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| brian m. bot| senior scientist | community manager |
Synapseenabling transparent, reproducible research
| michael kellen | director, technology platform and services |
a tool to improve transparency and reproducibility of data intensive
science by recording analyses in real-time
Synapse
a collection of living research projects enabling researchers to contribute to large-scale
collaborative science pre- and post-publication
Synapse
Attractor Metagenes
Columbia Professor Dimitris Anastassiou
MPEG-2 compression of digital audio and video signals
Modules of co-expressed genes shared across cancers
Belief that these ‘attractors’ represent underlying biological mechanisms (bioinformatic ‘hallmarks of cancer’1)
1D. Hanahan, R. A. Weinberg. Hallmarks of cancer: The next generation. Cell 144, 646–674 (2011)
21 february 2013
17 april 2013
21 february 2013
17 april 2013
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TCGA Pan-Cancer Consortium
Attractor Metagenes openly evolving research projects
collaboration around common data
Omberg, et al. Nature Gene*cs
•Analysis of: 12 Tumor types, 6 molecular profiling platforms •Focus series of: 4 papers in Nature Genetics, with 14 more to follow in other NPG journals
TCGA Pan-Cancer Consortium
18papers in press
68core projects
248researchers
28institutions
1070datasets
1723results
versioned data, analysis freezes
data versioning versus data provenance
TCGA Pan-Cancer Consortium collaboration around common data
CRC Subtyping Consortiumcollaboration around common question
CRC Subtyping Consortium
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analysis groups
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CRC Subtyping Consortium
Phase I: per-group subtyping ‣ subtyping calls on common data ‣ assess agreement between methods ‣ assess associations with phenotypic traits
Phase II: meta-analysis and de novo subtyping ‣ consensus subytping ‣ assess associations with clinical outcomes ‣ strategy for adoption from clinicians
enables transparency and reproducibility
facilitates large scale collaboration
encourages communication pre- and post-publication
summary
commenting / peer review mechanisms
recognition metrics for individuals and teams
deeper integration with cloud compute services
project snapshots linked to publications
future directions
Acknowledgements
Sage Bionetworks Synapse Development Team Alfred P. Sloan Foundation Nature Publishing Group
AAAS-Science PLoS