Modeling Tools

From IMAG_Wiki

BioPP - tool for web-publication and hosting of large-scale, annotated signaling pathway diagrams

http://tsb.mssm.edu/pathwayPublisher/broadcast

CompuCell3D

CompuCell3D is an open source modeling environment and pde solver, primarly used to study cellular behavior. CompuCell3D was initially developed to help researchers (biologists and physicists) model materials and tissues without having to dedicate resources to developing code that will reproduce existing software. The code is built on C++ with a Python wrapper. Users can easily define model parameters in an XML file and run the simulation with our GUI, the CompuCell Player. The GUI gives users an easy interface to complex models as well as real time visualization of their simulations. CompuCell3D is freely downloadable from: http://www.compucell3d.org/

DEDiscover - cross-platform tool for building and understanding differential equation models of antiviral immunity

https://cbim.urmc.rochester.edu/software/dediscover

DREM - models dynamic protein-DNA regulatory networks

http://www.sb.cs.cmu.edu/drem/

JSim - multi-platform environment (Linux, Windows, MacOS) targeting modeling analysis of data (ODES, PDEs and DAEs)

-includes automated unit balance checking

http://nsr.bioeng.washington.edu/jsim/

Karyote

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.

https://systemsbiology.indiana.edu/karyote

Multiscale Systems Immunology (MIS) simulation - models early immune response to vaccination or infection

http://galen.dulci.org/msi

Modeling archival sites - models available for dowhloading and runnning:

http://physiome.org The University of Washington Physiome Project: ~300 models and related tutorials on physiological topics (mechanical, transport and biochemical) See this site for LINKS to many modeling sites. Run models over the Web.

http://www.ebi.ac.uk/biomodels Public, free, searcheable database of published models. Features over 450 models, of which currently 240+ have been hand-curated and annotated with links to various free databases. Models are available for downloading in SBML and other formats. Developed by the EBI and Caltech, and maintained by the EBI.

http://sbml.org/SBML_Software_Guide Tools for use with SBML

http://physiome.org.nz/ The IUPS Physiome Project and the home for CellML

http://cellml.org/ CellML: Markup Language for cellular Physiology and Biophysics: ~400 models

NMI Build and Test Lab - reliable, automated building & testing of software

http://nmi.cs.wisc.edu/

SBW: Systems Biology Workbench

The Systems Biology Workbench (SBW) is a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' capabilities via a fast binary encoded-message system. Numerous plugins exist for the SBW, including simulators, model editors, visualizers and analysis systems. All plugins accept (or export) standard SBML.

http://sys-bio.org/sbwWiki/doku.php?id=sysbio:sbw

STEM - analysis of short time series (3-8 time points) gene expression data

http://www.cs.cmu.edu/~jernst/stem/

TinkerCell: Engineering platform for building and testing cellular circuits

TinkerCell is an extensible platform for editing and simulating cellular networks. Users can operate the software at different levels including graphical point and click or via an interactive console. It has the ability to interact with databases such as RegulonDB to provide the user with parts for the construction of new or existing networks from which the DNA sequence can be generated for later fabrication. TinkerCell is cross platform and written in C++. A Python console is provided for interactive control.

http://www.tinkercell.com/Home

TRND

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.

https://systemsbiology.indiana.edu/trnd

Uncertainty and Sensitivity Analysis - Kirschner Lab

http://malthus.micro.med.umich.edu/lab/usadata/

Macro-to-Micro Scale Tools for Respiratory System Simulation - Penn State Applied Research Laboratory--Kunz (WG3)

OpenFOAM Abstract

Presentation Slides