The objective of this cluster is to colaborate on analyzing bioinformatic application and designing accelerators/co-processors/new ISA in order to improve the most time-consuming parts of important bioinformatic applications like protein structure prediction, protein structure alignment and sequence alignment algorithms (FTDock, S&W, BLAST, FASTA).
This collaboration is important to share our analysis in order to see if there are similarities between bioinformatic applications that may not be very related. That analysis can help us to create a set of possible bio-accelerators that will be analyzed in the Cell simulator, developed under UNISIM at UPC and in the MOLEN platform as well (from TUDelft).

In particular, the student (UPC) we are asking foundation for is going to focus on one specific area of bioinformatics: protein docking, and will analyze the performance of different application to solve the protein docking problem. That will be done in a real Cell machine, the Cell simulator and also other actual processors (duration of this part:6-8 months).
The results of those analysis should contribute to some hardware proposals that will be implemented in the simulator and analyzed. That last work will start at 8-9th month, after the second meeting. In any case, it would be good that the two students (the one from UPC and the one from Delft, Isaza) can have foundation to spend some time at UPC and Delft. In the case of the UPC student we are thinking on a duration of 3 months (may help the student to have the European Ph.D) that can be divided intotwo visits. In the case of Delft student, we are thinking on two visits of two weeks, one visit at the beginning and another some month later. This will be essential to understand the common features of the several targeted bioinformatic applications and to fully understand the advantages and disadvantages of the architectures and simulation platforms being used.

First (phone->no founding) meeting will be at the beginning so that we can explain each other the bioinformatic areas we want to focus on, and the main ideas some applications (2nd month). Another point to discuss is the architecture aspects we think we should evaluate, and the architecture of the simulator we have.

Second meeting (8-9th month) will be after sharing the analysis results we have obtained of the analysis of those applications. In this meeting there will be a braimstorming about proposals that may be useful to one or other applications, and which will be useful for all of them.

A third meeting will be at the end of the cluster in order to analyze the performance results of the applications once we have implemented some of the proposals done during the second meeting. Also, discussing can help to prepare some papers and think about the extension of the duration of this cluster.

The project would start on September (student from UPC is finishing her last year and would finish on September). However, we may start before if that is an inconvenient.

Doctor Degree Fellowship for UPC student:
1200 euros/month x 12 months = 14400 Euros

2 Meetings x 4 personas * 1000 EUR = 8000 EUR

Intership: 7000 EUR
UPC Student 5000 EUR three month visit
Delf Student 2000 EUR two two-week visits

Total: 14400 + 8000 + 7000 = 29400 EUR

Delf Student: Sebastian Isaza
UPC Student: To determine