Project Portal: Briefly tell us about your project.

Thomas Rattei: SIMAP is a database of protein similarities. It contains about all currently published protein sequences and is continuously updated.

Protein similarities are computed using the FASTA algorithm which provides optimal speed and sensitivity. SIMAP is to our knowledge the only project that combines comprehensive coverage with respect to all known proteins and incremental update capabilities.


PP: Why did distributed (or grid) computing get brought up in the course of your research? How did you become aware of the technology?

TR: The computational costs to calculate the similarity data depend on the square of the number of contained sequences. So the computational effort for keeping the matrix up-to-date is constantly increasing. Our internal resources that perform calculations for SIMAP since years are no longer sufficient to keep track of all new sequences. That's why we implemented a SIMAP-client for the BOINC platform (Berkeley Open Infrastructure for Network Computing) which is based on the FASTA algorithm to detect sequence similarities. We became aware of the BOINC technology just because of the very famous SETI@home project.


PP: There are a lot of worthy projects that distributed computing has brought to us. Why should we choose yours?

TR: SIMAP supports many different projects in life sciences. Choosing SIMAP accelerates not only our project but many research projects all over the world.



More . . .

Thomas Rattei

Mailing address:

Dr. Thomas Rattei
Technische Universität München
Department of Genome Oriented Bioinformatics
Am Forum 1
85354 Freising, Germany

Curriculum Vitae:

• 1969 born in Dresden
  


• 1990-1995 Study of chemistry at the Dresden University of Technology
  


• 1995 Diploma degree in chemistry
  


• 1995-1999 PhD work in Prof. van Pee's Lab at the Dresden University of Technology
  


• 1999-2001 Head of my own IT service and consulting company
  


• 2002 PhD in chemistry, Thesis: "Development and characterization of complexes of Cetrorelix and biophilic base materials"
  


• 2001-2006 Staff scientist at the Chair of Genome Oriented Bioinformatics, Technische Universität München

Since 2006 Assistant Professor "Habilitand" at the Chair of Genome Oriented Bioinformatics, Technische Universität München.

mmmhhh... german researchers save the world and italians feed them with pasta... everyone has his place in the story


good job Sid