Do you know any platform/program/programming language or libraries for in silico cell modelling? It would be great to makevisualisations too.
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[?][?]
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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)
MCell can produce some great visualizations in combination with DREAMM e.g. http://www.youtube.com/watch?v=KQgydF-fXvc
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.
I haven't tried it yet, but "Systems Biology Markup Language" (SMBL) http://sbml.org/ seems to be related to what you think. The page has a lot of links to tools that support the language.
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:
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 there's COPASI ... which can read in SBML files and simulate the corresponding models. Although it tends to be a little slow.
Theres also CUDASIM. This is the link to their paper.
It 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.
I think SBML software matrix or the software category will be a good place to start. You can easily select tool for your analysis based on various criterias using the matrix.
Is there any easy way to model in silico if a peptide derived in my lab will get held up in the cell membrane in transit to the nucleus? I have the entire peptide sequence and after looking for a while it seams like in silico can be quite complex if it is not a common model. any help would be much appreciated!
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I took a workshop on CellDesigner a couple of years back and was really impressed with it then. It had a lot of capability at that time, it's probably got even more now.