Scientific Programmer in the field of Metabolomics-vacancy Leiden University, LACDR/ABS/NMC

Faculty of Science

LACDR

The Leiden / Amsterdam Center for Drug Research (LACDR) is part of the Faculty of Science. The LACDR is a leading institute which performs fundamental and strategic scientific research in the field of innovative drug research.

The Division of Analytical BioSciences (ABS) at the LACDR is a key player in the paradigm shift in Life Science research towards biosystem discoveries as a systems approach to biology will have a major impact on medicine of the future. The main research goals of the Division are improved diagnostics and understanding the onset of multi-factorial diseases. Since 2008, the Division is a key driver in the realization of the Netherlands Metabolomics Centre (NMC), a public/private funded multidisciplinary research network (www.metabolomicscentre.nl).

The Division of Analytical Biosciences of LACDR and the Data Support Platform (DSP) of the Netherlands Metabolomics Centre (NMC) have a position for a

Scientific Programmer in the field of Metabolomics, 38 hrs. per week

Metabolomics is a rapidly growing discipline, relying on bioinformatics for processing the large amounts of data that are being generated. The process of extracting biological information can be seen as an integrated workflow that can benefit highly from coordinated (and automated) handling and processing of the data. The need for tools and applications to support the data handling and biological interpretation is huge but online availability of these tools is poor. 

The Netherlands Metabolomics Centre aims at the creation of a world-class metabolomics knowledge infrastructure to improve personal health and quality of life. To strongly stimulate exchange of software, tools and expertise within the NMC and with researchers and centres outside the NMC, the Netherlands Bioinformatics Centre (NBIC) and NMC established the NMC-DSP. The DSP includes a flexible data warehouse infrastructure for experimental metabolomics data and provides all kinds of integrated tools for data processing. To strengthen the existing DSP team of scientific programmers, we are looking for a scientific programmer that will work on the integration of computationally intensive software in the metabolomics data processing tool chain. This project is part of the e-BioGrid program which objective is to create functional problem-solving environments for life-science application domains that consist of a coherent arrangement of bioinformatics components and connective e-science elements with access to grid/cloud computational power, storage and connectivity. As a consequence direct involvement of SARA in this project is ensured. 

We are seeking an experienced scientific programmer who will implement a number of metabolomics bioinformatics tools that require high performance computing in an environment that will be accessible to biologists. This will remove two major barriers: one is that the tools can currently only be run by skilled bioinformaticians with knowledge of the system, and the second is that performance is currently limited due to use of these tools in desktop environments. The resulting computing environment will be primarily focused on NMC biologists and biostatisticians, but will also be made available to interested users from outside NMC.

Two case studies are at present the most urgent. One deals with optimally and reproducibly extracting compound signals from raw metabolomics data (coming from different instrumental platforms and laboratories). At present a set of related tools for signal extraction is developed within the NMC which focuses on Liquid Chromatography – Mass Spectrometry (LC-MS) data. Main issue with this set of tools is that it requires a more advanced computing environment to handle the hundreds of LC-MS datasets simultaneously. The second case study involves an example from the statistical analysis part of the pipeline. More advanced statistical tools also need more powerful computing. Some experience has already been gained of running biomarker discovery software calculations on different grid nodes but collecting the results from the grid turned out to be rather complicated. An additional task will be to make this tool available to a broader audience, by integrating it into the NMC-DSP tool chain

Your profile

Applicants should have a Bachelor or Master degree, while affinity with research in the life sciences (e.g metabolomics) is appreciated. Furthermore experience with webservices and workflow management systems, programming (C, Java, Groovy, Grails, Python, Perl and/or Shell programming) and/or experience with bioinformatics / biostatistics software (R, Matlab) is preferred. Applicants should possess well developed communication and cooperation skills.

What do we offer?

Appointment will be according to the terms of the Collective Labour Agreement of Dutch Universities (CAO Nederlandse Universiteiten), initially for the duration of one year. The function is validated in the University Function Ordening system (UFO) under the profile “Ontwikkelaar ICT 3”. The salary will be set, depending on education and work experience, between the gross minimum of € 2379,- and gross maximum of

€ 3755,- per month, based on fulltime employment (salary scale: 10). Leiden University offers an attractive benefits package which includes an end-of-year premium of 8.3%, opportunities for personal development and possibilities for ‘personalized’ benefits via our Cafeteria model. More information about employment at Leiden University can be found at: www.leidenuniv.edu.

Further information and applications

For more information, please contact Dr. T.H. Reijmers, telephone: +3171-5274320, e-mail:  t.reijmers@lacdr.leidenuniv.nl. Additionally, you can visit the websites of the Faculty of Science and the LACDR: www.science.leidenuniv.nl and www.lacdr.nl.


Do you identify with the profile above and are you looking for an interesting job? Please apply by sending your written application before November 28th 2011, using the vacancy number, including a full Curriculum Vitae, and a list of publications to:

Faculty of Science

To the attention of: Prof.Dr. Thomas Hankemeier

Via e-mail: hankemeier@lacdr.leidenuniv.nl