The European Network of Excellence, ENFIN, is committed to providing a Europe-wide integration of computational approaches in systems biology

WP8: Graduate Level teaching

Activity type: COORD

Principal Partner(s):

Objectives

  • Develop course materials for an intensive graduate course in systems biology
  • Run one course within the first 18 months

Description

We will leverage the successful European School of Bioinformatics established by the BioSapiens network and will provide extensions to their cirriculum for Computational approaches in Systems Biology. The European School of Bioinformatics is held twice a year in a different country every time and will be followed, in the same location, by a workshop on one of the topics of interest of the network. It will consist of a six days entry level for inexperienced users and newcomers to the field. We have already contacted the BioSapiens coordinators to coordinate activities such that we would provide one of the two courses from our second year of activity. The course will have both theoretical and practical components, and the course materials will also be available from the ENFIN web site (and linked from the BioSapiens web site). The aim would be to provide a seamless educational environment from Genome Annotation (BioSapiens) to Systems Biology (ENFIN). The materials will also be of use to individual Masters courses in bioinformatics and biological information.

This course would also make extensive use of the documentation resource developed by Workpackage 9.

  • WP 1: Development of the ENFIN Core

    Objectives:

    • Assess workplan to develop the ENFIN core infrastructure
    • Develop starting ENFIN core infrastructure with ArrayExpress, Intact and Reactome
    • Roll the system out to the first set of alpha testers
    • Gather requirements from the ENFIN Analysis Layer groups

  • WP 2: Curation of appropriate pathway knowledge and hypotheses

    Objectives:

    • Capture new pathway information of interest to Network participants
    • Revise current pathway information in Reactome where appropriate
    • Develop structured hypothesis capture

  • WP 3: Development and management of new experimental data standards

    Objectives:

    • Assess current data standards and ontologies
    • Gather requirements from experimental and computational groups
    • Formulate new experimental standards in consultation with international groups

  • WP 4: Discrete Function Prediction

    Objectives:

    • Develop methods for discrete function prediction
    • Execute methods for named experimental areas
    • Integrate computational and experimental outlooks on the problem
    • Provide requirements to ENFIN Core working groups

  • WP 5: Network Reconstruction

    Objectives:

    • Develop methods for network reconstruction
    • Execute methods for named experimental areas
    • Integrate computational and experimental outlooks on the problem
    • Provide requirements to ENFIN Core working groups

  • WP 6: Systems-level modeling

    Objectives:

    • Develop methods for Systems Level Modeling
    • Execute methods for named experimental areas
    • Integrate computational and experimental outlooks on the problem
    • Provide requirements to ENFIN Core working groups

  • WP 7: Critical Assessment and Integration

    Objectives:

    • Run cross-workpackage workshops to assess prediction effectiveness
    • Approach interested groups for open critical assessment conference
    • Run workshop on structuring open critical assessment conference

  • WP 8: Graduate Level teaching

    Objectives:

    • Develop course materials for an intensive graduate course in systems biology
    • Run one course within the first 18 months

  • WP 9: Documentation from a wet laboratory perspective

    Objectives:

    • Assess best way to structure multi group documentation writing
    • Start the documentation writing on ENFIN

  • WP 10: SME focused outreach

    Objectives:

    • Investigate specific needs of SMEs in documentation and courses

The relationship between the different workpackages is shown in the graphic below:

ENFIN workpackages

Milestones

Milestone No. Milestone Name Delivered Date
M8.10 Organization of Advanced-level teaching of systems biology Tue, 2010-06-01
M8.9 Organization of Basic-level teaching of systems biology Tue, 2010-06-01
M8.8 Organization of Advanced-level teaching of systems biology Tue, 2010-06-01
M8.7 Organization of Basic-level teaching of systems biology Tue, 2010-06-01
M8.1 Running one graduate level course Wed, 2006-11-15
M8.2 Running one graduate level course Fri, 2007-06-15
M8.3 Organization of Basic-level teaching of systems biology Fri, 2008-02-15
M8.4 Organization of Advanced-level teaching of systems biology Sat, 2008-03-15
M8.5 Organisation of Basic-level teaching of systems biology Sun, 2009-02-15
M8.6 Organization of Advanced-level teaching of systems biology Sun, 2009-03-15