Project members

• Kees Van Bochove (owner)
• Michael Van Vliet (owner)
• M S Vanvliet (owner)

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.

Quick start

Be sure to check out our ​online demo. 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.

Source access

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.

You can become a developer by ​registering yourself if you haven't already done so, and requesting write access on the ​gscf-users mailing list.

Modules

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

Mailing lists

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).

Documents

Detailed information on the use of Javascript classes can be retrieved from ​Technical Documentation.
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.