Bioinformatics and Advanced Programming

Date/Time:
Thursday 11 December 2014, 6.00pm - 8.00pm

Venue:
The Davidson Building, 5 Southampton Street, London WC2E 7HA. The nearest underground stations are Covent Garden and Charing Cross.

Speaker:
Jan Kim

Summary:

Bioinformatics can be defined as the science of information in biological systems, or more broadly as developing and applying computational tools for analysing biological data. The biological processes that generate this information, particularly evolution, are highly complex, and therefore analysis of biological information is often computationally challenging. I will present the following selected topics and highlight the advanced computing challenges they involve, and also outline advances in the biosciences that have been enabled by tackling these challenges.

Many bioinformatics analyses are based on DNA sequences which today can be determined at very high volume through "Next Generation Sequencing" (NGS) techniques. As a result, the volume of publicly available sequence data has reached the range of petabytes. Searching this body of data requires highly optimised computational approaches, such as BLAST ("Basic Local Alignment Search Tool").

More recently, NGS methods that generate very large numbers of "short reads", i.e. strings of sequence. The central computational challenges resulting from these new technologies are "de novo assembly" of the original long sequence(s) from short reads, and mapping very large numbers of short reads to a known reference sequence.

Phylogeny analysis, i.e. reconstruction of ancestry relationships among species, is a classical field of bioinformatics which typically involves two steps, first a multiple alignment of the sequences is computed which subsequently is used to compute a tree. Computing multiple alignments is an optimisation problem that can only be approximately solved.

About the speaker:
Jan Kim is head of BioInformatics at the Pirbright Institute

This meeting will be followed by a buffet reception with wine; new members are welcome.

Admission is free, but to reserve your place please email our Membership Secretary, Algirdas Pakstas, at algirdas.pakstas@gmail.com as soon as possible, giving the title of the meeting and your name in the subject line of your e-mail.

Slides:

View the slides for this event (PDF)

YouTube video of the event