IDW2022: A decades experiences in transparent and interactive publication of FAIR data and software via an end-to-end XML publishing platform
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The document outlines the advancements in publishing fair data and software using an end-to-end XML platform, highlighting experiences and methodologies from significant publications like Gigascience and Codecheck. It discusses the importance of transparent practices, open peer review, and interactive content to enhance reproducibility and trust in scientific research. The document also suggests a new approach to publishing that prioritizes data, software, and workflow over traditional static versions of published records.
IDW2022: A decades experiences in transparent and interactive publication of FAIR data and software via an end-to-end XML publishing platform
- 1. A decades experiences in transparent and interactive publication of FAIR data and software via an end-to-end XML publishing platform Scott Edmunds 0000-0001-6444-1436
- 2. https://www.telegraph.co.uk/technology/2020/05/16/neil-fergusons-imperial-model-could-devastating-software-mistake/ Scientists: need to convince public + politicians The “Infodemic” Era Imperial College: Report 9
- 3. GigaSolution: rewarding open data & code http://gigasciencejournal.com/ Publishes “Data Notes” for CC0 data, “Tech Notes” for OSI software. Transparent: Open Peer Review and linked to preprints. Mandates code in repo.
- 4. Integrated GigaDB repository: DataCite DOIs, no size limits, code snapshots, APC covers curation http://gigadb.org/ GigaSolution: rewarding open data & code
- 5. 0 1 2 4 2 5 6 6 8 2 0 0 0 0 0 0 3 2 1 0 0 0 0 0 0 0 1 1 2 1 0 0 0 0 0 0 0 5 0 2 2 1 2 8 7 28 35 34 48 45 0 10 20 30 40 50 60 70 GigaScience software/workflow papers (Technical Notes), 2012-2021 Galaxy Snakemake Nextflow CWL Other Changes in how research is shared: workflows
- 6. gigagalaxy.net Experience publishing Galaxy workflows: 2013
- 7. https://doi.org/10.1186/2047-217X-3-23 • Downloadable as virtual hard-disk/available as Amazon Machine Image • Unclear how to describe licensing & security issues? Experience publishing VMs: 2014
- 8. https://doi.org/10.1186/s13742-015-0087-0 https://doi.org/10.1186/s13742-015-0073-6 • From 2015 increasing submissions leveraging containers • Promoted experiments in standardization such as bioboxes • Integrated with CodeOcean & tested with Gigantum • Carried out reproducibility case-studies (can be expensive) Experience publishing containers: 2015
- 9. Independent execution of computations underlying research articles. Experience publishing CODECHECK: 2020 CODECHECK tackles one of the main challenges of computational research by supporting codecheckers with a workflow, guidelines and tools to evaluate computer programs underlying scientific papers. The independent time-stamped runs conducted by codecheckers will award a “certificate of executable computation” and increase availability, discovery and reproducibility of crucial artefacts for computational sciences. https://codecheck.org.uk/
- 10. Experience publishing CODECHECK: 2020 http://gigasciencejournal.com/blog/codecheck-certificate/ https://doi.org/10.1093/gigascience/giaa026
- 11. Experience publishing CODECHECK: 2020 https://www.nature.com/articles/d41586-020-01685-y http://doi.org/10.5281/zenodo.3865491
- 12. Tech really the bottleneck Process much too slow & expensive Still too focused on narrative and static “version of record” Still not very FAIR Lessons learned in a decade of data & software publishing:
- 13. D ATA C O D E E N T I T I E S FA C T S S TA B I L I T Y A new approach Follow the Software Paradigm? C O D E R E L E A S E F O R K U P D AT E R E P E AT Deconstruct the “Version of Record”?
- 14. Move to new XML end-to-end pipeline Custom end-to-end workflow makes integrations simpler with one integration point
- 15. Features of new journal: Main advantage of workflow is XML from start to end https://gigabytejournal.com/ Several modules acting as one platform: no import/export of files, so fast and accurate Cutting out production allows huge time & cost saving (currently as little as 3.5hrs per paper) Any number of versions can be published instantly, including typographic quality PDF or updates/forks Allows instantaneous switch of views Leverage embeddable dynamic content/widgets Initial focus on forkable open source products: data + software + update papers
- 16. Focusing beyond VoR allows different views… 16 What does focusing on Data + software + XML allow us to do? https://doi.org/10.46471/gigabyte.1
- 17. https://doi.org/10.46471/gigabyte.6 High quality rich XML CC-BY open licensed, open citations, open corpus Structured schema.org metadata No hiding of material in supplemental files Maximise use of persistent identifiers (PIDs) Who ORCID IDs CASRAI contributorship Funder (Fundref) Institution (ROR) What Species (NCBI, fishbase) Cell/strain (RRID) How Equipment (RRID) Software (RRID, bio.tools) Output Data (accessions, DOIs) Results (DOIs) Helping to make research “AI-ready” Thinking about users: machines
- 18. Interaction: increasing understanding & trust https://doi.org/10.46471/gigabyte.13 Do you trust an immunoinformatics tool to predict whether memory T cells generated from previous exposure to common cold coronaviruses are cross-reactive against SARSCoV2?
- 19. Interaction: software and code via Stencila and CodeOcean http://gigasciencejournal.com/blog/gigabyte-executable-research-articles/ Code Ocean “Compute Capsule”: readers can directly interact with software via an embedded version in the article; or deploy and run in their own cloud computing environment. Popout Stencila “Executable Research Article” where figures are accompanied by editable code blocks that can be edited and re- executed to immediately see the changes.
- 20. Interact with Stenci.la “code chunks” & Code Ocean “compute capsules” of COVID-19 immunoinformatics papers https://doi.org/10.46471/gigabyte.13
- 21. A new way of publishing FAIR research with new tech • Share & get credit for updatable data & software papers • Follow the software paradigm, bring your research to life • XML makes it much easier to embed interactive content • Use automation & interaction to increase scrutiny & trust • XML only workflow cuts time and cost to publish • Rethink “Version of Record”: focus on facts/data/code & discard the packaging Help us change scientific publishing, contact: editorial@gigabytejournal.com https://gigabytejournal.com/
- 22. Thanks to: @GigaByteJournal facebook.com/GigaScience http://gigasciencejournal.com/blog/ Follow us: + Weibo & WeChat Laurie Goodman, Publisher Nicole Nogoy, Editor Hans Zauner, Assistant Editor Hongling Zhao, Assistant Editor Peter Li, Head of IT Chris Hunter, Lead BioCurator Chris Armit, Data Scientist Mary Ann Tulli, Data Editor Rija Ménagé, Senior Software Engineer Ken Cho, Systems Programmer Analyst Chen Qi, Shenzhen Office. https://gigabytejournal.com/ editorial@gigabytejournal.com
- 23. Questions?