Scientific Programmer

Organization
EMBL-EBI
Job Location
EMBL-EBI Wellcome Trust Genome Campus Hinxton
Cambridge
CB10 1SD
United Kingdom
Benefits

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation.

We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.

If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.

Job Description

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.

Useful links

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 )

Requirements

 

We are looking for a person who has the right skill set and is happy collaborating on a range of projects. Our new Scientific Programmer should have:
• Experience in developing software
• Education to degree level or equivalent
• Proficiency in C and/or C++
• Experience with studying advanced data structures and algorithms, both on paper/pseudocode, and in implementation
• Experience with code profiling tools, code correctness tools, version control.
• Competence with Linux
• Excellent communication skills - essential to effective collaboration within the team and users of our software

The following would be highly desirable, but not essential

• Experience with numerical or statistical algorithms

• Experience of working in a scientific setting.

How to Apply

To apply please submit a covering letter and CV, with two referees, through our online system.

About Our Organization

EMBL-EBI, the UK site of the European Molecular Biology Laboratory (EMBL), has been a global leader in computational biology research since its inception in 1994. Located on the Wellcome Genome Campus, we are at the centre of one of the highest concentrations of technical and scientific expertise in the world. Our research spans fundamental methods in sequence analysis, multi-dimensional statistical analysis and data-driven biological discovery, from plant biology to mammalian development and disease. We are highly collaborative and interdisciplinary, regularly publishing high-impact works on sequence and structural alignment, genome analysis, basic biological breakthroughs, algorithms and methods of widespread importance.

Students whose classmates are interested in science are more likely to think about a career in science, technology, engineering, and mathematics, a new study says.

CNBC reports that the genetic counseling field is expected to grow as personalized medicine becomes more common.

Gladys Kong writes at Fortune that her STEM background has helped her as a CEO.

Social scientists report that the image of the 'lone scientist' might be deterring US students from STEM careers.