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Latest status (

...

16 August 2018 - 12:00 UTC)

The server is loaded with data and ready for testing.

We have set a new test server up on AWS and assigned a DNS entry to it. The updated link is below. Please resume testing.loaded a set of basic studies and the latest 16.3 war file.

Data Loaded. Details below:

  • Cell-line use case data is loaded as public data (see table for details) including variant data for VCF and RNAseq
  • Browse tab data is loaded for selected studies. Suggestions on values for "Not applicable" fields - either true values, or useful values for testing filter functionallity - are welcome.
  • Additional data loaded for eTRIKS Asthma and Rheumatoid Arthritis studies..

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  • GWAS data is in preparation loaded for 5 magic analysis files. SNP data is being loaded for all SNPs in the loaded MAGIC datasets. Gene names have been added where available for each analysis.
  • VCF  data

Known Issues

See JIRAhttps://jira.transmartfoundation.org/secure/RapidBoard.jspa?rapidView=12

Server address

http://postgres-test.transmartfoundation.org/transmart 

TranSMART version

Release 16.2 3 (built 14/Dec/2016; 16:20:52August 2018)

Database created

November 2016 May 2018 - using release 16.2 3 version of transmart-data

...

GWAS data loading is in preparation

Top LevelDiseaseStudyDatatypesNotes
 Across Trials    
eTRIKS Studies AsthmaGSE23611Expression 
  Rheumatoid arthritisGSE10024Expression 
  GSE10500Expression 
Private StudiesCell-lineCell-line

ACGH

expression

MicroRNA

proteomics

RNAseq

VCF

ACGH data under "High-throughput molecular profiling \ Copy number aberrations"

Expression data under "High-throughput molecular profiling \ Expression (mRNA)" ("...array")

MicroRNA data under "High-throughput molecular profiling \ Expression (miRNA)"

Proteomics under "High-throughput molecular profiling \ Expression (protein)"

RNAseq under "High-throughput molecular profiling \ Expression (mRNA)" ("Illumina... RNAseq")

VCF under "High-throughput molecular profiling \ Small Variants (DNA)" and "... (RNA)"

Loaded as a private study - login as administrator to use this study.

Public StudiesAcute Lymphoblastic LeukemiaGSE4698Expression  
 AsthmaGSE34466 clinical only  
  GSE13168Expression  
  GSE31773 clinical only  
 Brain CancerGSE4271Expression 
 Breast Cancer GSE4922 Expression  
  GSE5327 Expression  
  GSE1456 Expression  
  GSE4382Expression 
 COPD GSE8581Expression 
 Melanoma UvealGSE27831Expression  
 PsoriasisGSE11903Expression  
 Pulmonary SarcoidosisGSE19976Expression 
 Rheumatoid ArthritisGSE20690 Expression 
 Type 2 DiabetesGSE38642 Expression  Test Studies test_GSE4382_incrementalclinical only (incremental load)Data loaded incrementally - adding nodes, populating nodes, adding patients  test_mannheim_with_samples clinical only   test_mass_spec_proteomics MsProteomics    test_metabolomicsMetabolomics   test_miRNAseq_WittenmiRNA-RNAseq    test_qPCR_miRNA_GSE37424miRNA-qPCR   test_qPCR_miRNA_GSE37425miRNA-qPCR   test_qPCR_miRNA_GSE42468miRNA-qPCR

TraIT Cell-lineCell-line

ACGH

expression

MicroRNA

proteomics

RNAseq

VCF

ACGH data under "High-throughput molecular profiling \ Copy number aberrations"

Expression data under "High-throughput molecular profiling \ Expression (mRNA)" ("...array")

MicroRNA data under "High-throughput molecular profiling \ Expression (miRNA)"

Proteomics under "High-throughput molecular profiling \ Expression (protein)"

RNAseq under "High-throughput molecular profiling \ Expression (mRNA)" ("Illumina... RNAseq")

VCF under "High-throughput molecular profiling \ Small Variants (DNA)" and "... (RNA)"

 Type 2 DiabetesGSE38642 Expression  
TCGA StudiesBreast CancerBRCAExpression

Lung AdenocarcinomaLUADExpression

Ovarian CancerOVExpression
Test Studies V1.3 Test diabetes largeclinical only
  Test mannheim with samples clinical only 
  test mass spec proteomics MsProteomics  
  test
_qPCR_miRNA_GSE49520miRNA-qPCR (no clinical data) 
merged data typesExpression Metabolomics MsProteomics 
 
test_rbm_adniRBMproteomics 
 
  test_RNAseq_GSE48213RNAseq    test_serial_high_dimExpression (no clinical data) 
test mRNA microarrayExpression 
  test_
serial
qPCR_
high
miRNA_
dim_ricercaExpression
GSE37425miRNA-qPCR 

 Dictionaries loaded

DictionaryReleaseNotes
Entrez geneNov 2016Updates to data loaded with transmart-data
Gene ontologyNov 2016Where is this used in tranSMART 16.2?

HMDB

Aug 2015Human metabolite database
KEGGJan 2011Last pre-subscription release
MeSH2016Medline subject headings, diseases
MiRBase

Release 21

Aug 2015

MicroRNA database
UniProt/SwissProt Nov 2016Human entries only 
Observation-Diabetes entry for GWAS
VCFdbSNP 146SNP data for GWAS MAGIC datasets