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Postdoc in Software Engineering for Scientific Programming at Technical University of Denmark

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 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 and tailoring personalized treatment schemes. Additionally, it is important for the design of cell factories, where 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.

  • 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 omics data (genomics, transcriptomics, proteomics, metabolomics) into accurate and simulatable models to guide treatment and design.

T
his 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 cellular metabolism.

Research field
This position involves research in the following areas:



  • Software engineering

  • Computational statistics

  • Computational biology

  • Cellular metabolism


Responsibilities and tasks
As a member of the multi-disciplinary and international 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:



  • Develop and maintain an application for large-scale kinetic modelling.

  • Implement novel equation solving algorithms with a view to high performance and incorporate them into the application.

  • Progressively improve the application's scalability and performance by exploiting parallelism, GPU access and threading.

  • Contribute to related open-source software projects like Stan, Sundials and AMICI.

  • Encourage the application's adoption at DTU Biosustain and in the wider scientific community through user-friendly design, effective documentation and publicity.


Qualifications
Candidates should have a PhD degree or equivalent. These qualifications are essential:



  • Your write high-quality, structured and maintainable code.

  • You have experience of implementing scientific algorithms with high-performance software.

  • You are at ease working in teams as well as working independently.


Experience in the following areas is a plus:



  • Probabilistic programming and automatic differentiation

  • Scientific programming in C++

  • Equation solving algorithms

  • GPU computing

  • MPI and/or openMP

  • HPC environments

  • Docker and similar virtualization technologies

  • Developing web applications and services


We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and terms of employment
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 4 years.

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

You can read more about career paths at DTU here

Further information
Further information may be obtained from Scientific Director Lars Keld Nielsen, lakeni(A)biosustain.dtu.dk.

You can read more about The Novo Nordisk Foundation Center for Biosustainability on www.biosustain.dtu.dk/english

Application procedure
Please submit your online application no later than 18 September 2020 (local time)

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out 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.

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

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