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Rewarding Reproducibility and Method Publishing the GigaScience Way

Rewarding Reproducibility and Method Publishing the GigaScience Way. Scott Edmu n ds GigaScience scott@gigasciencejournal.com @ gigascience / SCEdmunds. The Issue :. Data-driven science era brings: Huge opportunities Huge challenges with: data curation , review/QA, handling, sharing.

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Rewarding Reproducibility and Method Publishing the GigaScience Way

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  1. Rewarding Reproducibility and Method Publishing the GigaScience Way Scott Edmunds GigaScience scott@gigasciencejournal.com @gigascience/SCEdmunds

  2. The Issue: • Data-driven science era brings: • Huge opportunities • Huge challenges with: data curation, review/QA, handling, sharing = growing reproducibility gap

  3. GigaSolution: deconstructing the paper • Take data publication approach further and reward: • Data availability • Metadata/curation • Interoperability • Availability of workflows • Transparent analyses Analyses Metadata Methods Data

  4. GigaSolution: deconstructing the paper Combines and integrates: Open-access journal Data Publishing Platform Data Analysis Platform Utilizes big-data infrastructure and expertise from: Worlds largest genomics organisation with: 17PB storage, 20.5K cores, 212TFlops, >1000 bioinformaticians www.gigadb.org www.gigasciencejournal.com

  5. How are we supporting data reproducibility? Open-Data Open-Paper Data sets DOI:10.5524/100038 Linked to 78GB CC0 data DOI Open-Pipelines DOI Open-Workflows Linked to DOI:10.1186/2047-217X-1-18 Analyses DOI:10.5524/100044 >6500 accesses Open-Review 8 reviewers tested data in ftp server & named reports published Enabled code to being picked apart by bloggers in wiki http://homolog.us/wiki/index.php?title=SOAPdenovo2 Open-Code Code in sourceforge under GPLv3: http://soapdenovo2.sourceforge.net/ >4000 downloads

  6. SOAPdenovo2 workflows implemented in galaxy.cbiit.cuhk.edu.hk

  7. SOAPdenovo2 workflows implemented in Implemented entire workflow in our Galaxy server, inc.: • 3 pre-processing steps • 4 SOAPdenovomodules • 1 post processing steps • Evaluation and visualization tools Also available to download by >25K Galaxy users in galaxy.cbiit.cuhk.edu.hk

  8. “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal

  9. “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal

  10. “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal

  11. “Deconstructed” Journal “Regular” Journal “Conscientious” Online Journal Image Source: http://commons.wikimedia.org/wiki/File:System-Mechanic-California.jpg

  12. Ultimate Goal: Executable papers Data Papers Executable (Methods) Papers Analysis Papers

  13. What is needed to make it happen? Give us your data & pipelines!* Contact us: scott@gigasciencejournal.com editorial@gigasciencejournal.com database@gigasciencejournal.com * APC’s currently generously covered by BGI www.gigasciencejournal.com

  14. Thanks to: team: Funding from: Our collaborators: Peter Li Chris Hunter Jesse Si Zhe Nicole Nogoy Tam Sneddon Alexandra Basford Laurie Goodman RuibangLuo (BGI/HKU) ShaoguangLiang (BGI-SZ) Tin-Lap Lee (CUHK) HuayenGao (CUHK) QiongLuo (HKUST) Senghong Wang (HKUST) Yan Zhou (HKUST) CBIIT @gigascience Follow us: facebook.com/GigaScience blogs.openaccesscentral.com/blogs/gigablog/ www.gigadb.org galaxy.cbiit.cuhk.edu.hk www.gigasciencejournal.com

  15. Thanks to: team: Funding from: Our collaborators: Peter Li Chris Hunter Jesse Si Zhe Nicole Nogoy Tam Sneddon Alexandra Basford Laurie Goodman RuibangLuo (BGI/HKU) ShaoguangLiang (BGI-SZ) Tin-Lap Lee (CUHK) HuayenGao (CUHK) QiongLuo (HKUST) Senghong Wang (HKUST) Yan Zhou (HKUST) CBIIT @gigascience Follow us: facebook.com/GigaScience blogs.openaccesscentral.com/blogs/gigablog/ www.gigadb.org galaxy.cbiit.cuhk.edu.hk www.gigasciencejournal.com Happy New Year!

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