Job:Scientific Software Developer - Cell Factory Design Methods
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6.7 years ago

The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) at the technical university of Denmark (DTU) is seeking a highly motivated and skilled postdoctoral researcher to help build a web-based software platform for data-driven design of microbial cells and communities.

The Center conducts research on metabolic engineering and synthetic biology of microbial and mammalian cell factories for chemical and therapeutic protein production. The position will be within the DD-DeCaF project, which was recently funded by the European Commission to develop new bioinformatics approaches that leverage system-level data for biotechnological applications.

With advances in synthetic biology, genomes can now be edited at unprecedented speed and fidelity allowing making multiple changes in the same genome at the same time. This increases the need for computational tools to design cells and communities of cells analogous to the tools used in Computer Aided Design (CAD) of cars, buildings and other man-made objects. The European Commission has awarded 6.3 million Euros to a four-year collaborative project to build a CAD tool, DeCaF, for data-driven design of cells and microbial communities. Applications will range from human health to sustainable production of chemicals.

As a successful applicant, you will be part of a diverse team of scientists and engineers from leading academic institutions and innovative companies that will work towards this common goal. Your main responsibility will be establishing the computational resources for designing microbial cell factories and artificial communities of organisms. If you enjoy solving scientific problems programmatically, write code that others can reuse, and are disappointed in the current state of scientific software but would like to help make a difference, then we would like to hear from you.

Responsibilities and tasks

  • Implement existing and novel methods for designing microbial cell factories.
  • Optimize, test, and benchmark tools developed by academic and industrial partners within the project.
  • Collaborate with partners in integrating these tools into it into the DeCaF platform.
  • Participate in end-user requirement gathering and testing related to the design components of the DeCaF platform.
  • Maintain a consortium-wide code repository of well documented and tested methods, algorithms, software, and web-services.
  • Establish modern software development practices in the project and help educate scientists and engineers within the project.


  • The candidate needs to hold a M.Sc. or Ph.D. degree in a STEM (science, technology, engineering, mathematics) field.
  • The candidate should have significant previous experience with the development of scientific software with a strong focus on algorithm development, code optimization, parallel computing, numerical methods etc.
  • Prior experience with modeling large-scale biochemical networks is highly desirable.
  • Experience in analyzing omics data sets (metabolomics, fluxomics, transcriptomics, proteomics etc) is desirable.
  • The candidate should be able to write high-quality, structured and maintainable code.
  • Applicants with knowledge of Python and its scientific programming stack (Numpy, Scipy, scikit-learn, Pandas, Jupyter notebook, etc.) will be preferred.
  • Applicants that utilize modern software development practices, like test-driven development and continuous integration, in their day-to-day work will be preferred.
  • Experience with determining and alleviating computational bottlenecks by re-implementing them in a more efficient language (e.g. C/C++) and making them accessible through language bindings (swig, cython, etc.) is a plus.
  • Familiarity with popular programming languages used by scientists and engineers (Matlab, R, Mathematica, etc.) is a plus.
  • Experience with the basics of web development and databases is not required but a plus.

If you have public profiles in the development community such as on GitHub or StackOverflow, please include the links with your CV or cover letter.

We offer

We offer an interesting and challenging job in an international environment focusing on education, research, public-sector consultancy and innovation, which contribute to enhancing the economy and improving social welfare. We strive for academic excellence, collegial respect and freedom tempered by responsibility. DTU is a leading technical university in northern Europe and benchmarks with the best universities in the world.

Salary and terms of employment

The appointment will be based on the collective agreement with the Confederation of Professional Associations (AC). The allowance will be agreed with the relevant union.

Workplace and period of employment

The place of work is in Hørsholm just north of Copenhagen until mid-2016 and in Lyngby at the main DTU campus from thereon.

The period of employment is 4 years.

Further information

Further information may be obtained from Prof. Markus Herrgard ( or Dr. Nikolaus Sonnenschein (

You can read more about DTU Biosustain on

Application procedure: Please submit your online application no later than 15 February 2016. Apply online at

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 (an official translation into English)
  • List of publications

Applications and enclosures received after the deadline will not be considered.

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.

The Center is based upon a long term grant from the Novo Nordisk Foundation to DTU and it was inaugurated in 2011. It has now more than 220 employees and is still growing.

DTU is a technical university providing internationally leading research, education, innovation and public service. Our staff of 5,800 advance science and technology to create innovative solutions that meet the demands of society; and our 10,300 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.

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