TranSMART
1.2 & 2.0 Roadmap
riza@thehyve.nl
@rizanugraha
TranSMART
1.2 & 2.0 Roadmap
In the next 15 mins
- What & Why
- Our involvements
- Future tranSMART
- Demo(s)
What is tranSMART?
TranSMART
Data warehouse bringing together scientists from clinical sciences, preclinical research and discovery – around the data
Combination of internal datasets & documents with public datasets & knowledge
Tailored to both biologists/clinicians & bioinformaticians
Dual nature: in use for translational research in both pharma & hospitals/clinics
clinical data
biomarker
contextual info
tranSMART
biochemical observations
dosing
adverse events
demographics
outcomes
elisa/rbm
snp/cnv
'omics'
genomic
pathways
genomics/sequence
protein functions
literatures
ETL/CURATION
ETL/CURATION
ETL/CURATION
INFORMATION STANDARS: 1) ONTOLOGIES, TAXONOMIES, VOCABULARIES 2) SYNTACTICAL STANDARDS
mining
search
open source - GPLv3
+100 computer scientists, physician scientists
community driven
+150 downloads by academic, industrial, governmental, and private research
multiple collaborations between non-profits, academic medical centers, pharmaceutical companies, and commercial groups.
2009
2012
2013
2014
2015
J&J, Recombinant
Open Source!
v1.1
v1.2
v1.3
v2.0 ?
tranSMART 1.2.x
login: guest/transmart2015
Our Involvements
&
Contributions
+ Genome Browser
+ tranSMART Installer
+ proteomics support
+ metabolomics support
+ RNASeq data
+array CGH data
+ RESTful API
+ RClient
+ Core API
tranSMART 1.2.x
+ tranSMART Batch
+ many more ..
+ many more ..
Hackathons
Trainings
Seminars
Conferences
User groups
Wiki
annual meetings
Posters
Speakers
Boston
London
Paris
Amsterdam
annual meetings
Hackathons
Speakers
What's next?
October 19-21, 2015 in Amsterdam at the Netherlands Cancer Institute.
Modular architecture, responsive, interactive, better performance
Audit Logging, SNP, GWAS Improvements, Advanced Analysis Improvements
TranSMART REST-API
Analytical Tools
(RShiny, OpenCPU)
UI Client
transmart-base-ui
MobileApp
3rd party
2.0 Roadmap
oAuth
oAuth
oAuth
oAuth
VU MC
Imperial College
TranSMART REST-API
VU MC
transmart-base-ui
CrossfilterJS
DC.JS
DC.JS
We need you
Resources
- https://github.com/transmart
- https://github.com/thehyve/
- @TheHyveNL
- @tranSMART_org
- https://www.youtube.com/user/transartfoundation
- https://www.youtube.com/user/TheHyveNL
- https://www.linkedin.com/company/transmart-foundation
- http://thehyve.nl/category/solutions/transmart
- http://transmartfoundation.org/
- http://wiki.transmartfoundation.org