Call for Summer Trainees 2015

We offer the following internship positions for summer 2015. Applications to the positions should be submitted through the call for summer trainees by HIIT and Department of Computer Science in University of Helsinki.

1) Software tools for DNA sequencing / Työkaluja DNA-sekvenointidatan analyysiin

This project develops algorithms and software for DNA sequencing. The summer trainee is expected to participate in the experimental evaluation and comparison of new algorithms or, alternatively, to develop a software package and user interface that integrates several algorithms into a coherent tool for biologists. The trainee should have knowledge of basic algorithms of biological sequence analysis.

More information: Esko Ukkonen, Leena Salmela

2) Gene regulatory models / Geenisäätelymallit

This project develops probabilistic models that can be used for predicting gene regulatory structures ('patterns', 'motifs') in DNA. We are developing a huge probabilistic model to be used as a scanner that traverses through a DNA sequence and finds out where each putative regulatory motif is. The summer trainee is expected to participate in the software development, testing and validation of the scanner. The trainee should  have basic knowledge of Hidden Markov Models and algorithms of biological sequence analysis.

More information: Esko Ukkonen, Janne Korhonen, Jarkko Toivonen

3) Experimenting with Automata Processor / Kokeellista tutkimusta automaattiprosessorilla

Micron’s Automata Processor (AP) is a reconfigurable processing architecture that enables programmers to easily exploit massive parallelism. The AP is purpose-built to address the processing challenges associated with graph analysis, pattern matching, and data analytics. The summer trainee is expected to experiment with AP by programming some pattern matching algorithms and evaluating their performance on AP. The trainee should have interest in program development for non-standard processor architectures. For more information on AP, see [www.micronautomata.com].

More information: Esko Ukkonen, Leena Salmela, Juha Kärkkäinen