Scott Edmunds flashtalk on "Rewarding Reproducibility and Method Publishing the GigaScience Way" from Beyond the PDF 2 "Making it Happen" session. 20/3/13

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

2. The Issue:
(Mo Data, Mo Problems…)
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
Metadata Analyses
• Interoperability
Methods
Data
• Availability of workflows
• Transparent analyses

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

6. How are we supporting data
reproducibility?
Open-Data
Open-Paper Data sets DOI:10.5524/100038
78GB CC0 data
Open-Pipelines
DOI:10.1186/2047-217X-1-18
Open-Workflows
>6500 accesses Analyses DOI:10.5524/100044
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

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

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

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

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

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

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

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

14. 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

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