RSG-India at HGM 2008!

We are very happy to inform you all that RSG-India has been given an
opportunity to have a booth at the Human Genome Meeting 2008 to be
held at Hyderabad from 27th-31st September 2008!

Regional Student Group – India (RSG-India) is a student organization
dedicated to the development of the Bioinformatics and Computational
Biology student community in India. RSG-India is part of an initiative
by the Student Council of the International Society of Computational
Biology [ISCB-SC] to improve Computational Life sciences’ research and
learning around the world at a closer and more involved level.

HGM is the annual conference organized by the Human Genome
Organization HUGO, designed to update and increase knowledge in the
field of Human Genome research. HGM is one of the ‘must-attend’
conferences in the international conference calendar. We at RSG-India
are very excited about this opportunity. As far as we know, this is
the first time a student organization has been allowed its own booth
at an international Conference of this stature.

CAIcal is a web server that performs several computations in relation to
codon usage and the codon adaptation of DNA or RNA sequences to host
organisms.

This web server is freely accessible at http://genomes.urv.cat/CAIcal

For more details see the article Puigbo P, Bravo IG and Garcia-Vallve S.
(2008) CAIcal: a combined set of tools to assess codon usage adaptation.
Biology Direct, 3:38.

dear sir,
I am working as senior lecturer at sastra university,
tanjore. I am interested in bioinformatics. If you send me
the perl code for multiple sequence alignment. It would be
great help for my academeic endeavour.
with regards
m.a.k Jailani
senior lecturer
sastra university
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Dear all,

I am a beginner for VMD software, and currently try to practice VMD to get
electrostatic grid of protein of my interest. I try to use the example of
potsel.tcl usage in (http://www.ks.uiuc.edu/Research/vmd/script_library/)

source potsel.tcl
mol pdbload 1bnf
set sel [atomselect top "not water"]
potSel $sel 63 2 80

But, it did not work out, and written

couldn't execute "touch": no such file or directory

Do you know how I can get the "touch" file?
If you have more examples for me, I will really appreciate it.

Thanks a lot in advance.

Best regards,
Yusdy

Dear Group members,

a recent Science publication:
"A Global View of Gene Activity and Alternative Splicing by Deep
Sequencing of the Human Transcriptome"
[url]http://www.sciencemag.org/cgi/content/abstract/1160342[/url]

demonstrates capabilities of two products from Genomatix
[url]www.genomatix.de[/url]

Genomatix delivers powerful turnkey solutions downstream of Next
Generation Sequencing (NGS) devices, following the Genomatix tradition
of highest scientific standards and cutting edge technology.

Genomatix solutions work with data from all available NGS system
providers: Illumina´s Genome Analyzer (Solexa), Roche (454), The SOLiD
TM System by Applied Biosystems, and HeliScope by Helicos.

Dear All
Due to I am working on a project I need some information.
Any of you are working on Grid computing And/Or Nanomedicine Or
Nanoinformatics?
Thanks!

Dear all,

We announce the release of NQ-Flipper, a public service for the
visualization and correction of unfavorable/incorrect asparagine
and glutamine side-chain rotamers. For further information on the
NQ-rotamer problem and the NQ-Flipper service see

Weichenberger, Byzia & Sippl (2008), Visualization of unfavorable
interactions in protein folds.
Bioinformatics Advance Access published online on March 29, 2008.
http://dx.doi.org/10.1093/bioinformatics/btn108

Weichenberger & Sippl (2007) Recognition and Correction of Erroneous
Asparagine and Glutamine Side Chain Rotamers in Protein Structures.
Nucleic Acids Res., 35(Web Server issue), W403-406.
http://dx.doi.org/10.1093/nar/gkm263

NQ-Flipper is available as a public web service at
http://flipper.services.came.sbg.ac.at or may be downloaded as a
standalone application for Linux systems.

Enjoy!

Dear all,

We announce the release of NQ-Flipper, a public service for the
visualization and correction of unfavorable/incorrect asparagine
and glutamine side-chain rotamers. For further information on the
NQ-rotamer problem and the NQ-Flipper service see

Weichenberger, Byzia & Sippl (2008), Visualization of unfavorable
interactions in protein folds.
Bioinformatics Advance Access published online on March 29, 2008.
http://dx.doi.org/10.1093/bioinformatics/btn108

Weichenberger & Sippl (2007) Recognition and Correction of Erroneous
Asparagine and Glutamine Side Chain Rotamers in Protein Structures.
Nucleic Acids Res., 35(Web Server issue), W403-406.
http://dx.doi.org/10.1093/nar/gkm263

NQ-Flipper is available as a public web service at
http://flipper.services.came.sbg.ac.at or may be downloaded as a
standalone application for Linux systems.

Enjoy!

We are pleased to announce the release of TopMatch-web, a public web
service for the alignment and superposition of protein structures and the
instant visualization of structural similiarities.

We believe that TopMatch is an exceptionally effective, accurate, and
enjoyable program for the investigation of protein structure similarities.

For further information and instructive examples see
Sippl & Wiederstein (2008)
A Note on Difficult Structure Alignment Problems.
Bioinformatics 24, pp. 426-427

TopMatch-web is available as a public web service at
http://topmatch.services.came.sbg.ac.at.

Enjoy!

The TopMatch Team
Center of Applied Molecular Engineering
University of Salzburg
Austria

Meeting Announcement
Automated Biorepositories: Successful Models

Dear colleagues,

LRIG will host a second annual meeting on biorepositories with an emphasis
on how automation has been successfully applied to solve problems with
managing collections. The meeting consists of a technology exhibition, tours
of RUCDR and social period followed by presentations and discussion. It will
take place at Rutgers, the State University of New Jersey in Piscataway, NJ
from 3:00-9:00 PM on February 28, 2008. The web page with full details may
be found at <http://lab-robotics.org/Mid_Atlantic/meetings/0802.htm>.

An abbreviated agenda:

Tours: Rutgers University Cell and DNA Repository (RUCDR)
Dr. David Toke, Associate Managing Director, Rutgers University Cell & DNA
Repository (RUCDR)

University Cell and DNA Repository.

Presentation: Development and validation of the UK Biobank sample handling,
processing and archiving protocol
Tim Peakman, Executive Director, UK Biobank