Human Immunology Project Consortium links-niaid-data

NIAID Supported Data Analysis & Modeling Tools

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_prog

Misty Mountain is a fast unsupervised clustering algorithm designed for flow cytometry gating. http://tsb.mssm.edu/primeportal/?q=misty_mount_algor
FLOCK is an algorithmic application for the identification of unique cell populations in multi-dimensional flow cytometry data. Available through ImmPort. https://www.immport.org/immportWeb/home/home.do?loginType=full#

Biological Pathway Publisher (BioPP) is a web-based application for biological networks publication that facilitates sharing of pathway knowledgebases and interactive curation for research teams and scientific communities. The BioPP software suite consists of four interrelated elements: a Pathway Publisher, an Upload Web-Interface, a Pathway Repository, and a Pathway Navigator. http://tsb.mssm.edu/primeportal/?q=bioPP

DEDiscover 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/software/dediscover/