6 months master 2 projects at the European Bioinformatics Institute (EBI)
Camille
The European Bioinformatics Institute (http://www.ebi.ac.uk/), British
outstation of the European Molecular Biology Laboratory (http://
www.embl.org/) provides internship placements for undergraduate
students, usually as part of a Master's degree or equivalent. The
interns join a group at the EBI and are involved in an ongoing
research project. They will gain experience by working in an
international environment. Limited funding is provided to cover for
living expenses.
The Computational Neurobiology group (http://www.ebi.ac.uk/compneur/)
is looking for one or several trainees to work on one of the projects
described below. The internships should last 5-6 months, starting
anytime from January 2010.
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BioModels: A Database of Annotated Published Models
BioModels Database is a free and open-source database for storing,
exchanging and retrieving published quantitative models of biological
interest. Deposition of models upon publication is supported by
several publishing companies.
http://www.ebi.ac.uk/biomodels/
The student will work on one or several of the following features:
- Mirror synchronisation: development of a complete solution in
order to conveniently manage (during releases and other updates) the
software and content available on the mirrors of the resource.
- Search engine: development of a "one field search engine" where
users can perform complex queries by using simple keywords.
- Annotation helper: improvement of the model annotation interface
in order to present suggestions (based on external resources) for the
curators.
Knowledge of Java, XML and relational databases is required.
The student will preferably have a strong background in Informatics
and Bioinformatics.
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SBML to SBGN converter
The Systems Biology Graphical Notation (SBGN, http://sbgn.org/) is
an effort to standardise the graphical notation used in maps of
biochemical and cellular processes studied in systems biology. SBGN
maps can be generated from files encoded in SBML.
The student will work on:
- Improving the automatic layout of the graphs.
- Providing a tool to help the curators to modify easily and
quickly the generated graphs.
- Improving the possible interactions with a graph.
The final goal is that the SBGN representation of an SBML file
becomes the main entry point to visualise a model in BioModels
Database web interface.
Knowledge of XSLT is required.
The student will preferably have a strong background in Informatics
and Bioinformatics.
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KiSAO : Kinetic Simulation Algorithm Ontology
The KiSA Ontology covers the most important simulation algorithms
and simulation methods used to simulate biological kinetic models and
puts those algorithms and methods into relation.
http://www.ebi.ac.uk/compneur-srv/kisao/
The student will work on extending the ontology and enrich its
structure (in particular moving from OBO to OWL).
Knowledge of OBO and OWL is required.
The student will preferably have a strong background in Mathematics
and Bioinformatics.
Please send your detailed English CV to Nicolas Le Novère (lenov AT
ebi.ac.uk) and Camille Laibe (camille.laibe AT ebi.ac.uk).