PhD scholarship in Automation and Integration of Quantitative Fermentation Data - DTU Biosustain

Harnessing the power of biotechnology to address the many pressing environmental crises of the 21st Century will be impossible without better quantitative understanding of certain crucial metabolic processes. New models, algorithms, measurement techniques and laboratory innovations promise to meet this challenge, but their application is impeded by a lack of tools for orchestrating and integrating them. For example, there is currently no publicly available schema for the results of a quantitative metabolomics analysis of a fermentation experiment.

This project offers a unique chance to create the missing tools, providing both the human and technological infrastructure for developing them and testing them in metabolic engineering projects as well as the freedom to share them with the whole scientific community, satisfying FAIR principles.

Responsibilities and qualifications
Your overall focus will be to develop software, protocols, workflows and resources for the automation and integration of fermentation datasets, with an emphasis on data required to create accurate kinetic models of metabolic pathways. 

Working alongside a team of specialist software developers, you will develop a range of new tools, including but not limited to:

• A library of data models, validators and schemas for common kinds of fermentation data including quantitative metabolomics, fluxomics and proteomics.
• A library of datasets implementing these schemas.
• A curated, structured database recording key information about the kinetics of important metabolic pathways.

You will contribute to the development of these tools, demonstrate their usefulness by applying them to metabolic engineering projects and publicise them through academic papers and conference presentations.

The project will be keenly aware of the pitfalls of software development in an academic context, emphasizing the importance of lightweight, modular software with a low long-term maintenance footprint.

Essential qualifications:

• Collaborative programming skills in Python, demonstrated by contributions to at least one , open source data focused biology project.
• Hands-on wet lab experience with fermentation and quantitative metabolomics and fluxomics data generation. 
• Knowledge of enzyme kinetics, 13C metabolic flux analysis, demonstrated by practical experience using these modelling techniques.
• Understanding of Bayesian statistical inference, demonstrated by courses in this area.
• Excellent interpersonal skills and communication in both spoken and written English, demonstrated by a track record of relevant work experience.

The following qualifications will benefit your application:

• Knowledge of sustainable laboratory practices.
• Experience developing data models for biological data.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment  
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see DTU's rules for the PhD education . 

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 appointment terms 
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 3 years.

Kindly note that the selected candidate is expected to begin at the latest in January 2025. Or by mutual agreement.

You can read more about career paths at DTU here .

Further information  
Further information may be obtained from Teddy Groves by email: [email protected] .

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark . Furthermore, you have the option of joining our monthly free seminar “PhD relocation to Denmark and startup “Zoom” seminar ” for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU. 

Application procedure 
Your complete online application must be submitted no later than 27 September 2024 (23:59 Danish time) . 

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file . The file must include:

• A letter motivating the application (cover letter)
• Curriculum vitae 
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale

You may apply prior to ob­tai­ning your master's degree but cannot begin before having received it. 

Applications received after the deadline will not be considered.

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

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.