Doing Useful Research with Synapse

Synapse (www.synapse.org) is a free and open source informatics platform for data-driven collaborative research. Built from the ground up for a rich data sharing experience, Synapse provides tools for versioning, annotating data combined with provenance tracking and fine grained access control. We will demo some of these features with real examples.

Transcript

1. Useful Research ! Abhishek Pratap (Abhi)! Sage Bionetworks! apratap@sagebase.org @abhishekpratap! @Sagebio!
2. Science publishing: The golden club
3. Science publishing: The golden club mostly not useful 85% Chalmers and Glasziou 2009
4. “The biotechnology firm Amgen...tried to confirm published findings of 53 'landmark papers' … scientific findings were confirmed in only 6 (11%) cases.” Begley & Ellis. Nature (2012) “Bayer HealthCare in Germany last year reported that only about 25% of published preclinical studies could be validated to the point at which projects could continue.”
5. the status quo tolerates poor communication of findings 6% 21% 8% 11% 54% cannot reproduce can reproduce in principle can reproduce w/discrepancies can reproduce from processed data w/ discrepancies can reproduce partially Ioannidis A. et al. Repeatability of published microarray gene expression analyses. Nature Genetics 41, 149-155 (2009) | doi:10.1038/ng.295
6. Connecting the Dots Summary
7. collaborative workspaces Free Well supported Open source C O N T R I B U T E t o t h e C U R E Synapse Data Versioning Provenance Tracking Data Annotation Data Queries Governance Data Security www.synapse.org
8. The Cancer Genome Atlas DNA-Seq Methylation RNA-Seq miRNA-Seq Protein expression 1070 Datasets 258 researchers 1900 results 68 projects 28 institutions 21 papers
9. The Cancer Genome Atlas DNA-Seq Methylation RNA-Seq miRNA-Seq Protein expression 1070 Datasets 258 researchers 1900 results 68 projects 28 institutions 21 papers 10 Months
10. PCBC Project Overview
11. Common Mind
12. Cell line analysis Data Summary Files Folders syn123456 syn85656 syn47858 raw.csv proc.csv syn48788 syn4785 data results ! ! • Cell growth look normally distributed ! • There is evidence of inverse growth between these two cell lines ! Project Project Wiki
14. Synapse python API demo Today we will be using tutorial 1 : http://bit.ly/syn123-1
15. Publish your analysis to web Collaborate https:/ /synapse.org/#synxx used executed track your analysis
16. Just manage Data My notes your next Paper cud live here My research facebook
17. Lets do reproducible research
19. Thank You ! Abhishek Pratap! apratap@sagebase.org @sagebio! @abhishekpratap!