Postdoc position in computer science or bioinformatics with focus on Hadoop for large scale sequence analysis

at the Department of Information Technology
Application no later than 2012-10-15. UFV-PA 2012/2414

Background: The emerge of high-throughput technologies such as next-generation sequencing has turned life science into a data-intensive domain, which places high demands on an e-infrastructure in order to be analysed. UPPMAX ( is UppsalaUniversity’s center for high performance storage and computations that via the project UPPNEX ( offers resources for storage, computations, software and user support in bioinformatics and primarily sequence analysis. We are now seeking a Postdoc to evaluate how technologies like cloud computing and Hadoop can complement the current infrastructure and offer improved services in storage and analysis of bioscience data.

Brief description of the project: The successful applicant will conduct research and development in biological sequence analysis using the Apache Hadoop framework. The project includes evaluation of the usefulness and utility of running Hadoop on different file systems, on clusters contra cloud computing, and the possibilities of integrating Hadoop woth the SLURM queueing system as well as the metadata system iRODS. An important area is to evaluate existing Hadoop-applications for sequence analysis, and assess how this technology can complement the current research infrastructure at UPPMAX. The applicant will have a tight connection with Science for Life Laboratory ( that will contribute with use cases, testing, and feedback in analysis of life science data.

Qualifications: Applicants should have a PhD degree or equivalent scholarly competence in a relevant branch of computer science or bioinformatics. The applicants PhD degree must have been obtained no more than three years prior to the application date. The PhD can be older than three years if there are special circumstances. Such special circumstances can be periods of sick leave, parental leave etc, which are deducted from the three-year period.Good knowledge in UNIX/Linux and programming is a requirement. Experience of high-performance computing, storage solutions, cloud computing, Hadoop, and bioinformatics tools is meriting but not a requirement. Good knowledge in English is a requirement. Other important competences include ability to work independently and to set up and meet deadlines. Good knowledge in English is a requirement.

Others: The position is for 2 years with placement at UPPMAX, Uppsala University, Sweden. The position is financed by the Swedish strategic research program eSSENCE (

UPPMAX is Uppsala Univeristy’s resource for high-performance storage, computing, and related know-how. UPPMAX has aboout 20 employees, including system experts, application experts, and software engineers. The project UPPNEX provides resources for bioinformatics, including over1 PB high-performance storage, over 1 M computational hours per month, and a large ecosystem of bioinformatics software. Over 250 projects has utilized UPPNEX resources since the start in 2008.
For further information regarding this position, please contact Ola Spjuth, tel. +46 – (0)70 – 425 06 28 or Hans Karlsson, tel. +46 (0)701 679287. Union representatives are: Anders Grundström, SACO-rådet, tel +46 18-471 5380, Carin Söderhäll, TCO/ST, tel +46 18-471 1996, Stefan Djurström, SEKO, tel +46 18-471 3315.

You are welcome to submit your application no later than Oct 15 2012, UFV-PA 2012/2414. Use the link below to access the application form.

Postdoc position in computer science or bioinformatics with focus on Hadoop for large scale sequence analysis