Scott Edmunds flashtalk slides from Beyond the PDF2
15
Rewarding Reproducibility and Method Publishing the GigaScience Way Scott Edmunds GigaScience [email protected] @gigascience/SCEdmunds
-
Upload
gigascience-bgi-hong-kong -
Category
Technology
-
view
107 -
download
0
description
Scott Edmunds flashtalk on "Rewarding Reproducibility and Method Publishing the GigaScience Way" from Beyond the PDF 2 "Making it Happen" session. 20/3/13
Transcript of Scott Edmunds flashtalk slides from Beyond the PDF2
Rewarding Reproducibility and Method Publishing the GigaScience Way
Scott EdmundsGigaScience
[email protected]@gigascience/SCEdmunds
The Issue:(Mo Data, Mo Problems…)
= growing reproducibility gap
Data-driven science era brings:
• Huge opportunities
• Huge challenges with: data curation, review/QA, handling, sharing
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
GigaSolution: deconstructing the paper
www.gigadb.orgwww.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
How are we supporting data reproducibility?
Data sets
Analyses
Linked to
Linked to
DOI
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-PipelinesOpen-Workflows
DOI:10.5524/100038Open-Data
78GB CC0 data
Code in sourceforge under GPLv3: http://soapdenovo2.sourceforge.net/>4000 downloads
Enabled code to being picked apart by bloggers in wiki http://homolog.us/wiki/index.php?title=SOAPdenovo2
SOAPdenovo2 workflows implemented in
galaxy.cbiit.cuhk.edu.hk
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
“Deconstructed”Journal
“Regular”Journal
“Conscientious” Online Journal
“Deconstructed”Journal
“Regular”Journal
“Conscientious” Online Journal
“Deconstructed”Journal
“Regular”Journal
“Conscientious” Online Journal
Image Source: http://commons.wikimedia.org/wiki/File:System-Mechanic-California.jpg
“Deconstructed”Journal
“Regular”Journal
“Conscientious” Online Journal
Ultimate Goal: Executable papersData
Papers
Executable (Methods)
Papers
Analysis Papers
www.gigasciencejournal.com
Give us your data & pipelines!*
What is needed to make it happen?
[email protected]@[email protected]
Contact us:
* APC’s currently generously covered by BGI
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:
@gigasciencefacebook.com/GigaScienceblogs.openaccesscentral.com/blogs/gigablog/
Peter LiChris HunterJesse Si ZheNicole NogoyTam SneddonAlexandra BasfordLaurie Goodman
Follow us:www.gigadb.org
galaxy.cbiit.cuhk.edu.hkwww.gigasciencejournal.com
CBIIT
Funding from:Our collaborators:team:
