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

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

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

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

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

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

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

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

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

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

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

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

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

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

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