Joel Hedlund

Joel Hedlund, Ph D student

Linköping University, Sweden

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MDRs, HMMs and Biogrid – A Bioinformatician's Experiences.

Life sciences have undergone an immense transformation during the recent years, where advances in genomics, proteomics and other high-throughput techniques produce floods of raw data that need to be stored, analysed and interpreted in various ways. Biology and medicine have become information sciences and new areas of comparative biology have opened. Bioinformatics is crucial by providing tools to efficiently utilize these gold mines of data in order to better understand the roles of proteins and genes and to spark ideas for new experiments.

BioGrid is an NDGF-supported effort to establish a Nordic grid infrastructure for bioinformatics, aiming both to gridify computationally heavy tasks and to coordinate bioinformatic infrastructure efforts in order to use the Nordic resources more efficiently. The widely used bioinformatic software packages BLAST and HMMer have now been gridified in an optimised way and allowing for multicore support. The frequently used databases UniProtKB and UniRef have been made available on the distributed and cached storage system within the Nordic grid. Further applications are in the pipeline to be gridified including multiple sequence alignment, molecule dynamics and phylogeny.

The BioGrid has already contributed to provide computational power for analysis of the medium-chain dehydrogenase/reductase (MDR) superfamily. The size and complexity of this superfamily has recently been shown to far surpass the means of subclassification that have traditionally been employed for this task. Instead, more computationally demanding methods must be employed, such as profile Hidden Markov Models, implemented in the HMMer package and employed on the grid. This talk will focus on user experiences from this endeavour.

Authors:
Joel Hedlund1,
Olli Tourunen2,
Erik Sonnhammer3,
Ann-Charlotte Berglund Sonnhammer4,
Inge Jonassen5,
Pär Andersson6,
Michael Grønager2,
Josva Kleist2
and Bengt Persson1,6,7

Affiliations:
1 IFM Bioinformatics, Linköping University, Sweden
2 Nordic Data Grid Facility (NDGF), Kastruplundgade 22, DK-2770 Kastrup, Denmark
3 Stockholm Bioinformatics Center (SBC), Stockholm University, Sweden
4 Linnaeus Center for Bioinformatics (LCB), Uppsala University, Sweden
5 Computational Biology Unit, BCCS, University of Bergen, Norway
6 National Supercomputer Centre (NSC), Linköping, Sweden
7 Dept of Cell and Molecular Biology, Karolinska Institutet, Sweden

yohell.mdr.nordunet.apr2008.pdf
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Biography

• Ph D student in Bioinformatics.
• M. Sc. in Engineering Biology.

• Branch of studies:
  Bioengineering physics/Microsystems&Biosensors
• Thesis subject: Bioinformatics
  Familiar - A tool for de novo protein family definition

• Scholarship Work

• Control/Data acquisition/Analysis software for research applications:
  FRAPpeal (FRAP software),
  Izaeus (ICS software),
  Familiar