[CPM-SPIRE-L] WCTA 2015 Call for Presentation Abstracts

[Travis Gagie]

Dear Colleague,

This is a reminder presentation abstracts for WCTA (described in the email
below) are due this Friday, August 7th.  Please forward this email to any
researchers, especially students and post-docs who are not yet well-known
in our community, who you think might have results that would be of
interest to our community.

Best regards,
Travis Gagie
Tatiana Starikovskaya


On 18 July 2015 at 02:46, Travis Gagie <travis.gagie at gmail.com> wrote:

> Dear Colleague,
>
> The 2015 Workshop on Compression, Text and Algorithms (WCTA,
> http://www.dcs.kcl.ac.uk/events/spire2015/workshops.html) will take place
> at King's College, London, the day after the Symposium on String Processing
> and Information Retrieval (SPIRE), i.e., September 4.
>
> We invite abstracts for presentations (15--25 minutes) of recent results
> and surveys of interest to the string-processing community.  We
> particularly encourage submissions from junior members of our community.
> Since WCTA has no proceedings, presenting results there should not preclude
> submitting them to other conferences or publishing them in journals.
> Please submit abstracts by emailing copies (preferably PDF) to *both* WCTA
> co-chairs (addresses below).
>
> Submission deadline: August 7th, 2015 (anywhere on Earth)
> Notification: August 21st, 2015
>
> WCTA will feature an invited talk on "Using Suffix Array Based Data
> Structures in Computational Genomics" by Richard Durbin, FRS, from the
> Wellcome Trust Sanger Institute, and a tutorial on "Compact and Succinct
> Data Structures -- From Theory to Practice" by Simon Gog from the Karlsruhe
> Institute of Technology (abstracts below).  WCTA will be free for SPIRE
> attendees; there may be a small fee for those attending only the workshop.
>
> Best regards,
>
> Travis Gagie,
> University of Helsinki
> <travis.gagie at gmail.com>
>
> Tatiana Starikovskaya,
> University of Bristol
> <tat.lastname at gmail.com>
>
> (WCTA co-chairs)
>
> ==========
>
> Title:
> Using Suffix Array Based Data Structures in Computational Genomics
>
> Abstract:
> This talk will describe how the BWT and FM-indexes are used in read
> mapping (e.g., with BWA), sequence assembly (e.g., with SGA and Fermi),
> and haplotype matching and storage (with the Positional BWT).
>
> BWA: http://www.ncbi.nlm.nih.gov/pubmed/19451168
> http://www.ncbi.nlm.nih.gov/pubmed/20080505 http://bio-bwa.sourceforge.
> net/
> SGA: http://www.ncbi.nlm.nih.gov/pubmed/22156294
> https://github.com/jts/sga
> Fermi: http://bioinformatics.oxfordjournals.org/content/28/14/1838
> https://github.com/lh3/fermi
> PBWT: http://www.ncbi.nlm.nih.gov/pubmed/24413527 https://github.com/
> richarddurbin/pbwt
>
> Bio:
> Richard Durbin, FRS, is Acting Head of Computational Genomics at the
> Wellcome Trust Sanger Institute and leader of the Genome Informatics group.
> He studied mathematics at Cambridge and earned a PhD on the development and
> organization of the nervous system in C. elegans. He has developed numerous
> methods for computational sequence analysis, co-authored a textbook on this
> subject, and co-leads the international 1000 Genomes Project. He was a
> joint winner of the Mullard Award of the Royal Society in 1994 (for work on
> the confocal microscope), won the Lord Lloyd of Kilgerran Award of the
> Foundation for Science and Technology in 2004, and was elected a Fellow of
> the Royal Society in 2004 (for contributions to computational biology) and
> a member of the European Molecular Biology Organization (EMBO) in 2009.
>
> ==========
>
> Title:
> Compact and Succinct Data Structures -- From Theory to Practice
>
> Abstract:
> For decades index structures where build on top of the data to enable
> users to efficiently carry out queries. For instance suffix trees or arrays
> were built on top of a text to answer pattern matching queries in a time
> complexity which is independent from the text length.
>
> Unfortunately, these traditional pointer-based index structures often take
> significantly more space than the original data and therefore can not be
> used in scenarios where the data itself is not much smaller than the
> available main memory. In the last 25 years researches invented
> space-efficient counterparts for many index structures which use not much
> more space than the original data and have the same query complexity in
> theory. In this talk we will review popular examples of compact and
> succinct structures -- ranging from bit vectors over wavelet trees to
> compressed suffix trees -- and show how they can be easily used in
> applications by employing the Succinct Data Structure Library (SDSL). We
> will further show how to use the library's facilities to analyse, measure,
> and monitor time and space requirements of structures. Finally, we will
> learn how more complex structures can be composed and integrated in the
> existing framework.
>
> SDSL: https://github.com/simongog/sdsl-lite
>
> Bio:
> Simon Gog obtained his PhD from Ulm University where he was working on
> space-efficient index data structures with applications in Bioinformatics.
> The Succinct Data Structure Library project was started in Ulm and
> continued at the University of Melbourne, where he was working as a PostDoc
> on compressed external index structures. Currently, Simon is working at the
> Karlsruhe Institute of Technology on compact index structures for
> applications in the area of Information Retrieval.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: https://fenris.cs.ucr.edu/pipermail/cpm-spire-l/attachments/20150802/99813f9c/attachment.html