Question: In Silico Cell Modelling Platform
gravatar for Vova Naumov
7.0 years ago by
Vova Naumov210
Russia, Moscow
Vova Naumov210 wrote:

Do you know any platform/program/programming language or libraries for in silico cell modelling? It would be great to makevisualisations too.

software modeling • 3.9k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 7.0 years ago by Vova Naumov210
gravatar for Fred Fleche
7.0 years ago by
Fred Fleche4.2k
Paris, France
Fred Fleche4.2k wrote:

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[?][?]


ADD COMMENTlink written 7.0 years ago by Fred Fleche4.2k

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.

ADD REPLYlink written 7.0 years ago by Mary11k
gravatar for Mateusz Kuzak
7.0 years ago by
Mateusz Kuzak70 wrote:

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)

ADD COMMENTlink written 7.0 years ago by Mateusz Kuzak70

MCell can produce some great visualizations in combination with DREAMM e.g.

ADD REPLYlink written 7.0 years ago by Kraut220
gravatar for Melanie
7.0 years ago by
San Diego
Melanie620 wrote:

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.

ADD COMMENTlink written 7.0 years ago by Melanie620
gravatar for Pablo
7.0 years ago by
Pablo1.8k wrote:

I haven't tried it yet, but "Systems Biology Markup Language" (SMBL) seems to be related to what you think. The page has a lot of links to tools that support the language.

ADD COMMENTlink written 7.0 years ago by Pablo1.8k
gravatar for Herbert Sauro
7.0 years ago by
Herbert Sauro10 wrote:

There is a very long list of modeling tools listed at the 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:

  2. CellDesigner
  3. SBW (systems biology workbench)
  4. TinkerCell
  5. 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.

ADD COMMENTlink written 7.0 years ago by Herbert Sauro10
gravatar for Lars Juhl Jensen
7.0 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

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.

ADD COMMENTlink written 7.0 years ago by Lars Juhl Jensen11k

Thank you! But I mean that naybe someone can give advice about software, he recently used

ADD REPLYlink written 7.0 years ago by Vova Naumov210
gravatar for Nathan Harmston
7.0 years ago by
Nathan Harmston1.1k
Nathan Harmston1.1k wrote:

So theres COPASI: ... which can read in SBML files and simulate the corresponding models. Although it tends to be a little slow.

Theres also CUDASIM 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.

ADD COMMENTlink written 7.0 years ago by Nathan Harmston1.1k
gravatar for Khader Shameer
7.0 years ago by
Manhattan, NY
Khader Shameer17k wrote:

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.

ADD COMMENTlink written 7.0 years ago by Khader Shameer17k
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