The public server

Public server provides you with a large variety of studies ranging from demographic, clinical information and microarray gene expression data. All this data can be viewed with tranSMART or Galaxy application tools. The data is extracted from public data repositories and curated by eTRIKS before being made available on the public server. Click on the right hand side widget to explore these datasets using the eTRIKS platform.

Want to see which studies are available to you?

Here below is an overview of the patient-centric as well as cell line-focused data we have currently available on our eTRIKS Public server. Stay tuned : Additional omics data types will be added in the future.

Patient data:

Systemic Lupus Erythematosus:
27 Studies from GEO
Asthma:
25 Studies from GEO
Psoriasis:
24 Studies from GEO
Rheumatoid Arthritis:
23 Studies from GEO
Macrophages:
18 Studies from GEO
Parkinson Disease:
16 Studies from GEO
Inflammatory Bowel Disease:
15 Studies from GEO
Cancer:
CCLE (1070 cell lines)
GSK (950 cell lines)
4 Studies from TCGA
3 Studies from GEO on Brest Cancer
1 Study from GEO on Multiple Myeloma
Lupus Nephritis:
2 Studies from GEO
Multiple sclerosis:
1 Study from GEO

Cell line data:

CCLE:
1070 cell lines
GSK:
950 cell lines
Want to know from which public repository the studies are originating from?

The studies provided in the public server originate from the following Public data repositories:

Gene Expression Omnibus (GEO) Geo logo
The Cancer Genome Atlas (TCGA) TCGA logo
GSK Cell Line data GSK logo
Cancer Cell Line Encyclopedia (CCLE) TCGA logo
eTRIKS-brand-logo

Public Server

tranSMART eTRIKS v4.0
eTRIKS Platform version: 4.0
tranSMART core version: 16.2
R version: 3.2.5

eTRIKS Documentation

eTRIKS provides you with a large variety of documents which can help you to use platform. Click on the widget below to explore.


Downloadable documents
Guide to user registration and password modification
Introduction to the ticketing system
Getting started on ETL
documentation

eTRIKS Labs

With large, complex datasets becoming the norm staging, exploring and analyzing translational research data can be challenging and resource intensive. eTRIKS is working to change that by providing platforms, services, and guidance for the use and re-use of translational research data.
Our newest development is the creation of an online space, eTRIKS Labs, where new projects that are being worked on will be made available for review and feedback. The intent is for this to be a means of co-creating tools, services, training and guidelines for translational research.

SmartR

SmartR Demo image

SmartR is aimed to provide a highly dynamic and interactive way of visualizing and analyzing data within tranSMART.

Disease Map

Services :

  • Access here to the documentation

    • SmartR Demo image

    An integrated knowledge repository to provide biological context to data emerging from experimental studies for selected IMI projects.

    SNF

    SmartR Demo image

    SNF is a novel computational method for genomic data integration that was developed by Wang et al., in the lab of Anna Goldenberg. ... See More

    WGCNA

    SmartR Demo image

    Weighted Gene Correlation Network Analysis. Image reference: Jiang et al. BMC Genomics 2014 15:756

    EHS

    SmartR Demo image

    The eHS addresses the needs of eTRIKS current and prospective users for data harmonization and support ... See More

    Hi Dome

    SmartR Demo image

    The High Dimensional and omics data exploration project is an extension to tranSMART which allows the creation ... See More

    GSVA

    GSVA image

    Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method which estimates the relative enrichment of ... See More

    Disclaimer

    The eTRIKS Labs modules are offered to the public as freely available resources, for non-commercial research use. Some aspects of these experimental modules may still be under development, and there are no warranties about the completeness, reliability, accuracy, and security of any of the software packages. Please bear this in mind, especially if you wish to analyse personal and/or confidential data. Some of the services provided use public data sources that are available through third parties on the internet – these are identified by links provided under ‘Acknowledgements’ on the respective module pages. If you use or re-distribute these public data for any purposes, you are responsible for adhering to the license requirements of these public data sources.

    Hosted Projects

    Currently, eTRIKS platform in CC-IN2P3/CNRS hosts three projects. Only project members can click on the project to access the proposed services. For visitors who wants to know more about the specific projects, please click on the "hosted project" link in the navigation bar above.

    eTRIKS-brand-logo

    Services :

    Production tranSMART eTRIKS v4.0
    Forgot or change your password

    Production Platform Version:

    eTRIKS Platform version: 4.0
    tranSMART core version: 16.1
    R version: 3.2.5
    bioaster-logo
    eTRIKS-brand-logo

    Services :

    Production tranSMART eTRIKS v4.0
    Forgot or change your password

    Production Platform Version:

    eTRIKS Platform version: 4.0
    tranSMART core version: 16.1
    R version: 3.2.5

    eTRIKS deployment tools for services and applications

    eTRIKS project provides several ways to deploy applications and services such as tranSMART, etc. Beware, these deployment tools are not designed for data centers that want to host production eTRIKS platform. If you are planning to deploy the eTRIKS platform in your data center, please contact us by clicking on the link user support on the navigation bar. We will provide you with more support.

    bioaster-logo

    Docker file for eTRIKS-flavour of tranSMART

    Services :

    Download docker file
    The purpose of this repository is to provide a Docker-based installation of tranSMART. More information are available from the download page.
    etriks-logo

    eTRIKS-flavour tranSMART Java war file

    Services :

    Download tranSMART eTRIKS v4.0 war file
    This is an all-in-one tranSMART deployment tool for test purpose only. This war file needs a compute host with Java application server on it (e.g. tomcat, JBoss, etc.).
    bioaster-logo

    Virtual Machine for tranSMART application

    Services :

    tranSMART Foundation Virtual Machine deployment
    This is an all-in-one tranSMART virtual machine image. This deployment needs a compute host with virtual machine framework on it (e.g. virtualbox, vmware). The linked page will give you more information.