing a package that accesses an API.Mark tackled the task of translating what \"good\" means in a statistical package and how a reviewer can assess it.He recruited a new set of editors with the expertise to tackel this work and turned insights into a concrete set of statistical software standards and the guide that accompanies them (rOpenSci Statistical Software Testing and Peer Review Community Call).Mark also built the machinery to go with this new type of review: pkgstats gathers information about a package's structure, helps authors and editors see what a submission contains and how it is organised; srr allows package authors to document their adherence to statistical software standards.
The result of all this work was our first peer-reviewed statistical packages, published in November 2022, and to date we've had over 26 statistical packages go through this review!Anyone who has gone through statistical software review has benefited from the groundwork Mark laid.
Peer review at rOpenSci is a human process, but it runs on a lot of automation, and a good part of that automation is Mark's work.
Mark built and maintained pkgcheck, which runs automated checks on submitted packages, and the GitHub Action that allows anyone to run the same checks on their own repository.pkgcheck uses goodpractice, another package maintained by Mark, that recently rolled out a host of updates and extension.Mark maintained Buffy, the bot behind our chat review system on GitHub, which lets editors assign reviewers, track deadlines and move submissions along with simple comments, and many other pieces of infrastructure that make the whole system work.
In early 2025, Mark became our new Software Review Lead.In this role he was in charge of editorial management, curating the current editorial board and planning its future.Mark helped guide peer-review through new challenges, such as how review should handle AI-assisted contributions, resulting in rOpenSci's first AI policy; or how to deal with large software submissions, resulting in our first group peer review.
Mark's care for rOpenSci goes beyond software.He researched alternatives to GitHub, sharing the results in Beyond GitHub, a thoughtful look at what it would mean for a community like ours to depend less on a single platform.
He has also served on our Code of Conduct committee, work that helps ensure rOpenSci remains a welcoming and safe community.
Mark also builds tools that help the wider R community.The allcontributors package, inspired by the allcontributors project, makes it easy to recognise everyone who contributes to a project, not just those who write code.His work on repometrics explores how to understand the health and activity of software repositories, and his work on deposits looks at how research data and software can be deposited in trusted repositories.
Mark's work has shaped how we review software, support contributors, and build a more reliable and sustainable open science ecosystem.Thank you, Mark, for building so much of the infrastructure and process that we rely on, and for leaving it in a much better shape than you found it.
If you have benefited from Mark's work, reach out to Mark and let him know!You can keep following his work through his website and social media.
","doi":"https://doi.org/10.59350/hbr59-wee08","guid":"https://doi.org/10.59350/hbr59-wee08","language":"en","license":"https://creativecommons.org/licenses/by/4.0/legalcode","published_at":1792540800,"rid":"pph7s-cc368","summary":"Mark Padgham is leaving rOpenSci at the end of October, and we want to take this moment to recognize his impact and say thank you for helping to shape rOpenSci.","tags":["Staff","Statistical-software","Software Peer Review"],"title":"Mark Padgham: Building the Machinery of Software Peer Review","updated_at":1792654210,"url":"https://ropensci.org/blog/2026/10/21/mark-building-machinery-software-review/","version":"v1"}],"out_of":57848,"page":1,"per_page":10,"total-results":57848}