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Student projectsThe Steinbeck group offers computational student projects embedded within the Services and Research team. All students are supervised by experienced staff members and have access to a broad array of local experts for the technologies used. All applicants should have a good computational background.The following projects are currently on offer. Automatic Structure Diagram Generation (SDG) In cheminformatics it is often necessary to create 2D coordinates for compounds which either have wrong coordinates or none at all. This task is difficult because on the one hand the algorithm needs to lay out arbitrary structures, but on the other hand there are certain conventions on how certain cases should be handled. In this project, the student would work on the existing code for SDG in the Chemistry Development Kit (CDK) and improve it with respect to e. g. handling of stereochemistry, deterministic layout, IUPAC-conforming alignment of final structure (major ring sytem/largest chain horizontally placed) and globally optimized layout. This requires good programming skills in general, best in an object-oriented fashion, and a basic command of the Java language. The project would include assesment of the literature with respect to standards, specification of the requirements and implementation of a solution.
Kemia Javascript editor We are looking for someone to contribute to Kemia, a pure Javascript editor for editing 2D chemical structures and reactions. Kemia uses the Google Closure library extensively. It is an open source project (shared on Github) to which our group is contributing. The editor is still to be finished, and many features could be added in the future. Some more links:
We are interested in mining biological resources which reference our source database Chemical Entities of Biological Interest (http://www.ebi.ac.uk/chebi). ChEBI is a dictionary and ontology of small molecules. We would like to use ChEBI identifiers as a means to investigate biological knowledge stored in our sister databases but not easily visible to our users. One such example could be which species does a specific molecule exist in or whether a molecule occurs at pH 7. This project would involve firstly learning about the different resources and what information they have, then defining what information would be useful for users. The technical implementation would require a system which would query each data source and display the relevant information within a web interface. Different interfaces will be built for user testing. Such a project would require a 6 month internship with good Java skills.
We would like to investigate different ontology visualisation methods to best harness the ChEBI ontology. ChEBI is a dictionary and ontology of small molecules. The ChEBI ontology is quite in depth and detailed for the average user to comprehend. Hence, we would like to develop prototypes which will simplify our visualisation of the ChEBI ontology. Each prototype will then be user tested and further alterations will be required to refine the results. Such a project would require a 4 month internship and preferably some programming skills. |
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