PhD - High-performance algorithms for processing genomic data

Centro Nacional de Análisis Genómico

Barcelona, Spain

 

Description

 

The CNAG (www.cnag.eu) started operating in March 2010 and is aimed to carry out large-scale DNA sequence analysis projects in human and other species in collaboration with researchers in Catalonia, Spain and internationally. The CNAG operates ten Illumina HiSeq2000 sequencers and has a dedicated 13 Tflop compute cluster with a 2 petabyte disk storage array, becoming one of the major Genome Sequencing Centers in Europe. The Ph.D. will take place within the Algorithm Development team, whose mission is to design and deploy practical methods to process the hundreds of gigabases of DNA sequencing data produced daily by the Center. The CNAG seeks a talented young student that is expected to establish, under the supervision of Dr. Ribeca, a research line focused on the development of high-performance algorithms for the processing of genomic data, with particular emphasis on their implementation and deployment on FPGA-based hardware architectures.

 

Requirements

 

- Solid theoretical background in computer science, with particular emphasis on algorithmics (data structures, programming languages, theory of parsing and formal languages), string manipulation algorithms (indexing, compression, pattern matching, searches) and program optimization. Detailed knowledge of FPGA hardware architectures, and previous experience with FPGA programming, will be considered a plus.

- Previous practical programming experience in medium-scale software projects (~10 Klines of code). Mastery of the C/C++ programming languages, with particular reference to advanced programming techniques, is required. Some proficiency in the Java programming language will be considered a plus.

- Previous exposure to biology and bioinformatics (in particular, theoretical and practical knowledge of sequence alignment tools).

- In general, enthusiasm, rigor and motivation along with scientific curiosity and good team spirit will be appreciated. The candidate should also show a marked propensity to find original solutions to problems and to “think big”.

 

Applications

 

Interested candidates may submit a CV and a brief statement of experience and interests before 15th of December 2012 indicating the offer reference in the message subject (PHD_Algorithm) subject to borsadetreball@pcb.ub.cat