In my library I have the book Introduction to Systems Biology which should be a good starting point. [?]Moreover at the appendices section there are the follwoing resources in the category [?]modeling[?][?]
- CellML 1.1
- SBML (System Biology Markup Language)
- SBML Editor
- SBML Toolbox
- Virtual Cell
Depending on what you are looking for, you might find one of these interesting:
MCell A Monte Carlo Simulator of Cellular Microphysiology
E-Cell Project a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell
CompuCell3D based on the Cellular Potts Model (CPM)
I think that you're going to have to be more specific than "cell modeling". Some tools work best for electrophysiological models, some work best for pathway models, some are best for bacteria, others will also do eukaryotes, some make pretty pictures and handle qualitative models, others will run full on simulations if you provide the math.... In other words, what exactly are you trying to do? I haven't been involved in the field for many years, so I can't really tell you which tool to use in any given situation, but unless there has been a massive leap forward in the years since I last checked in, no one tool can handle all of the situations. The list that Fred provided is a decent starting place, and which thing you use will depend on what you want to do.
CellML and SBML are just languages to describe the models (disclaimer- I was involved with CellML many years ago). There are repositories of models in both languages. You could start with their websites and see what tools and models they link to and go from there.
There is a very long list of modeling tools listed at the SBML.org web site. As another contributer mentioned, it all depends on what kind of modeling you would like to do. For modeling biochemical networks I would recommend the following:
- SBW (systems biology workbench)
- Virtual Cell
These are probably the most popular. Other than these you also have more general tools such as Matlab or Mathematica. Whatever you use however I would make sure the tool can import and export SBML and/or CellML. This will allow you to move your model to another tool if need be.
DISCLAIMER: SBW and TinkerCell is developed by people in my group.
No offense, but did you try using Google? A simple search for cell modelling software immediately gives me links to multiple different software platforms/tools for in silico modeling of cells.
So theres COPASI: http://www.copasi.org/ ... which can read in SBML files and simulate the corresponding models. Although it tends to be a little slow.
http://sourceforge.net/apps/mediawiki/cuda-sim/index.php?title=CUDA-SIM which allows you simulate models of biochemical networks on CUDA-enabled GPUs and is very .. very fast. Kind of depends what you're looking for and have available.
DISCLAIMER: CUDA-SIM is developed by people from my group.