Bioinformatics Systems Biology

• 3D Reconstruction Via Stereoscopy for the Study of Mosquito Swarms
• Dose Response Analysis Pipeline (DRAP)
  A web-based application for high-throughput dose response analysis.
• Immune Epitope Database and Analysis Resource (IEDB)
  
  • B Cell Epitope Prediction Tools
    These tools are intended to predict regions of proteins that are likely to be recognized as epitopes in the context of a B cell response.
  • T Cell Epitope Prediction Tools
    These tools predict IC50 values for peptides binding to specific MHC molecules.
• Modeling Immunity for Biodefense
  This program brings together immunologists, microbiologists, bioinformaticians, and modelers to develop mathematical models of immunity to infection or vaccination.
• Simmune
  Simmune is the name of a suite of software tools that guides the user through the multiple hierarchical scales of cellular behavior, facilitating the generation of comprehensive models. It was originally created to simulate immunological phenomena — hence its name, Simmune — but it is applicable to a very broad class of cell biological models.
• Systems Approach to Immunology
  
  • Computational Core
    Aggregates and integrates data from consortium Cores; constructs pipelines for automated data processing; disseminates consortium data to the scientific community.
  • Signalling Core
    The aim of this investigation is to identify the temporal activation of intracellular signaling proteins in response to TLR activation.

• Systems Biology for Infectious Diseases
  
  • Systems Biology of Enteropathogens
    This program, a multi-institution center, was established to deepen our fundamental understanding of the complex processes of microbes and their interactions with the host.
    • COBRA Project
      Physiochemical constraints to model a biological network.
    • Omics Datasets
  • Systems Influenza
    
    • Exon microarray data sets
    • SILAC Proteomic Data
    • Viral Host protein interactions
      The goal of this project is to identify the compendium of host proteins that interact directly with influenza viral proteins.
  • Mycobacterium tuberculosis Systems Biology
    
    • CSDeconv
      A computational method to locate TF binding from ChIP-seq data using blind deconvolution.
    • GenomeView
      Genome editor and viewer with dynamic visualization of aligned short read sequences.
    • E-Flux
      A method to model metabolic states using whole cell measurements and extend flux balance analysis.
    • Mycobacterium tuberculosis ChipSeq regulatory binding sites
      This page allows you to search for regulatory binding interactions based on ChIP-Seq data.
  • Systems Virology
    
    • Systems Virology Agilent Microarray datasets
    • Proteomics datasets
    • Seqbias
      Graphical per-position bias correction of quantitative sequence abundance in RNA-Seq experiments
    • Peptide Abundance Analysis Toolbox (PAAT)
    • QC workflow for Proteomics Data: RMD
      A statistical program to determine if LC-MS peptide abundance data are statistical outliers.

Contact Information

For more information on Bioinformatics Systems Biology, email
Bioinformatics and Computational Sciences Branch