enabling transparent, reproducible research

| 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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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