ADAPT - Windows
A computational modeling platform for pharmacokinetic/pharmacodynamic analysis and systems pharmacology. Contains high-level software tools for early- through late-phase drug development, as well as clinical pharmacology applications. MSR (bmsr.usc.edu)
BioPP - tool for web-publication and hosting of large-scale, annotated signaling pathway diagrams
BSim - BSim is an agent-based modeling tool designed to allow for the study of bacterial populations. By enabling the description of bacterial behaviors, it attempts to provide an environment in which to investigate how local interactions between individual bacterium leads to the emergence of population level features, such as cooperation and synchronisation. More information is available at: http://bsim-bccs.sourceforge.net
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/
Continuity
Continuity is a problem-solving environment for multi-scale modeling in bioengineering and physiology — especially cardiac biomechanics, transport and electrophysiology — distributed free for academic research by the National Biomedical Computation Resource, an NIGMS Biotechnology Research Center. Continuity is portable, object-oriented, has separate GUI client and computational server components, and 64-bit versions under Windows, MacOS or Linux, including Linux clusters. It includes a client to a model library maintained by the NBCR.
DEDiscover - cross-platform tool for building and understanding differential equation models of antiviral immunity
DREM - models dynamic protein-DNA regulatory networks
EONS - Windows, Mac, Linux
The EONS (Elementary Objects of the Nervous System) software allows in-depth study of a number of synaptic components (presynaptic terminal, postsynaptic spine and astrocytic ensheathment), as well as their complex spatial and temporal interactions. BMSR (bmsr.usc.edu)
fastFVA - MATLAB
fastFVA is an efficient Matlab implementation of flux variability analysis (FVA) optimized for the GLPK and CPLEX solvers.
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.
LYSIS - Matlab - Windows, Mac, Linux
LYSIS is an interactive set of modular programs that provide an integrated computing environment for data analysis and system modeling, emphasizing input-output nonlinear system modeling and the novel methodology of “Principal Dynamic Modes”. BMSR (bmsr.usc.edu)
MIST - MIST stands for MIcro Simulation Tool. This software is a modeling framework aimed at disease modeling and supports Monte-Carlo micro-simulation of parallel state transition processes. It supports High Performance Computing environments - MIST runs over the cloud! This modeling tool is free to the public and released with source code under GPL license.
- The project web site is: https://github.com/Jacob-Barhak/MIST
- Presentation in SciPy 2013: http://www.youtube.com/watch?v=AD896WakR94
- See abstract and additional information in: https://github.com/scipy/scipy2013_talks/tree/master/talks/jacob_barhak
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
PDCO: Primal-Dual Convex Optimizer - A primal-dual interior method for solving linearly constrained optimization problems with a convex objective function. Available at http://www.stanford.edu/group/SOL/software/pdco.html. Please see http://www.stanford.edu/group/SOL/multiscale/software.html for other relevant software packages.
PNEUMA - Matlab-Windows, Mac, Linux
PNEUMA consists of a set of Simulink modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. BMSR (bmsr.usc.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
StochSS - Mac, Linux, Windows
Integrated development environment for discrete stochastic biochemical simulation. Currently features algorithms for well-mixed systems and ODEs. Problems can be specified via a graphical user interface (or imported as StochKit2 models). Planned to include algorithms for characterization of rare events, stochastic parameter estimation, spatial stochastic simulation and exploration of simulation data. Runs on your workstation or on the cloud.
TARGETgene - Matlab-Windows, Mac, Linux
Identification of mutation drivers, possible therapeutic targets and drug candidates in cancer. The GUI allows users to find, select, and explore identified target genes and compounds. Predictions can be validated via user-defined benchmark or curated cancer genes. BMSR (bmsr.usc.edu)
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
Virtual Cell: A Modeling environment for computational cell biology and physiology
Virtual Cell (aka VCell) allows users to create and run simulations of biochemical networks, membrane transport and electrophysiology. These can be formulated as compartmental ordinary differential equation models and numerically solved with a choice of ODE solvers. A unique feature of VCell is that it permits the incorporation of realistic experimental geometries within full 3D spatial models. Thus, the effects of diffusion and flow can be explicitly incorporated into models, and simulations provide solutions to the corresponding partial differential equations. Furthermore, simulations, both compartmental and spatial, can be performed using stochastic reaction probabilities and Brownian dynamics. An intuitive JAVA interface includes options for database access, geometry definition (including directly from microscope images), specification of compartment topology, species definition and assignment, chemical reaction input, membrane transport mechanisms (including voltage dependence), initial conditions, boundary conditions, simulation solver choices, and computational mesh. At the same time, VCell provides a mathematical interface that allows theoreticians to examine and elaborate models through purely mathematical formulations. It allows for the direct entry of mathematical equations that describe a model, through a declarative language (Virtual Cell Mathematics Description Language, VCMDL). The mathematics is then automatically translated into C++ programming code that can than be sent to the numerics solvers. Thus, modelers are relieved of the drudgery of writing ad hoc code for every new modeling task. Furthermore, a VCMDL description of a model can be produced directly and automatically from a model that has been created within the biological interface. This dual interface has the additional benefit of encouraging communication and collaboration between the experimental and modeling communities. http://vcell.org
- Paper of Interest:
Macro-to-Micro Scale Tools for Respiratory System Simulation - Penn State Applied Research Laboratory--Kunz (WG3)