1. | brian m. bot| senior scientist | community manager |
Synapse
enabling transparent, reproducible research
| michael kellen | director, technology platform and services |
2. a tool to improve transparency and
reproducibility of data intensive
science by recording analyses in real-time
Synapse
3. a collection of living research projects
enabling researchers to contribute to large-scale
collaborative science pre- and post-publication
Synapse
4. 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)
13. 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
29. 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
30. enables transparency and reproducibility
facilitates large scale collaboration
encourages communication pre- and post-publication
summary
31. commenting / peer review mechanisms
recognition metrics for individuals and teams
deeper integration with cloud compute services
project snapshots linked to publications
future directions