3rd international symposium on Computational Life Science
October 4-5, 2007 University of Utrecht, The Netherlands
 

 

CompLife Application Tutorials

Four application tutorials will be held in two blocks after the main conference on Friday 5th October in the afternoon. We will decide which tutorials will be held in parallel once we have received registrations. Therefore, please indicate your wishes in the registration form. Participation is free of charge! Each tutorial will last about 2 hours.

  1. C a n c e l e d
    NGS - National Grid Service (http://www.ngs.ac.uk)

    This tutorial will introduce participants to the basic concepts of grid computing and the UK’s National Grid Service (NGS). The NGS offers both compute power and data storage to all UK based academics.

    The Applications Repository, which is introduced in this tutorial, allows users to execute personal applications and applications that are hosted and configured by the NGS, including life science software such as Amber and Gromacs through an online graphical interface.

    Grid computing is a growing area, with many ‘grand challenge’ projects making use of the NGS. One such ‘grand challenge’ is being studied by the Integrative Biology Project, which aims to understand the two biggest causes of death in the UK - heart disease and cancer - by developing detailed multi-scale computational models of the heart and of cancer tumours.

    Tutors: David Meredith & Katie Weeks
    Note: Participants need to bring their own laptops

  2. Bioclipse (http://www.bioclipse.net/) & CDK

    Bioclipse is an open source workbench for chemo- and bioinformatics with rich functionality for molecules, sequences, proteins, spectra, and scripts. Bioclipse has an advanced plugin architecture, which facilitates integration of new functionality, such as algorithms, editors, visualizations, Web services, and third party applications.

    Bioclipse is now published including "features" and packaging plugins and views for a certain type of functionality in one easy download.

    Features that can be downloaded include QSAR, Chemoinformatics and Bioinformatics.

    The Complife Tutorial will demonstrate the features of Bioclipse, the power of the plugin architecture, and how to integrate new features into the framework.

    We would also like to show new developments in The Chemistry Development Kit (CDK) – a freely available open-source Java library for Structural

    Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics. It is available at http://cdk.sourceforge.net.

    Tutor: Ola Spjuth & Egon Willighagen
    Note: Participants should preferably bring their own laptops

  3. C a n c e l e d
    Cytoscape (http://www.cytoscape.org/)

    This tutorial is intended to introduce CompLife '07 delegates to the open source software "Cytoscape", a network visualisation and analysis tool.

    We will introduce you to the Cytoscape Graphical User Interface and then Construct and Load Biological Networks. Then we will visualize and analyze the networks. Integration of Molecular State Data with the Biological Networks is also covered, as well as advanced sub-network identification. The tutorial will close with biological analysis and questions and answers.

    Tutors: Guy Warner & Yeyejide Adeleye
    Note: Participants need to bring their own laptops

  4. KNIME - Konstanz Information Miner (http://www.knime.org/)

    The first part of the tutorial will introduce the Data Analysis Platform KNIME. We explain KNIME's workflow concept, present some of the data processing and data mining nodes and demonstrate one of KNIME's key features, known as "visual brushing".

    The second part of the tutorial will deal with extending KNIME by writing custom nodes. Here, we will provide a short introduction about the API and then write a new node, starting with creating the necessary classes through to bundling the node in a new Eclipse plugin, which can be integrated into any KNIME installation.

    Tutors: Thorsten Meinl
    Note: Participants need to bring their own laptops