--- author: - contributor_roles: [] family: Edmunds given: Scott url: https://orcid.org/0000-0001-6444-1436 blog: authors: null community_id: 52db0518-e228-4260-8c54-c4e323b2569d created: 1675555200 current_feed_url: null description: Data driven blogging from the GigaScience editors doi: https://doi.org/10.59350/gigablog favicon: https://rogue-scholar.org/api/communities/52db0518-e228-4260-8c54-c4e323b2569d/logo feed_format: application/atom+xml feed_url: http://gigasciencejournal.com/blog/feed/atom/ filter: null generator: Other home_page_url: https://gigasciencejournal.com/blog issn: null language: eng license: https://creativecommons.org/licenses/by/4.0/legalcode prefix: '10.59350' relative_url: null secure: false slug: gigablog status: archived subfield: '1311' title: GigaBlog updated: null use_api: null container: GigaBlog date: '2014-02-06T00:00:00+00:00' date_updated: '2025-12-06T10:42:33+00:00' guid: http://finaloriginalblogs.dev/gigablog/?p=971 identifier: https://doi.org/10.59350/w8kyr-0e629 image: http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21-300x257.png images: - height: '257' sizes: '(max-width: 300px) 100vw, 300px' src: http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21-300x257.png srcset: http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21-300x257.png, http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21-768x658.png, http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21.png width: '300' - height: '588' sizes: '(max-width: 744px) 100vw, 744px' src: http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/Screen-shot-2014-02-05-at-4.31.52-PM.png srcset: http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/Screen-shot-2014-02-05-at-4.31.52-PM.png, http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/Screen-shot-2014-02-05-at-4.31.52-PM-300x237.png width: '744' - src: http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21.png - src: http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/Screen-shot-2014-02-05-at-4.31.52-PM.png issn: null keywords: - Publishing - Technology - Usegalaxy - Conferences - Galaxy lang: en license: https://creativecommons.org/licenses/by/4.0/legalcode reference: - id: https://doi.org/10.1186/2047-217x-2-17 unstructured: Bedoya-Reina, O. C., Ratan, A., Burhans, R., Kim, H. L., Giardine, B., Riemer, C., Li, Q., Olson, T. L., Loughran, T. P., vonHoldt, B. M., Perry, G. H., Schuster, S. C., & Miller, W. (2013). Galaxy tools to study genome diversity. Gigascience, 2(1). - id: https://doi.org/10.1186/2047-217x-3-1 unstructured: 'Hiltemann, S., Mei, H., de Hollander, M., Palli, I., van der Spek, P., Jenster, G., & Stubbs, A. (2014). CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy. GigaScience, 3(1).' - id: https://doi.org/10.5524/100069 unstructured: Bedoya-Reina, O. C., Ratan, A., Burhans, R., Kim, K. L., Giardine, B., Riemer, C., Li, Q., Olson, T. L., Loughran, T. P. J., vonHoldt, B. M., Perry, G. H., Schuster, S. C., & Miller, W. (2013). GigaGalaxy workflows and histories from "Galaxy tools to study genome diversity" [Data set]. GigaScience Database. - id: http://www.gigasciencejournal.com/series/galaxy unstructured: Unknown title - id: http://gigasciencejournal.com/blog/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/ unstructured: Unknown title - id: http://gigasciencejournal.com/blog unstructured: Unknown title rid: s4kwq-jfb94 rights: https://creativecommons.org/licenses/by/4.0/legalcode summary: Push the button! GigaScience moves toward more interactive articles Research articles are being published with increasingly large and complicated supporting datasets, together with the software code used in analyses of the data. title: 'Rewarding Reproducibility: First Papers in our Galaxy Series utilizing our GigaGalaxy platform' url: https://wayback.archive-it.org/22098/2025-05-01T17:13:42Z/http://gigasciencejournal.com/blog/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform version: v1 --- **Push the button! *GigaScience* moves toward more interactive articles**\ [![](http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21-300x257.png){.alignleft .size-medium .wp-image-987 loading="lazy" decoding="async" srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21-300x257.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21-768x658.png 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21.png 783w" sizes="(max-width: 300px) 100vw, 300px" width="300" height="257"}](http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/bgi-galaxy-21.png)\ Research articles are being published with increasingly large and complicated supporting datasets, together with the software code used in analyses of the data. However, there is a [growing](http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124){target="_blank" rel="noopener"} [number](http://www.nature.com/ng/journal/v41/n2/full/ng.295.html "Ioannidis microarray paper"){target="_blank" rel="noopener"} of studies reporting the inability to reproduce previously published findings which may, at least in part, be responsible for the increasing rate of retractions that [Bjorn Brembs has calculated](http://bjoern.brembs.net/2013/07/the-looming-crisis-in-science/ "B Brembs blog on retractions"){target="_blank" rel="noopener"} will overtake the number of papers published some time in the mid-2040s. Furthermore, there is an awareness of the \"reproducibility gap\" within the scientific community, with Francis Collins of the NIH [just publishing](http://www.nature.com/news/policy-nih-plans-to-enhance-reproducibility-1.14586 "Collins NIH reproducibility drive"){target="_blank" rel="noopener"} a statement expressing concern about this issue. Whilst this has provoked [some](http://news.cell.com/cellreports/cell-reports/in-defense-of-science "Cell: reproducibility isn't a problem piece"){target="_blank" rel="noopener"} [to deny](http://www.nature.com/news/reproducibility-the-risks-of-the-replication-drive-1.14184 "Nature: reproducibility isn't a problem article"){target="_blank" rel="noopener"} this is a serious issue (ironically in journals with the [highest retraction rates](http://iai.asm.org/content/79/10/3855.abstract "Retraction Index paper"){target="_blank" rel="noopener"}), *[GigaScience](http://www.gigasciencejournal.com/ "GigaScience"){target="_blank" rel="noopener"}* has joined initiatives such as [Sage Bionetworks Synapse](https://www.synapse.org/ "SAGE synapse homepage"){target="_blank" rel="noopener"} and [Science Exchange](https://www.scienceexchange.com/ "Science Exchange website"){target="_blank" rel="noopener"} [reproducibility initiative](http://reproducibilityinitiative.org/ "Reproducibility initiative"){target="_blank" rel="noopener"} in attempting to do something about this through building platforms and procedures to assist and reward authors who are keen on their work being reproducible and actually used. The [Galaxy community](http://usegalaxy.org/ "Galaxy homepage"){target="_blank" rel="noopener"} is one that shares similar goals, with a computational platform which allows users to share workflows, histories and wrapped tools in an easy-to-use and open source interface that even people without coding experience can use. On top of our [GigaDB repository](gigadb.org/ "GigaDB homepage"){target="_blank" rel="noopener"} to host large scale datasets, we have also set up our own Galaxy server called [GigaGalaxy](http://galaxy.cbiit.cuhk.edu.hk/ "GigaGalaxy server page"){target="_blank" rel="noopener"} to similarly present and host the computational outputs and methods of studies published in *GigaScience*. Attending the [Galaxy Community Conference in Oslo](https://wiki.galaxyproject.org/Events/GCC2013 "GCC2013 homepage"){target="_blank" rel="noopener"} last summer (see the write-up [here](http://blogs.biomedcentral.com/gigablog/2013/07/09/usegalaxy-lights-up-northern-skies/ "#usegalaxy conference write-up"){target="_blank" rel="noopener"}), we and the conference committee announced a [call for papers](http://blogs.biomedcentral.com/gigablog/2013/04/05/call-for-papers-for-a-special-gcc2013-galaxy-series/ "Galaxy CfP blog"){target="_blank" rel="noopener"} for a special thematic focused series on studies utilizing large-scale datasets and workflows. The initial results of this are now available, with the first two papers just out and available from the [new series page](http://www.gigasciencejournal.com/series/Galaxy "Galaxy Series Page"){target="_blank" rel="noopener"}. Whilst the series considers best practice papers, discussion, as well as novel uses of Galaxy, these first papers are examples of Galaxy toolkits, with a [genome diversity tool collection](http://dx.doi.org/10.1186/2047-217X-2-17 "Galaxy Pop Genomics paper"){target="_blank" rel="noopener"} presented from the Webb Miller lab at Pennsylvania State, and a [set of analytical and visualisation tools for Complete Genomics sequencing data](http://dx.doi.org/10.1186/2047-217X-3-1 "CGtag paper"){target="_blank" rel="noopener"} from the Stubbs lab at Erasmus Medical College. What differentiates this series from other traditional journals are doing is the focus on reproducibility, and the use of permanent DOIs and our own Galaxy server that can archive and present wrapped tools and workflows and histories from the papers. **DOIs for workflows**\ Following on from our experiences allocating [DOIs](http://en.wikipedia.org/wiki/Digital_object_identifier "Digital Object Identifier (wikipedia page)"){target="_blank" rel="noopener"} to software from papers, we helped lobby [DataCite](http://www.datacite.org/ "DataCite schema"){target="_blank" rel="noopener"} to include \"workflow\" as a similar resource type, and they have now [included this](http://schema.datacite.org/meta/kernel-3/example/datacite-example-workflow-v3.0.xml "Workflow metadata example"){target="_blank" rel="noopener"} in the release of their latest [metadata schema](http://schema.datacite.org/ "DataCite schema"){target="_blank" rel="noopener"}. We have been testing our GigaGalaxy platform by [implementing workflows](galaxy.cbiit.cuhk.edu.hk/galaxy/u/peter/p/soapdenovo2-tutorial-1 "SOAPdenovo2 workflows"){target="_blank" rel="noopener"} from our [SOAPdenovo2 publication](http://www.gigasciencejournal.com/content/1/1/18 "SOAPdenovo2 paper"){target="_blank" rel="noopener"}, and we presented much of this work at our \"[What Bioinformaticians need to know Beyond the PDF](http://blogs.biomedcentral.com/gigablog/2013/08/09/more-on-our-ismb-workshop-what-bioinformaticians-need-to-know-about-digital-publishing-beyond-the-pdf/ "WBN2NBtPDF2 blog post"){target="_blank" rel="noopener"}\" workshop at ISMB (which incidentally will be [continued again](http://www.researchobject.org/news/ "News on WBN2NBtPDF2"){target="_blank" rel="noopener"} at the 2014 meeting). The genome diversity toolkit is our first example of a DOI that resolves purely to a workflow. From the landing page in GigaDB, you can download the Galaxy XML files, or click the link to appropriate part in the [\"Papers\" section of our GigaGalaxy server](http://galaxy.cbiit.cuhk.edu.hk/paper/list_published "GigaScience papers in GigaGalaxy"){target="_blank" rel="noopener"} to [browse and run the workflows discussed in the paper](http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/g/obedoyareina2013 "Galaxy Pop Genomics paper workflows"){target="_blank" rel="noopener"}. Presenting a handy toolkit covering a number of popular population genetics tools, the paper provides diverse examples of their application on the genetics of Lemurs, and Canines and Cave Bears (oh my!). Seven of these examples are viewable on our [GigaGalaxy page](http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/g/obedoyareina2013 "Galaxy Pop Genomics paper workflows"){target="_blank" rel="noopener"}. Whilst the latest versions of the tools and further examples are available from the [main Galaxy server](http://usegalaxy.org/ "Galaxy homepage"){target="_blank" rel="noopener"} and the authors website, the *GigaScience* Galaxy server provides access to static versions of the tools used within the examples of the paper. To make it a little more interactive and understandable for users, we have produced SVG graphs to help visualize how input datasets, workflows and histories are related to each example analysis. [![](http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/Screen-shot-2014-02-05-at-4.31.52-PM.png){.aligncenter .size-full .wp-image-972 loading="lazy" decoding="async" srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/Screen-shot-2014-02-05-at-4.31.52-PM.png 744w, http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/Screen-shot-2014-02-05-at-4.31.52-PM-300x237.png 300w" sizes="(max-width: 744px) 100vw, 744px" width="744" height="588"}](http://gigasciencejournal.com/blog/wp-content/uploads/2014/02/Screen-shot-2014-02-05-at-4.31.52-PM.png) As a step on the road to executable papers, this is aiming to be a more interactive and two-way experience than traditional publication models still rooted in the print era, so please feedback to us at editorial@gigasciencejournal.com on on any bugs or features you would like to see. We would like to thank our collaborators at [CBIIT (the CUHK-BGI Innovation Institute of Trans-omics)](http://www.cuhk.edu.hk/cbiit/research.html "CBIIT research page"){target="_blank" rel="noopener"} who helped us set up our Galaxy server, [BioMed Central](http://www.biomedcentral.com/ "BMC homepage"){target="_blank" rel="noopener"}, [DataCite](http://www.datacite.org/ "DataCite homepage"){target="_blank" rel="noopener"}, as well as the authors and reviewers for working with us to get these examples out and online. The [series](http://www.gigasciencejournal.com/series/Galaxy "Galaxy Series Page"){target="_blank" rel="noopener"} is still open and we are continuing to take and review submissions, so watch the series page for future additions. Please contact us if you are interested in submitting your work or submit through our submission system [here](http://www.gigasciencejournal.com/manuscript "Submit page"){target="_blank" rel="noopener"}. Thanks to support from the [BGI](http://www.genomics.cn/en/index "BGI homepage"){target="_blank" rel="noopener"} our article processing charges are still currently free and, as we are again silver sponsors of the [2014 Galaxy Community Conference](https://wiki.galaxyproject.org/Events/GCC2014 "GCC2014 homepage"){target="_blank" rel="noopener"}, we hope to meet many of you there. ### **References** [1.](http://dx.doi.org/10.1186/2047-217X-2-17 "Galaxy Pop Genomics paper"){target="_blank" rel="noopener"} Bedoya-Reina et al.: Galaxy tools to study genome diversity. GigaScience 2:17 [http://dx.doi.org/10.1186/2047-217X-2-17](http://dx.doi.org/10.1186/2047-217X-2-17 "Galaxy Pop Genomics paper"){target="_blank" rel="noopener"} [2.](http://dx.doi.org/10.1186/2047-217X-3-1 "CGtag paper"){target="_blank" rel="noopener"} Hiltemann et al.: CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy. GigaScience 2014 3:1 [http://dx.doi.org/10.1186/2047-217X-3-1](http://dx.doi.org/10.1186/2047-217X-3-1 "CGtag paper"){target="_blank" rel="noopener"} [3.](http://dx.doi.org/10.5524/100069 "Galaxy Pop Genomics paper workflow DOI"){target="_blank" rel="noopener"} Bedoya-Reina, OC; Ratan, A; Burhans, R; Kim, HL; Giardine, B; Riemer, C; Li, Q; Olson, TL; Loughran Jr, TP; vonHoldt, BM; Perry, GH; Schuster, SC; Miller, W (2013): GigaGalaxy workflows and histories from \"Galaxy tools to study genome diversity\" GigaScience Database. [http://dx.doi.org/10.5524/100069](http://dx.doi.org/10.5524/100069 "Galaxy Pop Genomics paper workflow DOI"){target="_blank" rel="noopener"} [4.](http://www.gigasciencejournal.com/series/Galaxy "Galaxy Series Page"){target="_blank" rel="noopener"} GigaScience Galaxy Series Page https://academic.oup.com/gigascience/pages/galaxy_series_data_intensive_reproducible_research The post [Rewarding Reproducibility: First Papers in our Galaxy Series utilizing our GigaGalaxy platform](http://gigasciencejournal.com/blog/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/){rel="nofollow"} appeared first on [GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.