Are you an experienced software developer with good working knowledge of fundamental algorithms and data structures? The Iqbal research group at the European Bioinformatics Institute (EMBL-EBI) is looking for a programmer to join their growing team, and play a vital role in developing software used to analyse the DNA of pathogens underlying global health threats such as TB and malaria.
Many problems in the analysis of DNA can be cast as algorithms on strings or graphs. Localised differences in DNA can cause bacterial and parasite strains to differ in medically and biologically important ways - for example being resistant to an antibiotic or being able to infect humans. Detecting and classifying these differences (either between genomes or between noisy experimental subsamples of genomes) can be translated into string and graph problems. The Iqbal group develops such methods. Their work ranges from development of novel algorithms and data structures, to concrete implementations translating research ideas into clinical practise. For example their Mykrobe predictor software has been integrated into Public Health England’s tuberculosis pipeline. Dr Iqbal spent 8 years in the software industry after his PhD, working in development and software management in embedded operating systems for mobile device and network drivers, before returning to academia. The rest of the group have degrees in maths, physics and biology.
As a Scientific Programmer, you would lead the development and maintenance of key scientific software developed by the Iqbal group. One important area of work is the further development of gramtools, a software suite for analysing genome sequence data based on a modified Burrows Wheeler transform.
Your specific goals and tasks would include:
• Develop, implement and maintain advanced algorithms and data structures, in particular in gramtools, but also in other applications related to genome graphs and succinct data structures.
• Collaborate closely with other team members who are developing modifications of and tools based on gramtools and/or other graph genome software.
• Apply these software to empirical datasets, profile, evaluate performance and update design, implementation and/or algorithms as appropriate.
Group home page: www.ebi.ac.uk/research/iqbal
Gramtools code: https://github.com/iqbal-lab/gramtools
Gramtools motivation and algorithm: https://goo.gl/E21Gi1
Other work from this group on de Bruijn graphs (https://goo.gl/69wrU) and antibiotic resistance prediction using graphs (https://www.youtube.com/watch?v=pM4yiirQD0c, https://github.com/iqbal-lab/Mykrobe-predictor, https://goo.gl/1ZxR7x )