Internship opportunities
Curation internship: Literature curation of Genome-Scale metabolic models
BioModels 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 the curation of constraint-based models including Genome-Scale Metabolic models (GEMs).
The internship is suitable for a student who is pursuing or completed master's or PhD degree and has experience in constraint-based modelling approaches including genome-scale metabolic model reconstruction, flux balance analysis or equivalent methods. The intern will apply the recently developed community standard FROG to assess the reproducibility of the constraint-based models and perform semantic enrichment to curate. Training will be given to understand the basics of FROG analysis and relevant tools. Potential possibilities exist for the intern to be a co-author of our community manuscript on FROG analysis.
This is an in-person internship at the EMBL-EBI Campus based in Hinxton, Cambridge, UK. The provisional starting date is September 2022, however, it can be adjusted. The position is for 6 months but can be extended up to one year. A fixed monthly allowance is provided to help towards living costs. Support for the visa will be offered to the selected candidate when required.
For further enquiries or to make an application (with your CV and a cover letter), please contact: Dr Rahuman Sheriff (sheriff AT ebi.ac.uk). The application is open until filled.
EMBL-EBI - IITM Internship on Curation of Machine Learning Models in BioModels
Machine learning (ML) models are widely used as tools in life science and medical research. However, ML models are scattered across various resources including personal websites, git-hub, bitbucket, and supplementary material, making it difficult to find, access, and reuse them. We aim to extend the BioModels to support Findable, Accessible, Interoperable, and Reusable (FAIR) dissemination of ML models in biomedical sciences. BioModels is a world-leading repository of mechanistic models of biological processes, hosted by EMBL-EBI. BioModels’s infrastructure was recently enhanced to support version-controlled dissemination and curation of a wide range of modelling frameworks and formats, providing capabilities to host and disseminate ML models.
The internship is ideal for a student who is pursuing or completed a master's or PhD degree and aiming to move towards the next step of their career. The applicant should have experience in machine learning approaches including deep learning neural networks and other equivalent methods. During the internship, the intern will rebuild ML models published in life science journals and submit them to the BioModels repository. Potential possibilities exist for the intern to be a co-author on our high-impact manuscript.
Prerequisite: very good programming skills in Python, R or equivalent languages, experience in building machine learning models, and a good background in biological science. Experience in deep learning will be a plus.
The first 3 months of the internship are based at the Robert Bosch Centre for Data Science and Artificial Intelligence & Dept. of Biotechnology, Indian Institute of Technology Madras at Prof. Raman’s lab, Chennai, India. The next 3 months will be based at the European Bioinformatics Institute (EMBL-EBI) Campus at Hinxton, Cambridge, UK. The position is for 6 months but can be extended up to one year. The provisional starting date is September 2022, however, it can be adjusted. A fixed monthly allowance is provided to help towards living costs. Support for a UK visa will be offered to the selected candidate.
For further enquiries or to make an application (with your CV and a cover letter), please contact Prof. Karthik Raman (kraman AT iitm.ac.in) and or Dr Rahuman Sheriff (sheriff AT ebi.ac.uk). The application is open until filled.