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bmBASE: Web Application & Database

Veselin Karaganev, a Computer Science summer student from the University has been working with our Research Software Engineers to develop a web database for the basement membraneBASE project from Wellcome Centre for Cell-Matrix Research.

Basement membranes are assemblies of many molecules that form thin sheet-like matrices which surround animal tissue. In addition to providing mechanical support, they also have many other critical functions. Studies in less complex animals such as C. elegans (a species of nematode worms) and Drosophila (a species of fruit flies) show that abnormalities in these membranes can result in a lethal outcome, and in humans, they can cause many different types of tissue-related disorders.

Prof. Rachel Lennon from the Wellcome Centre for Cell-Matrix Research, is studying the specifics of basement membrane function and composition, together with a group of other researchers from the University of Manchester and more recently, researchers from Duke University (USA).

The basement membraneBASE project (bmBASE) team was previously using several spreadsheets to collect and reference data for genes, their proteins, orthologs, and for one of the focal points of the project - localisation evidence, that indicates the involvement of the gene in basement membrane composition. The sheer volume and structure of the data made it difficult for them to publish their findings and to add new types of data. A lot of duplication was also present, due to the inherent constraints of the spreadsheet format.

Veselin, a summer student from the Department of Computer Science, was tasked with the end-to-end development of the supporting web application and database:

“I am very glad that I was given the opportunity to be a part of this project. It was a great learning experience that allowed me to practice many different skills and will be helpful for my career future. Due to COVID-19, being physically present at the Research IT office was not possible, so instead, I had weekly Zoom meetings with Andrew Jerrison from Research IT, who was always very helpful and approachable, and Prof. Rachel Lennon – who was very friendly and helpful as well.”

The data collected by the researchers is now normalized and split into more than a dozen tables. There is a public-facing website available at the bmBASE website, which shows their findings and allows other researchers to build on top of them. Prof, Rachel Lennon and the team behind the research also have access to a private administrative interface, through which they can manage that data in a way that is much more approachable than before.

“Overall it was a great experience that really gave my summer a meaning - especially in these times! I especially liked the focus on research projects, compared to the usual financial or e-commerce sector most other internship programs are involved with. I would definitely recommend anyone interested to apply for an internship in Research IT when applications open again next year”, Veselin explained.

Robert Haines, Head of Research IT said " Veselin has produced really good work over the 10 weeks that he has been with us. He has got to grips with the project really quickly, liaising with the research team to elicit requirements and working with Research IT colleagues to implement the system. It's been a real shame that Veselin hasn't been able to join us physically in Manchester, but that he has achieved what he has achieved remotely is even more impressive. We wish him all the best for the future!".

If you are interested in having a Research Software Engineer work with you on your research project please get in touch with us.

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