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Internship opportunities

Curation internship: Literature curation of mechanistic models of disease pathways

BioModels Database is a central repository of mathematical models of biological/biomedical processes. It is hosted at EMBL-EBI and is one of the resources of the molecular systems cluster. The models distributed through BioModels are extensively tested and encoded in standard formats (for example, SBML (Systems Biology Markup Language)) and are free to use. In addition, the models and their components are cross-referenced with external data resources and ontologies, which facilitates search and retrieval, and maximises the benefits of the growing number of already existing models.

Curating models of biological processes is an effective training in computational systems biology, where the curators gain an integrative knowledge on biological systems, modelling and bioinformatics. We have a number of internship opportunities available within the team, to carry out targeted curation of mechanistic models of certain disease pathways. The topics likely to be focused, but not limited to, are cancer, neurodegeneration, arthritis (inflammation & immunology), plant systems, and diabetes [1].

The internships might be ideal for a master degree thesis or for candidates who are in between their masters and PhD. An initial knowledge of biology, mathematics and computing is desirable. The successful candidate will be a master student in bioinformatics or systems biology. Training will be given to understand basics of modelling, and on modelling and simulation tools. The position is ideally for 6 months, but can be extended up to one year. A fixed monthly allowance is provided to help towards living costs.

For further enquiries or to make an application (attach your CV and a cover letter), please contact: Vijayalakshmi Chelliah (viji AT ebi.ac.uk).

  1. Ajmera I., Swat M., Laibe C., Le Novèrei N., Chelliah V. The impact of mathematical modeling on the understanding of diabetes and related complications. CPT: Pharmacometrics & Systems Pharmacology. Jul 10;2:e54. 2013.

Software development intership: Development of a model editor for drug discovery

We are looking for a talented student to develop an editing software tool for Pharmacometrics models. Those models describe and quantify interactions between xenobiotics and patients , including beneficial effects and adverse effects. They are applied to quantify drug, disease and trial information to aid efficient drug development, regulatory decisions and rational drug treatment in patients. Recently, a consortium of academic and industrial partners developed PharmML, a standard markup language to encode those models.

The standalone tool, written in the Java programming language, will permit to create, edit and export pharmacokinetics/pharmacodynamics (PKPD) models in PharmML. This includes the definition of the model (structural and statistical), the trial design and the modelling steps. The tool will use PharmML schemas and the Java API libPharmML. The student will be assisted by the developers of PharmML, libPharmML and software developers experienced in the creation of similar tools.

The successful candidate will be a master student in computing science or bioinformatics. He will be proficient in Java programming, and at home with all the usual software development productivity tools. Enthusiastic and industrious, he will be a independent worker but thrive in a team environment. The position is intended to last up to 6 months and should ideally be part of a degree.

For further enquiries or to make an application (attach your CV and a cover letter), please contact: Mihai Glont (mglont AT ebi.ac.uk).

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