Modeling Tools
From IMAG_Wiki
BioPP - tool for web-publication and hosting of large-scale, annotated signaling pathway diagrams
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
DREM - models dynamic protein-DNA regulatory networks
GENESIS - The GEneral NEural SImulation System was designed from the outset to support the biologically realistic modeling of neural systems at levels of scale ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. GENESIS 3 (G-3) is a complete redesign of GENESIS, with a modular plug-in architecture that facilitates the incorporation of new types of model components at any level of scale. This design allows the direct real time interaction or embedding of models (local or remote) at different levels of scale, and also provides a framework for collaborative modeling and software tool development. Both the current developer's release of G-3 and the stable GENESIS 2.3 release, documentation, and tutorials are available from the GENESIS web site
JSim - multi-platform environment (Linux, Windows, MacOS) targeting modeling analysis of data (ODES, PDEs and DAEs). The JSim Project file is a vehicle for "Reproducible Modeling" for it can contain all the elements of the modeling project: model description, source code, automated unit balance checking on equations and parameter calculations, verification suites to test the numerical methods, multiple numerical methods for ODEs, DAEs, and 1- and 2-dimensional PDEs, experimental data sets (many in a given project file), the fitting of models to data using manual or automated optimization by 8 methods, goodness of fit and parameter confidence range evaluation by covariance matrix and by MonteCarlo, a variety of graphics, notes for operating instructions and for data processing. These can be run over the web or downloaded. The models and the JSim simulation analysis platform is Open Source (BSD), and all 350 models can be downloaded freely.
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
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
NEURON - biologically realistic modeling of neural systems from molecular to network level. A recent improvement provides greater tools for reaction/diffusion modeling at the subcellular level. Program supports multiple types of synapses including learning. Also provides facilities for multiple types of cell models, including multicompartment cells, integrate&fire, event-based and others. Program utilizes a plugin compiled language (NMOD) as well as 2 alternative interpreters: Hoc and Python. URL: :http://www.neuron.yale.edu; 100s of simulations available at :http://senselab.med.yale.edu/ModelDB which also houses many simulations for other simulators and programming languages.
OpenMM - OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes. Benchmarks demonstrating OpenMM performance are available here: http://wiki.simtk.org/openmm/Benchmarks. OpenMM is open-source and is available for download from http://simtk.org/home/openmm.
OpenSim
OpenSim is a freely available, user extensible software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. Visit our website to find out more about the project, download the software, and joint the community of researchers using OpenSim.
- Learn about the OpenSim and its applications: http://opensim.stanford.edu/work/index.html
- Download the Software: https://simtk.org/home/opensim
- News about OpenSim: http://news.stanford.edu/news/2011/october/opensim-motion-software-102711.html
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
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
Macro-to-Micro Scale Tools for Respiratory System Simulation - Penn State Applied Research Laboratory--Kunz (WG3)
