Chair of Bioinformatics

    Dynamic modelling of protein networks

    Software required for our education due to version compatibility

     

    SQUAD 2: download

    Squad 2 requires Java SE runtime environment 6, not newer.

    Java SE 6 can be downloaded from here.

    Squad tutorial please read: http://www.enfin.org/wiki/squad-tutorial

    please cite the original paper and author:

    Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L. Dynamic simulation of  regulatory networks using SQUAD. BMC Bioinformatics. 2007 Nov 26;8:462. PubMed PMID: 18039375; PubMed Central PMCID: PMC2238325.

    Readme:

    To run squad under win7/8, you have to uninstall JRE 7 firstly if you have it installed before. Then download JRE 6 from Oracle (1.6.0_45) and install it. Attention! You are only allowed to download after filling out registration with Oracle and agree with the license, please follow the link: http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase6-419409.html.


     

    Celldesigner 3.5.1 (windows): download

    Celldesigner 3.5.1 (linux): download

    Original release please see: http://www.celldesigner.org/features/features351.html

    please cite the article and author: Oda K, Matsuoka Y, Funahashi A, Kitano H., A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol. 2005;1:2005.0010. Epub 2005 May 25.


    Readme:

    To run Celldesigner 3.5.1 under win 8, you have to follow this instruction

    step 1. framework 3.5 (2.0 and 3.0) is not included in win7 and win8 by default, since it is originally for winxp and vista. Go to Settings, choose Control Panel then choose Programs,
    step 2. choose second rows in the left, "Turn windows features On or Off", after 5 seconds, you will see a menuitem in the window. .NET framework 3.5 (includes .NET 2 and 3), click it and both submenuitems. Then OK button.
    step 3. after 3 minutes, it will finish.
    step 4. simulate Vista environment. install celldesigner 3.5.1, afterwards, with right mouse button please click the celldesigner icon.
    step 5. click the properties in the menu. find the compatibility tab-button, click it.
    step 6. in the drawbox menu, select the "Windows Vista", not "winXP", not "win7",  check the run the program with compatible mode, then click OK button.
    step 7. go to desktop, enjoy your Celldesigner.

     


    Jimena

    Jimena is available at jimena.bioapps.biozentrum.uni-wuerzburg.de

    Karl S, Dandekar T. Jimena: efficient computing and system state identification for genetic regulatory networks. BMC Bioinformatics. 2013 Oct 11;14:306. doi: 10.1186/1471-2105-14-306. PubMed PMID: 24118878.

     


    CNA: Cell Net Analyzer

    CNA 6.0 (and higher) is the successor and further development of FluxAnalyzer 5.3 . FluxAnalyzer was originally developed for analyzing stoichi- ometric (metabolic) networks. CNA extends the functionalities of FluxAnalyzer by providing also a framework for structural and functional analysis of cellular signaling and regulatory net- works. The way to construct, repr esent and analyze networks within CellNetAnalyzer is basically the same as in FluxAnalyzer and everyone who is familiar with FluxAnalyzer will quickly be able to use the facilities of CellNetAnalyzer as well. Since CNA distinguishes between mass- flow (i.e. stoichiometric or metabolic) networks and signal-flow (signaling and regulatory) net- works, the analysis of stoichiometric networks can be done in the same way as in FluxAnalyzer and a conversion of network projects compiled with earlier versions is not required.

    It can be downloaded at www2.mpi-magdeburg.mpg.de/projects/cna/cna.html

    A manual is public available at here

    Klamt S, Saez-Rodriguez J and Gilles ED (2007) Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 1: 2.


     

    Perl courses

    Course slides: Download

     

     

     

     

     

     

     

    Contact

    Lehrstuhl für Bioinformatik
    Am Hubland
    97074 Würzburg

    Tel. +49 931 31-84550
    Fax: +49 931 31-84552

    Find Contact

    Hubland Süd Hubland Nord Campus Dallenberg Fabrikschleichach Humangenetik Campus Medizin