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Welcome to project gscf
GSCF is an open source project in which a number of universities, companies and academic consortia participate. Most notably NuGO (The European Nutrigenomics Organization), NMC (Netherlands Metabolomics Centre) and of course NBIC (Netherlands Bioinformatics Centre) which hosts the project. For more information see http://dbnp.org. GSCF is licensed under the Apache 2.0 license.
Be sure to check out our online demo (log in with username 'user' and password 'useR123!'). If you want to try installing it yourself, the easiest way is to deploy the latest pre-compiled test war from the Downloads section in a Java servlet container such as Tomcat. Be advised that this uses an in-memory database and will destroy your input at each restart! To learn more about how to set up your own database and custom configuration, read Quickstart. If you want to set up your own dedicated GSCF server, read QuickStartServer.
You can do an anonymous readonly checkout using subversion as follows:
svn co https://trac.nbic.nl/svn/gscf gscf
Write access is only available to registered developers.
GSCF stores only study design (meta)data for studies. However, most of the time, you will also have data that were measured on samples, such as transcriptomics, metabolomics or sequencing data. These can be stored in so called 'dbNP modules' and can then be dynamically attached to GSCF and the studies described in GSCF. Modules maintained in NBIC Trac are:
- CTD: a module for storing transcriptomics data
- DSP metabolomics module: a module for storing metabolomics data
- SAM: a module for plain numerical data (e.g. clinical chemistry data)
- Mass Sequencing: a module for 454 sequencing data
This project provides the following mailing lists.
- gscf-users: a list intended for general discussion on the project.
- gscf-commits: a list that receives source code commit messages.
- gscf-devel: a list intended for discussion among developers (subscription is restricted to registered developers).
Other available documents are IDE Configuration, 1.0 Code Cleanup Troubleshooting and Development Guidelines.
Other NBIC software projects
All active NBIC software projects can be accessed from the project index.