Hackathon
Dates: Wed 5th February to Fri 7th February 9:00 to 17:00
Participants
eTRIKS/Imperial: Florian Guitton, Axel Oehmichen, Peter Rice
CTMM TraIT/The Hyve: Riza Nugraha, Ruslan Forostianov, Gustavo dos Santos Lopes, Kees von Bochove
University of Michigan: Terry Weymouth
Recombinant at Deloitte: Dave John plus others
Pfizer: Ami Khandeshi
Harvard: Michael McDuffie
Goals
Merge of Sanofi RC2 with public code branches into a clean v1.2alpha branch
Branches to be included are described in detail on a separate page
Develop an approach to publicly accessible testing and QA
TranSMART v1.2 Features Specification
Feature/Provider | Description |
---|---|
High-Dimensional data models Sanofi RC2, Hyve/Cognizant, eTRIKS |
|
Improved search and Browsing Sanofi RC1+RC2, Recombinant, Hyve/Cognizant |
|
Serial Data Sanofi RC2, Hyve/Cognizant | Accommodate serial low and high-dimensional data (time series, doses responses, etc.). Analysis of ‘serial’ data matrix. Analysis of individual columns (time points). Use of time dimension as a variable. |
Sample ID incorporation Sanofi RC2, Hyve/Cognizant | Definition of multiple samples per patient. Association of high and low dimensional data to a single sample. Display linking sample and patient ID in grid view. |
Oracle compatibility eTRIKS, Hyve, Recombinant | Maintain Oracle support in parallel with Postgres. Oracle and Postgres test systems and test suites. |
Incremental data load Sanofi RC2, Hyve/Cognizant | Enable incremental loading of data for a study: add new variables to existing study, add new patients to existing study, overwrite values for certain variables in an existing study, change label names of variables previously loaded. |
Variation/VCF support eTRIKS, OncoTrack, Hyve, Sanofi RC2 | Transmart NGS working group developments. Improvements in SNP variation automation and performance. |
Recombinant FDA Recombinant | Use of i2b2 modifiers. Cross-trial support. Personalized workspace features (e.g., analysis saving) ? |
Pfizer GWAS Recombinant | Pfizer GWAS 1.0 available. New version with minor changes expected – can be updated later. |
Faceted search JnJ, eTRIKS, Hyve, Recombinant | Already merged in multiple branches. To be merged with Sanofi RC1+2 Browse/Analyze tab functionality which was preferred in the community vote. |
Analytics improvements Sanofi RC2, eTRIKS, Recombinant |
|
R Interface Takeda, Hyve, eTRIKS, Recombinant | Presented by Takeda in Paris. Merge new R interface developments by Hyve for JnJ/eTRIKS. |
Core API Hyve | Update with latest new functionality |
Security improvements, eTRIKS, Sanofi RC2 | Improved security from eTRIKS and Sanofi exercise. Security models for APIs. |
Multiple cohorts eTRIKS | General support for more than 2 cohorts for comparison/analysis |
Postgres 9.3 support eTRIKS | Maintaining Postgres 9.3 as the main supported version |
Code review | Support for Grails 2.3.x. Code cleanup proposed in Paris hackathon to be applied to code base after Boston. |
Code Branches
- eTRIKS/Imperial
- CTMM TraIT/The Hyve
- Sanofi RC2 Functional Description
- Recombinant
- Pfizer
- JnJ
- Takeda
Test Data
Sanofi RC2 test data for hackathon internal use: examples for miRNAseq, qPCR miRNA, RNAseq, metabolomics and RBM proteomics. Expected also mass-spec proteomics.
eTRIKS script to extract and load pathway data from KEGG
Public studies curated by Rancho Biosciences
- Oncology: GSE1456 GSE4271 GSE4698 GSE4922 GSE20194 GSE27831
- Inflammatory: GSE8650 GSE13732 GSE24060 GSE17755
- Asthma: GSE13168