Software Engineer for Scientific Programming

Center for Biosustainability
onsdag 26 sep 18

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Frist 22. oktober 2018
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Quantitative Modelling of Cell Metabolism (QMCM) is a new section at the Novo Nordisk Foundation Center for Biosustainability, headed by Professor Lars Keld Nielsen and supported by a seven year Novo Nordisk Foundation Laureate Research Grant. In QMCM, we focus on developing mathematical models to explore and explain the molecular basis for homeostasis – the self-regulating processes evolved to maintain metabolic equilibrium in organisms.

Studying homeostasis is relevant for the understanding and treatment of complex diseases, particular with the emergence of personalized medicine. It is equally important when we seek to repurpose the cellular machinery for the production of desired chemicals, materials and pharmaceuticals. In this process, the cells’ homeostatic control mechanisms must be either disabled or exploited.

Cellular reactions are catalyzed by enzymes. In order to model homeostasis, we need to model the kinetics of all the enzymes involved in cellular metabolism and the regulation of their expression. The main objectives of this program are, thus, to:

  • develop the tools needed to formulate and fit large network kinetic models,
  • explore several aberrant metabolic phenotypes, including the Warburg Effect in cancer cells and common genetic disorders of red blood cell metabolism, and
  • explore several product models in E. coli and yeast in order to guide superior cell factory designs.
The ultimate aim is to be able automatically to convert the omics “parts” lists (genome, transcriptome, proteome, metabolome) now routinely collected for many individuals into accurate and simulatable models to guide treatment and design.

This is an opportunity for a scientific programmer with expertise in scientific computing and modern software engineering practices to join an interdisciplinary team working on biological network modelling, computer science and algorithmics, statistical computing and bioinformatics, to solve the fundamental challenge of formulating and fitting very large non-linear models of these organisms.

Responsibilities and tasks

As a member of the multi-disciplinary team, you will contribute your expertise towards formulating, fitting, and simulating large kinetic models. In particular, you will enable the team by building the necessary software tools and pipelines.
 
Examples of the challenges you will address include:
  • Independently develop a high-quality and maintainable software framework that will provide the basis for the project’s success.
  • Deploy models and simulation code to collaborators as well as external users in academia and industry by either leveraging their own HPC infrastructure or through IaaS providers such as AWS, Google Compute Engine, Microsoft Azure etc.
  • Ensure interoperability with other software engineering efforts at DTU Biosustain through regular software meetups and common technology choices, APIs etc.
Qualifications
Candidates should have a PhD degree or equivalent.
  • You write high-quality, structured and maintainable code.
  • You are an expert in at least one of the following programming languages and their associated scientific software stacks and generally comfortable dealing with one or two others: Python, Matlab, Julia, C, C++, Fortran, Mathematica, R.
  • You have extensive experience with operating in a HPC environment.
  • You are at ease working in teams as well as working independently.
  • Experience with machine learning and GPU computing is a plus.
  • Experience with MPI and/or openMP is a plus.
  • Experience with Docker and other similar virtualization technologies (especially in the context of scientific computing) is a plus.
  • Experience in developing web applications and services involving Javascript, HTML, and CSS is a plus.
What we offer in return
We offer an interesting and challenging job in an international atmosphere with the focus on research, teaching, innovation and scientific advice for the benefit of the surrounding community. We place emphasis on a high level of professionalism among our staff, so skills development is an integral part of our organization. We offer a great flexibility in the position. In the area of technical and natural sciences, DTU is one of the leading research and education institutions in Europe.

Salary and terms of employment

The appointment will be based on the collective agreement with the Confederation of Professional Associations. The allowance will be agreed with the relevant union.
 
Workplace and period of employment:

You will be based in the recently opened, custom-designed DTU Biosustain building at the DTU Lyngby Campus.

The period of employment is 3 years.

Application procedure and contact
Please submit your online application no later than 22 October 2018.

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online," fill in the online application form, and attach all your materials in English in one PDF file. The file must include:
  • Application (cover letter)
  • CV
  • Diploma (MSc/PhD)
  • List of publications 
Applications and enclosures received after the deadline will not be considered.

Further information may be obtained from Scientific Director Lars Keld Nielsen, lakeni@biosustain.dtu.dk.
 
You can read more about The Novo Nordisk Foundation Center for Biosustainability on http://www.biosustain.dtu.dk/english.

All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply.

DTU Biosustain is an international research center of excellence developing next generation cell factories and bioprocesses for sustainable production of high-value chemical compounds as well as protein-based products. The center uses advanced metabolic engineering techniques and computational biology ensuring efficient and cost-effective design and construction processes.

The center’s activities are a balanced mix of basic and translational research, complemented by an emphasis on business development to facilitate commercialization of new cell factories and associated technologies. DTU Biosustain offers state-of-the-art research facilities and assembles world leaders in the field thus offering a unique platform providing excellent talent development and career opportunities.

DTU is a technical university providing internationally leading research, education, innovation and scientific advice. Our staff of 6,000 advance science and technology to create innovative solutions that meet the demands of society, and our 11,200 students are being educated to address the technological challenges of the future. DTU is an independent academic university collaborating globally with business, industry, government and public agencies.