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University of Cambridge
The 2nd International Symposium on Computational Life Science
CompLife '06
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Life Science Free Software Session

CybercafeIn the last years more and more free and open source software has been developed for chemo- and bioinformatics, molecular modelling or other Life Science applications, but many of the programs are not well known. During the CompLife 2006 conference we will organize a special session dedicated to this type of free software. The demo session will be preceeded by a short session having room for brief introductory presentations whereas the demo session itself will allow attendees to see the tools in action. Authors of free software will have the opportunity to present their program to the CompLife audience which will consist of researchers and users from computer science, biology, chemistry and everything in between.

The following software will be presented on the first day of the conference in the CyberCafé, Department of Chemistry, Lensfield Road. After a presentation of each software program, you will have the opportunity to talk to the presenters in more detail about their software. Each software stand will be set up in and around the CyberCafé in the Dept. of Chemistry, lending the event a relaxed atmosphere. The conference reception will begin after the software presentations have taken place and we therefore hope you will enjoy testing the software, while sipping a glass of wine and enjoying the snacks that will be served!

27th September 17.00 – 20.00, Free software session (Chair: Thorsten Meinl)


  1. Cclib (http://cclib.sf.net): Cclib is an open source library, written in Python for parsing and interpreting results of computational chemistry packages.
  2. National Grid Service NGS, (http://www.ngs.ac.uk): The UK’s research Grid for e-Scientists.
  3. EMBL-EBI’s (http://www.ebi.ac.uk): The EMBL-European Bioinformatics Institute (EMBL-EBI) provides freely available biological data and bioinformatics services.
  4. DeltaProt (http://www.math.uit.no/bi/deltaprot/): Motivated by the need to create a flexible software platform that enables statistical analyses of proteins with special preferences of temperature, pH, salt concentration or pressure.
  5. Bioclipse (http://www.bioclipse.net/): Free, Java-based, open source workbench for chemo- and bioinformatics.
  6. CDK (http://cdk.sourceforge.net/): CDK is an open source chemo- and bioinformatics library, covering chemistry, pharmaceutical sciences and structural biology.
  7. COMPARE (http://dtp.nci.nih.gov/docs/compare/compare.html): COMPARE is a tool for exploring correlations across data from the NCI panel of 60 human tumor cell lines.
  8. KNIME (http://www.knime.org/): A modular, extensible information mining platform.
  9. SSAHA2 (http://www.sanger.ac.uk/Software/analysis/SSAHA2/): Very fast DNA sequence alignment tool.
  10. AMBIT (http://ambit.acad.bg/): Open source chemoinformatics software written in Java; standalone (desktop) and Web server (servlets) applications.
  11. Cytoscape (http://www.cytoscape.org/): Open-source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
  12. iBabel (http://homepage.mac.com/swain/Sites/Macinchem/applescripts.htm): A Mac GUI for the file conversion utility OpenBabel together with others tools built on the OpenBabel framework.

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