Data Scientist - DTU Biosustain

If your areas of interest and competence are genomic big data science and software development, and you are looking to gain experience while working on projects that will make an impact on the world, this is your chance. Your personal efforts will enable and accelerate works towards development of new environment friendly products, new medical treatments, climate friendly farming, etc using by applying the tools /pipeline of Big Data, AI and bioinformatics for the life sciences. All code that you will develop will have a permissive open-source license (e.g., MIT), hosted on GitHub, and will be promoted at the international level via publications and conferences. Through this, you will get the opportunity to utilize everything you know and help break new ground at the very forefront of what is possible.

Skill acquisition opportunities
At a more personal level, you will get the opportunity to learn the latest and greatest algorithms related to personalized medicine and synthetic biotechnology. You must be open to learning new information within the biology domain, and be open to contributing with your software engineering expertise and ideas at our regular meetings in the group. You will be building the foundation for world-class scientific results. We anticipate that by working with us, you will develop or hone the following skills:

• Programming in modern C++ (HPC languages), python and workflow language
• How to develop modern build/test/deploy infrastructure using CMAKE and continuous integration for all operating systems
• Multi-threading algorithm and logic
• Native GUI design and development
• Advanced deep learning and graph algorithms for life-science data (multi-omics)

The projects and tasks
Your mission is to develop and optimize a new software platform that can automate handling of large and heterogeneous data sets (i.e., Big Data) from biotechnology experiments (for example, long-read/Hi-C/single-cell sequencing). You will do so by developing new or transforming traditional algorithms into high-performance multi-threading including cloud infrastructures. The core algorithms utilize state-of-the-art optimization and deep learning techniques. You will

• Develop and maintain core software business logic and GUI components written in modern C++
• Develop and maintain core software build infrastructure using CMAKE and continuous integration infrastructure scripts
• Develop and maintain scripts for deploying the software on both end-user devices and HPC infrastructure
• Develop and maintain core software algorithms and workflows for data processing and analysis
• Translate algorithms and workflows prototyped into high-performance tools
• Gain knowledge in relevant biological domain, for example, metagenomics for sustainability, medical multi-omics (cancer, diabetes), complete genomics, etc.

Ideal competencies required for the projects
You are willing to work in an international environment with colleagues and partners from all over the world. Added to this, your CV comprises:

• Experience programming in C++ and scripting in Python
• Workflow/pipeline development and management
• Experience in using CMAKE
• Experience using version control with e.g. GitHub
• Experience setting up and working with continuous integration tooling
• Experience within and/or motivation for working with agile methods
• Experience with clean code knowledge and Software testing knowledge
• Prototyping in Jupyter notebooks
• Familiarity with best practices for software development/large-scale genomics data analysis
• Familiarity in deep learning frameworks like pytorch
• Motivation for software development/large-scale genomic data analysis/joining our lab
• A degree in software development/data science/computational biology/bioinformatics/deep learning or related
• Ability to work independently and as part of a team.
• Ability to successfully work on multiple concurrent projects and meet deadlines.

You can look forward to being part of a leading research and education institution in Europe where on-going development of skills and knowledge is a part of the foundation. You will have great flexibility, as trust and respect are some of the values we build our results on.

DTU Biosustain – your new department
At DTU Biosustain we use synthetic biology techniques for the development of advanced materials and chemicals, smart and sustainable agriculture, and personalized human health applications. We are breaking new land at the absolute forefront of what is possible.  We have the funding, the knowhow, and the latest state-of-the-art technology and equipment needed to succeed. You can learn more at biosustain.dtu.dk

Further information
If you have any questions, you are very welcome to contact Shilpa Garg, Senior Researcher/Associate Professor at [email protected] or [email protected] . If necessary, we will set up an additional phone call to ensure your understanding of the job and your many opportunities.

Google scholar link: https://scholar.google.com/citations?hl=en&user=_Sn07lgAAAAJ&view_op=list_works&sortby=pubdate .

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark .

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.

Starting date is 1 July or as soon as possible.

Application
Please submit your online application no later than 5 April 2023. Open the “Apply now” link, fill out the form and attach all materials to be given consideration including CV, cover letter, degree, motivation statement, demonstration of software/workflow development for genomic data types, and if relevant list of publications.

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

The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)
Recent progress in our ability to read and write genomic code, combined with advances in automation, analytics and data science, has fundamentally changed the scope and ambition of harnessing the potential of biological systems. Big data approaches and analysis of biological systems are key research instruments at the Center. DTU Biosustain utilizes these advances for microbial cell factory design to foster sustainable lifestyles in relation to three application areas: Sustainable Chemicals, Natural Products, and Microbial Foods.

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear mission to develop and create value using science and engineering to benefit society. That mission lives on today. DTU has 13,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.