• 3DVC

3DVC Community Catalor is a collaborative project between the 3DVC and the NIF (Neuroscience Information Framework). The initial existing resources in the 3DVC catalog were tagged from the NIF catalog as resources relating to the 3DVC Community. A special thanks to NIF for helping launch the catalog and providing supporting services; to Delsa.org for helping tag resources and to the working group members for hours of volunteer time and input.

http://www.3dvcell.org/catalog

• 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/

• CellX

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. For more information, contact Peter J. Ortoleva, Director of the Center for Cell and Virus Theory, at 812-855-2717

https://systemsbiology.indiana.edu/cellx

• FLAME

FLAME is an agent-based modelling framework developed at the University of Sheffield. It has been successfully used to model biological systems and has already uncovered useful results. The framework, which uses X-machines as the basic computational model is flexible enough to be applied to various disciplines from biology to economics. FLAME provides specifications in the form of a formal framework which can be used by developers to create models, and software tools, that are compatible with one another.

Media:FLAME_Documentation.pdf is a document which gives insights into the modelling framework, FLAME, and how it can be applied to biological systems modelling.

Free downloads of FLAME at: http://www.flame.ac.uk, and information about the Epitheliome Project (individual-based modelling of epithelial tissues from a cell-based perspective) at: http://www.dcs.shef.ac.uk/~rod/

For more information about FLAME, contact Rod Smallwood, Head of Computational Systems Biology research group at the University of Sheffield, at mailto:r.smallwood@shef.ac.uk.

• JSim

JSim is a Simulation interface supporting primarily the modeling analysis of data, from model development, through verification and validation, and comparisons among models, to parameterization of experimental data, and routine clinical data analysis. Coding can be done directly in JSim's MML (Mathematical Modeling Language). It provides a variety of numerical methods for ODEs and PDEs, sensitivity analysis, optimization of model fitting to data (several optimizers), repetitive operation (Loops) with automated parameter changes for model exploration.

Model code in JSim's MML can be automatically generated from SBML and CellML. In addition to parsing MML into Java for computation, JSim is also serving as a front end for models in FORTRAN, C, and Matlab, A course using it will be given September 8th to 15th at U.Washington. :Free download of models and JSim at:

https://www.physiome.org/jsim

23Aug07: MSM Consortium BREEZE presentation of Modeling with JSim, followed by Discussion on model sharing and archiving Media:IMAG23aug.ppt

Try JSim out, with or with out downloading it, at http://www.physiome.org.

• MASON

MASON is a discrete-event multiagent simulation library written in Java, designed to be a lightweight foundation for large custom simulations. It contains both a model library and an optional suite of visualization tools in 2D and 3D. MASON's focus is on computational efficiency, speed, and a minimal API, in contrast to packages that attempt to provide a complete platform with many convenience classes and constructs. This is made possible, in part, by the plethora of third party Java libraries available.

MASON development focuses on social system simulation, which places a heavy emphasis on discrete spaces and networks. But it is a fully general library with some convenience classes for continuous spaces and schedules.

http://cs.gmu.edu/~eclab/projects/mason/

• 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

• openCOBRA toolbox

MATLAB toolbox for constraint-based reconstruction and analysis (COBRA). Available from http://opencobra.sourceforge.net/openCOBRA/Welcome.html

• 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 freely available to the biomechanics community and enables advanced modeling and simulation of human and animal movement, including inverse dynamics analysis and forward dynamic simulation. The software provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through a world-wide collaboration. The software, complete models, and example simulations are available at the project website, https://simtk.org/home/opensim. The project page also includes tutorials to help you get started with the software.

• Ptolemy II

Ptolemy II is an open-source, actor-oriented, multi-formalism, co-simulation framework. Actors are software components that execute concurrently and communicate through messages sent via interconnected ports. A model is a hierarchical interconnection of actors. Model semantics are determined by a software component in the model called a director, which implements a model of computation, including directors supporting process networks (PN), discrete-events (DE), dataflow (SDF), synchronous/reactive(SR), rendezvous-based models, 3-D visualization, and continuous-time models. Multiscale, multi-formalism models are developed by nesting models using CompositeActors, whose semantics can be set by their own local directors.

Ptolemy II is implemented in Java, but is extensible to other languages (e.g. Python and Matlab) for Actor implementation. Models can be manually coded in Java or the MoML XML schema but are usually composed with a graphical programming tool called Vergil.

http://ptolemy.eecs.berkeley.edu/ptolemyII/

• 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

• StochSS: Stochastic Simulation Service

StochSS is an Integrated development environment for discrete stochastic biochemical simulation. It runs on Mac or Linux. StochSS currently features algorithms for well-mixed systems. It is planned to include algorithms for characterization of rare events, stochastic parameter estimation, spatial stochastic simulation and exploration of simulation data. StochSS runs on your workstation or on the cloud (and the transition is easy).

http://www.StochSS.org

• Swarm

Swarm is both a modeling platform for the construction of agent-based models as well as a set of libraries for experimentation with hierarchical (multiscale) discrete-event and discrete-time computational complex systems. It was designed to facilitate the study of artificial life and provides significant overlap with agent-based simulation. Its unique features beyond other such libraries are its dynamic class customization, logical concurrency model, and semi-automatic composition of objects into Swarms. These features assist in the rapid synthesis, execution, and iterative evolution of hierarchically composed algorithms which are usually used to simulate (in silico) natural systems and explore the complex maps between local mechanism and global phenomena.

Swarm is written in GNU Objective-C, but can be invoked through Java bindings. A preliminary Apple Objective-C configuration is available from the open source repository at Savannah. There is also an XPCOM layer that can be used to invoke the Swarm libraries from various languages. The GNU Objective-C and Java layers are accessible on Linux (or other Unix platforms supporting GCC) and Windows (with Cygwin) and on Mac OS X using the Apple Objective-C target.

http://swarm.org/index.php/Swarm_main_page

• 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

• 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