Rewarding Reproducibility and Method   Publishing the GigaScience Way             Scott Edmunds              GigaScience  ...
The Issue:(Mo Data, Mo Problems…)Data-driven science era brings:• Huge opportunities• Huge challenges with:    data curati...
GigaSolution: deconstructing the paperTake data publication approach further and reward:•   Data availability•   Metadata/...
GigaSolution: deconstructing the paperCombines and integrates:                Open-access journal                Data Publ...
How are we supporting data                       reproducibility?                                                         ...
SOAPdenovo2 workflows implemented in            galaxy.cbiit.cuhk.edu.hk
SOAPdenovo2 workflows implemented inImplemented entire workflow in our Galaxy server, inc.:• 3 pre-processing steps• 4 SOA...
“Regular”   “Conscientious” “Deconstructed” Journal     Online Journal     Journal
“Regular”   “Conscientious” “Deconstructed” Journal     Online Journal     Journal
“Regular”   “Conscientious” “Deconstructed” Journal     Online Journal     Journal
“Regular”                                     “Conscientious” “Deconstructed”     Journal                                 ...
Ultimate Goal: Executable papers  Data PapersExecutable(Methods)  Papers Analysis  Papers
What is needed tomake it happen?Give us your data &    pipelines!*Contact us:scott@gigasciencejournal.comeditorial@gigasci...
Thanks to:        team:        Our collaborators:                    Funding from:Peter Li             Ruibang Luo (BGI/HK...
Scott Edmunds flashtalk slides from Beyond the PDF2
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Scott Edmunds flashtalk slides from Beyond the PDF2

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

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  • That just leaves me to thank the GigaScience team: Laurie, Scott, Alexandra, Peter and Jesse, BGI for their support - specifically Shaoguang for IT and bioinformatics support – our collaborators on the database, website and tools: Tin-Lap, Qiong, Senhong, Yan, the Cogini web design team, Datacite for providing the DOI service and the isacommons team for their support and advocacy for best practice use of metadata reporting and sharing.Thank you for listening.
  • Scott Edmunds flashtalk slides from Beyond the PDF2

    1. 1. Rewarding Reproducibility and Method Publishing the GigaScience Way Scott Edmunds GigaScience scott@gigasciencejournal.com @gigascience/SCEdmunds
    2. 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. 3. GigaSolution: deconstructing the paperTake data publication approach further and reward:• Data availability• Metadata/curation Metadata Analyses• Interoperability Methods Data• Availability of workflows• Transparent analyses
    4. 4. GigaSolution: deconstructing the paperCombines and integrates: Open-access journal Data Publishing Platform Data Analysis PlatformUtilizes 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. 5. How are we supporting data reproducibility? Open-Data Open-Paper Data sets DOI:10.5524/100038 78GB CC0 data Open-PipelinesDOI: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
    6. 6. SOAPdenovo2 workflows implemented in galaxy.cbiit.cuhk.edu.hk
    7. 7. SOAPdenovo2 workflows implemented inImplemented entire workflow in our Galaxy server, inc.:• 3 pre-processing steps• 4 SOAPdenovo modules• 1 post processing steps• Evaluation and visualization toolsAlso available to download by >25K Galaxy users in galaxy.cbiit.cuhk.edu.hk
    8. 8. “Regular” “Conscientious” “Deconstructed” Journal Online Journal Journal
    9. 9. “Regular” “Conscientious” “Deconstructed” Journal Online Journal Journal
    10. 10. “Regular” “Conscientious” “Deconstructed” Journal Online Journal Journal
    11. 11. “Regular” “Conscientious” “Deconstructed” Journal Online Journal JournalImage Source: http://commons.wikimedia.org/wiki/File:System-Mechanic-California.jpg
    12. 12. Ultimate Goal: Executable papers Data PapersExecutable(Methods) Papers Analysis Papers
    13. 13. What is needed tomake it happen?Give us your data & pipelines!*Contact us:scott@gigasciencejournal.comeditorial@gigasciencejournal.comdatabase@gigasciencejournal.com* APC’s currently generously covered by BGI www.gigasciencejournal.com
    14. 14. 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) CBIITAlexandra Basford Senghong Wang (HKUST)Laurie Goodman Yan Zhou (HKUST) @gigascienceFollow us: facebook.com/GigaScience blogs.openaccesscentral.com/blogs/gigablog/ www.gigadb.org galaxy.cbiit.cuhk.edu.hk www.gigasciencejournal.com
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