NIAID Supported Data Analysis & Modeling Tools

Microarray/gene expression data

  • Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). http://www.cs.cmu.edu/~jernst/stem/
  • Dynamic Regulatory Events Miner (DREM) allows analysis and visualization of transcriptional gene regulation dynamics. http://gene.ml.cmu.edu/drem/
  • CorEx is a tool to identify possible transcription factors that regulate a given group of genes from transcriptional data. CorEx can, either jointly or separately, i) define the group of genes, ii) identify common transcription factor binding sites (TFBS) in the promoters of those genes, and iii) test the identified TFBS for enrichment/sharing. http://tsb.mssm.edu/primeportal/?q=corex

Multi-color flow cytometry

Mathematical Modeling

  • DEDiscover (Login Required) is a differential equation immune modeling software for scientists, statisticians and modelers. The software contains models of immunity to influenza that can be modified to fit specific immunologic and viral parameters. The software can also be customized to address additional areas of immunological research. https://cbim.urmc.rochester.edu/