Systems Biology

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Welcome to the Systems Biology Portal of the Center for Cell and Virus Theory at Indiana University. Below you will find descriptions of the different areas in our portal categorized by the scientific area. You may also use the bar at the top of the screen to quickly navigate between areas.
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• Cell Modeling - a suite of cell simulators:
  • Karyote is an integrated set of modules for building and simulating ordinary differential equation models of single cells and arrays of interacting cells. Karyote is hierarchical so that models can accommodate intracellular compartments for arrays of interacting cells. It allows automatic integration of simpler models to create more complete ones and has a set of example models.
• Network Discovery
  • TRND is an integrated workflow wherein user-supplied gene expression data generates transcriptional regulatory networks and derives their biological implications. TRND uses a built-in database of experimentally validated gene-transcription factor regulatory interactions and a non-linear dynamical systems analysis package for discovering transitions in cell behavior supported by a transcription-translation-post-translation process network.
    
    • Demo movie - a 15 minute overview of how to use the site
  • CellX is a database and platform for cooperative research on a particular cell type. Presently, transcriptional regulatory networks (TRNs) are available for a representative set of cell types of relevance to the NIH mission. These TRNs are intended to serve as a basis of user working groups who expand, curate, and use them as training-set TRNs that are transformed via bioinformatics, cell modeling, and gene expression and proteomic data to a TRN tailored for a particular cell line.
  • GeoGen, An interactive database of transcriptional regulatory information for Geobacter species.

These links provide static information about the Center for Cell and Virus Theory and related content. You may also use the bar at the top of the screen to quickly navigate between areas.

• Publications by CCVT researchers.
• Presentations from the CCVT.
• VTRI, The Viral Threat Reduction Institute is a collaborative effort of Indiana University and Purdue University dedicated to the use of advanced scientific and engineering approaches to address viral threats to global health and security.