CarbLoader: building 3D models of carbohydrate structures for simulation

Proposer: Michelle Kuttel

Abbreviation: CARBLOAD

Brief Description: In this project, you will create a software package, both standalone and with a web interface, to build reasonable models of carbohydrate molecules. Carbohydrates are very interesting molecules in that they have a very broad range of biological roles – from a food source (starch), through to structural support in plants (cellulose) to fundamental roles in infection (new “conjugate” vaccines consist primarily of carbohydrates). Carbohydrates are composed of a number of different sugar building blocks connected by a variety of different linkages – in this sense they resemble construction toys like Mechano. However, because carbohydrates are so flexible, it is very difficult to use experiments to determine their 3D structure. A software tool, both standalone and with a web interface, to do this would be very useful for simulation of carbohydrates.

Computer Science Content: Algorithm development and open-source software engineering.

Specific Learning Outcomes: You will learn about open source scientific software engineering, with the aim of incorporating the best aspects of the tools currently available. You will have experience with direct contact with the “clients” for requirements specification (Göran Widmalm and his group at the University of Stockholm, Sweden).

Skills Required by Team as a Whole:

• Theory: Absolutely no prior experience with chemistry or carbohydrates (except as a food source!) is required. However, you will have to learn the basics of molecular structure of carbohydrates (which are fascinating molecules).

• Implementation: Implementation will be of average difficulty for an Honours project. The emphasis will be on an interative design process to obtain a really useful and user-friendly product.

Facilities needed: Standard PC/laptop.

Supervision: We are very excited about this project, which has the potential to create a very useful tool. You will have weekly meetings with Michelle (who has experience with carbohydrate simulation), together with remote Co-supervision by Göran Widmalm (University of Stockholm, Sweden).

Number of Students: 2 (or optional extension to 3)