[Sussex] Talk about bioinformatics at Portsmouth LUG B-a-B meeting Saturday, August 16th, from 13:00 - 18:00

[Lisi Reisz]

You are all - but especially those down our end of Sussex - warmly invited to 
the next meeting of the Portsmouth Linux Users Group, which will be on 
Saturday, August 16th, from 13:00 - 18:00, in the Broadoaks Social Club.
http://www.broadoaksocialclub.net/where.html

Please note that this is in Hilsea, not Portsmouth.  It is very easily 
accessible from the A27 and is on the Brighton-Portsmouth railway line.  It 
is a mere 4 miles form the Sussex border.

It would be great to see a crowd of you.  Please remember it is a Bring-a-Box 
meeting. ;-)

Jan Kim is very kindly giving a talk on Bioinformatics.

Herewith what he says about it:
<quote>
Biological systems generate and process information, and new DNA
sequencing technologies [1] now provide unprecedented experimental
access to genetic information. The volume of sequence data necessitates
the use of high performance computing for its storage and analysis,
and the majority of sequence data is now held in public repositories
operated by global collaborations [2].

Linux is a major platform for the development of bioinformatics systems
and APIs, including EMBOSS [3], clustal [4], APIs for general purpose
programming systems such as Bioconductor [5] for R or Biopython [6],
and specialised high performance systems for "Next Generation Sequencing"
(NGS) data analysis [7, 8, 9]. These systems are generally developed
as Open Source projects and packaged for all major Linux distributions.

My general plan for this talk is to start with a brief background on
molecular genetics, and to then give a flavour of the use of some of
the systems above in scientific computing environments [10]. It will be
a group decision which of these we'll look into, and to which extent --
I'll bring my laptop and slides covering most of the systems above
but expect there won't be time for all of them.

[1] http://en.wikipedia.org/wiki/Dna_sequencing
[2] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013722/
[3] http://emboss.sourceforge.net/
[4] http://www.clustal.org/
[5] http://bioconductor.org/
[6] http://biopython.org/
[7] http://samtools.sourceforge.net/
[8] http://bio-bwa.sourceforge.net/
[9] https://www.ebi.ac.uk/~zerbino/velvet/
[10] 
http://www.software.ac.uk/collaborations-workshop-2014-cw14-software-your-reproducible-research
</quote>

Tea, coffee and a full bar are available, but please note that alcohol can 
only be bought by club members.  Temporary membership is available for £1, or 
you can ask one of the three of us who are members to do the buying for you.  
Food on a Saturday is sparse unless preordered.  (Scratchings, crisps etc.)

For newcomers:
There is plenty of parking just opposite the club, and Hilsea railway 
station is immediately adjacent.

The door to the club will probably be locked.  If so, you will need to 
ring the buzzer and ask for the Linux meeting.  Go up the stairs and 
through the bar to the door at the back left corner of the bar.

I shall aim to be there not later than 12:30.  If I am the only one left at 
any time after 5:00, I shall go.  So if you want to arrive ultra late, make 
sure that you let me know!

Lisi