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Cell-simulations portal

DOI: 10.1186/gb-2001-3-1-reports2002

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Navigation is reasonably straightforward and finding the different parts of the site is easy, although there is no dedicated search engine. The links back and forth are not uniform, however: good in some places but absent from others. Customization is possible in the modeling, simulation and image framework. Most pages print as they are seen on-screen, including the figures. No special software, other than a JAVA-enabled browser, is needed to access the site.The last update at the time of writing was 13 June 2001 with Version 3.0 of Virtual Cell.The availability of a modeling platform that frees biologists from having to invest in local computing resources is great. It realizes the vision of remote computing with bare-bones computers logged into central high-performance machines over the internet.At the moment, even small simulations take a very long time to run, without any indication of how long it will take. The response to feedback is poor, having taken over a working week for meBetter performance from the program and a fitting and optimization module added to the virtual cell software would certainly add to the attractiveness of the resources.Tools for similar simulations in cell biology are commercially available for work offline from Berkeley Madonna and the ordinary differential equations (ODE) and partial differential equations (PDE) solvers of MATLAB. Image libraries of cells are available at, for example, the Virtual Cell for plant cells. Data standards in computational cell biology are available at CellML and Systems Workbench Development Group.The National Resource for Cell Analysis and ModelingBerkeley MadonnaMATLABVirtual CellCellMLSystems Workbench Development Group


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