Nabble - Bio.net - Bionews

Bioprotocols online

2009-12-08T19:05:46Z

Sciclips has launched a unique database of bioprotocols for
researchers. Researchers will have free access to these bioprotocols
which have been extracted from published journal articles and patents/
patent applications. We are the first to list protocols from published
US patents, US patent and WO (PCT) applications. We have thousands of
protocols on molecular biology, proteomics, biological imaging,
virology, immunology, stem cells, drug discovery, immunoassays, cell
biology, epigenetics, genomics, plant biology, microbiology, tissue
microarrays and more. In addition to this, we have also listed new
sections on high throughput screening (HTS) and biopharmaceutical
assay protocols. All the protocols are linked to the articles or
patent/patent application . Please follow this link to see the
complete list of our bioprotocols online: http://www.sciclips.com/sciclips/bio-protocols.do

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Bionet Arthropod list is available, with Arthropod EST assemblies

2009-12-08T10:23:21Z

Dear scientists,

The new BIOSCI/Bionet newsgroup ARTHROPOD is available now
for discussion of the largest phylum of animals including
insects, arachnids, crustaceans, and others. Topics of
interest include Evolution, Genomics, and disease Vector arthropods.
List-mail: arthropod @ net.bio.net
Subscribe: http://www.bio.net/biomail/listinfo/arthropod
Usenet (as bionet.biology.vectors) and RSS news feeds are available

Early posts include upcoming meetings of interest, and new
Arthropod EST gene data. EST results include arachnid tick
Ixodes, crustacean waterflea Daphnia, insects Bombyx silk moth,
Drosophila fruitfly, Nasonia wasp and Acyrthosiphon aphid

- Which species has official gene models that missed over 50%
of EST assemblies?

- Which species has 3 times more ESTs split between scaffolds, and
a perhaps corresponding missed coding exon per gene model, on average?

You can get answers to these questions on the bionet.Arthropod news group,
just ask.

-- Don Gilbert
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd@...--http://marmot.bio.indiana.edu/

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Bionet seeks new Usenet service provider

2009-12-08T10:21:14Z

Dear Bionet readers,

Another Indiana university is turning off its Usenet service.
Bionet will lose its Usenet feed thru Purdue at the end of this
month. I appreciate this service that Purdue University has
provided to the Bionet community for the last few years.

If you know of any good Usenet providers who would help out with
Bionet, please let me know. This would be a Usenet provider that
supports NNTPS (secure network news protocol) which most should,
and also the ability to process moderated, PGP signed messages.

Usenet is waining due in part its unregulated, distributed
nature, that has been abused, yet it still provides value to many
in biology and outside. About 25% of Bionet postings are coming
in via Usenet, across all the groups.

THanks for any suggestions,

Don Gilbert
email: biosci-help@...
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd@...--http://marmot.bio.indiana.edu/

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DEXA'10/BIOKDD'10: Call for Papers

2009-12-06T11:18:58Z

CALL FOR PAPERS


2nd
International Workshop on

   Biological Knowledge Discovery
and Data Mining (BIOKDD'10)

Held in parallel
with

21st International Conference on Database and

Expert Systems Applications (DEXA’10)

www.dexa.org



Bilbao ,
Spain

August 30-September
3, 2010

With the development of Molecular Biology
during the last decades, we are witnessing an exponential growth of both the
volume and the complexity of biological data. For example, the Human Genome Project provided the sequence of the 3 billion DNA bases that
constitute the human genome. And, consequently,
we are provided too with the sequences of about 100,000 proteins. Therefore, we
are entering the post-genomic era: after having focused so many efforts on the accumulation
of data, we have now to focus as much effort, and even more, on the analysis of
these data. Analyzing this huge volume of data is a challenging task because,
not only, of its complexity and its multiple and numerous correlated factors,
but also, because of the continuous evolution of our understanding of the
biological mechanisms. Classical approaches of biological data analysis are no
longer efficient and produce only a very limited amount of information, compared
to the numerous and complex biological mechanisms under study. From here comes
the necessity to use computer tools and develop new in silico high
performance approaches to support us in the analysis of biological data and,
hence, to help us in our understanding of the correlations that exist between,
on one hand, structures and functional patterns of biological sequences and, on
the other hand, genetic and biochemical mechanisms. Knowledge Discovery and
Data Mining (KDD) are a response to these new trends.

Topics of BIOKDD'10 workshop include, but not limited to:



Data Preprocessing: Data Storage, Representation and Management, Data Cleaning,
Feature Extraction, Feature Selection.

   Data Mining: Biological Data Clustering/Biclustering, Biological Data
Classification, Biological Data Regression, Association Rule Learning from Biological
Data, Parallel/Cloud/Grid Computing for Biological Data Mining, Text Mining
and Application to Biological Sequences, Web Mining and Application to
Biological Data, Analysis
of Biological Networks.

Data Postprocessing: Knowledge Filtering, Knowledge Representation and
Visualization, Knowledge Combination and Integration, Error Rates and Numerical
Indicators.



PAPER SUBMISSION
DETAILS: Authors are invited to submit
electronically original contributions in English. Submitted papers should
not exceed 5 pages in IEEE format

<www.ieee.org/web/publications/authors/transjnl/index.html>. All accepted papers will be published in the
proceedings of DEXA’10 Workshops with IEEE CSP.
One of the authors of an accepted paper must register
to DEXA’10 conference and present the paper at BIOKDD’10 workshop. For paper registration and
electronic submission see <http://confdriver.ifs.tuwien.ac.at/dexa2010/>, starting from January 2010.

IMPORTANT DATES:      Submission of Full
Papers: March 30, 2010Notification of Acceptance: April 20, 2010

Camera-ready Copies: May 17, 2010

PROGRAM COMMITTEE:

Mourad Elloumi, UTIC, University of Tunis, Tunisia (PC Co-Chair)

Jin-Kao Hao, LERIA, University of Angers, France (PC Co-Chair)

El Ghazali Talbi, University
of Lille,

INRIA, CNRS, France

Albert Y. Zomaya, The
University of Sydney, Australia

Nadia Pisanti, University of Pisa, Italy

Sandrine Dudoit, University
of California, Berkeley, USA

Raffaele Giancarlo, Università degli Studi di
Palermo, Italy

Francesc Rosselló, University of the Balearic Islands
in Mallorca, Spain

Gabriel Valiente,

Technical University of Catalonia,
Spain

Giorgio Valentini, Università
degli Studi di Milano, Italy

Matteo Rè, Università degli Studi di Milano, Italy

Pierre
Peterlongo, IRISA-INRIA, Rennes, France

Alexandros Stamatakis, Technische
Universität München, Germany

Mohamed
Elati, University of Evry Val-d'Essonne, France

Michael
Ng, Hong Kong Baptist University , Hong Kong

Roderic Guigo, Genome
Informatics Research Laboratory, Spain

Alfredo Pulvirenti, University of Catania, Italy

Jason H. Moore, Dartmouth Medical School , USA

Dragan Bosnacki, Eindhoven University of Technology, The Netherlands

Carlo Cattani, University of Salerno, Italy

Giulio Pavesi, Università degli
Studi di Milano, Italy

Luonan Chen, Osaka Sangyo University, Japan

Chiara Epifanio, Università degli Studi di
Palermo, Italy

Graziano Pesole, University
of Bari, Italy

Elena Marchiori, Radboud Universityn, Nijmegen , The Netherlands

Alioune Ngom, University of Windsor , Ontario , Canada

Giulia Menconi, Istituto Nazionale di Alta Matematica,
Roma, Italy

Luca Bortolussi, Università di
Trieste, Italy

Jaume Bacardit, University of Nottingham , UK

Rosalba Giugno, University of Catania, Italy

Oleg Okun, The National Academy
of Sciences of Belarus, Belarus

Xiangchao Gan, University of Oxford, UK

Florin Leon , Technical University of Iaşi, Romania

Mihai Horia Zaharia, Technical
University of Iaşi, Romania

Xingming Zhao, Shanghai University, China

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GMOD Community Meeting, January 2010

2009-11-25T13:11:27Z

The next GMOD meeting will be held January 14-15 in San Diego, California,
USA, immediately after the Plant and Animal Genome (PAG) conference. There
is no registration fee for this meeting. However, there is limited space, so
please register early. See the meeting page for more information:
http://gmod.org/wiki/January_2010_GMOD_Meeting.

GMOD is a collection of interoperable open source software components for
visualizing, annotating, and managing biological data. GMOD is also a
community of users and developers asking diverse questions, and facing
common challenges, with their biological data. GMOD has many widely used
software packages, including GBrowse, Apollo, CMap, Chado, BioMart, MAKER,
Galaxy, Textpresso, and many others. The availability and affordability of
next generation sequencing (NGS) has made GMOD particularly timely to a wide
range of research groups.

As with previous GMOD meetings, there will be a mixture of project,
component, and user talks. There will also be a number of satellite meetings
focusing on particular areas of interest.

Thanks,

Dave Clements
GMOD Help Desk

--
http://gmod.org/wiki/January_2010_GMOD_Meeting
http://gmod.org/wiki/GMOD_News
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OSDD Connect to Decode Programme is Open for Registrations

2009-11-14T02:15:24Z

Dear Colleagues,

OSDD Launches the "Connect to Decode" 2010 Initiative to re-annotate
the Mycobacterium tuberculosis genome.

Open Source Drug Discovery (OSDD) Project in its quest towards
conquest of Tuberculosis, is launching a massive initiative to further
the understanding of the biology of the causative organism,
Mycobacterium tuberculosis. The objective is to accelerate the
discovery of novel drugs for TB, a disease neglected by Pharmaceutical
enterprises.
Though Mtb was sequenced a decade back, the standard databases have
not annotated in real biological processes, more than 1000 of the near
4000 genes encoded by the organism. This is symptomatic of the problem
of neglected diseases of the poor.

OSDD is taking up the challenge of annotating all possible genes in
Mtb and hopes that your Institution would join this massive effort.

The project requires a faculty coordinator and student contributors
from the college. For students this would be their summer project, the
successful completion of which would fetch them a certificate from the
Council of Scientific and Industrial Research (CSIR). All the projects
are managed by experts in the field. For the faculty coordinators, it
is an opportunity to interact with leading scientists working in this
field. Since the project has great significance in the conquest of TB,
we expect serious student involvement and competent faculty
monitoring. The best coordinators, student contributors and the best
college centers would receive awards. Prizes include Laptops, iPods,
holidays etc. The project is scheduled between December ‘09 and March
’10. The best students and faculty would be invited for an
international conference on TB in April ’10.

If interested, you are requested to go through the programme website
at https://sites.google.com/a/osdd.net/osdd-connect-2-decode-2010/home

Please feel free to spread the word and forward this to others who
might be interested in participating.

--
----------------------------------------------------------
Dr Vinod Scaria
Scientist
G N Ramachandran Knowledge Centre for Genome Informatics,
Institute of Genomics and Integrative Biology (CSIR),
Mall Road, Delhi 110 007, India
E-mail: vinods@...
Web: http://vinodscaria.rnabiology.org/
Mob: +91 9650466002

Lab Address: IGIB Extension Center at Naraina,
A93-94 Naraina Inds Area, Phase 1,Naraina, New Delhi -110 028, Ph-
+91-11-25895615, 45073677/88/99 | Fax no: +91-11-2766 7471
---------------------------------------------------------
What's New? Visit http://miracle.igib.res.in

NOTE
'This message, including any attachments, may contain confidential and
privileged information for the sole use of the intended recipient(s).
Review, use, distribution or disclosure by others is prohibited. If
you receive this message in error, please notify the sender by reply
e-mail and delete the message from all computers. Please note that
e-mails are susceptible to change. The sender will not accept
liability for the improper or incomplete transmission of the
information contained in this message.'

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International Conference - Genome Biology and Bioinformatics

2009-11-04T13:21:19Z

The program of the conference features talks of many leading
experts in the field Visit the speakers page of the website
[http://www2.isye.gatech.edu/binf2009/speakers_2009.php]

Thanks to financial support from a larger group of sponsors we
are happy to announce

that the registration fee is reduced to

$20 student/postdoc; $50 - academic; $100 - industry;

We hope to see you soon in the Georgia Tech Ferst Center for the
Arts . Visit the website.
[http://www2.isye.gatech.edu/binf2009/]

November 12 (starting at 5pm) Dr. Jeffrey Bennetzen, Member of
National Academy of Sciences, University of Georgia, Athens, GA,
USA

The Hyperevolution of Artifacts and Realities in the Structure
and Function of Higher Plant Genomes Dr. Jian Ma, University
of Illinois at Urbana Champaign, Urbana, IL, USA

Unraveling the Ancestral Mammalian Genome Yields Insights into
the Human Genome Dr. Igor Jouline (Zhulin), University of
Tennessee - Oak Ridge National Laboratory, Oak Ridge, TN, USA

Molecular Evolution of a Complex Signal Transduction System in
Prokaryotes Dr. Curtis Huttenhower, Harvard University, Boston
, MA, USA

Large Scale Genomic Data Mining Dr. Boris Lenhard, University
of Bergen, Norway

Long-, Short- and Mid-Range Gene Regulation: Lessons from Genome
-Wide Patterns of Sequence Conservation and Transcription Factor
Binding Inaugural Margaret O. Dayhoff lecture

Dr. David Lipman, Member of the National Academy of Sciences,
NCBI/NIH, Bethesda, MD, USA

Margaret Dayhoff and Molecular Evolution in the 21st Century

Dr. Joanna Masel, University of Arizona, Tucson, AZ, USA

The Origin of New Coding Sequences Dr. Nick Grishin, Howard
Hughes Medical Institute, University of Texas, Dallas, TX, USA

Evolutionary Classification of Protein Structures Dr. Eugene
Koonin, NCBI/NIH, Bethesda, MD, USA

Systems Biology and the Prospects of a Post-Modern Evolutionary
Synthesis Dr. Nikos Kyrpides, DOE Joint Genome Institute,
Walnut Creek, CA, USA

The Future of Microbial Genomics Dr. Andrei Osterman, Burnham
Institute for Medical Research, La Jolla, CA

USA Integrated Genomic Reconstruction of Metabolic and Regulatory
Networks in Bacteria November 14 Dr. Pierre Rouze, Gent
University, Gent, Belgium

>From Protists to Plants, Fungi and Animals: Eukaryote Genomes Are
Not Born Equal Dr. Jason Miller, J. Craig Venter Institute,
Rockville, MD, USA

Studies of the Human Microbiome Dr. Mark Borodovsky, Georgia
Tech and Emory University, Atlanta, GA, USA

Gene Finding in the Era of Next Generation Sequencing Dr. John
Reinitz, State University of New York at Stony Brook, NY, USA

When Two Plus Two Doesn't Equal Four: Modeling Non-Modular
Enhancer Behavior in the Eve Promoter Dr. Yael Mandel
-Gutfreund, Technion, Institute of Technology, Haifa, Israel

Deciphering the Role of Alternative Splicing in Modulating the
Human Gene Regulatory Network Dr. Andrey Mironov, Moscow State
University, Russia

Conserved Intronic RNA Secondary Structures Dr. Gill Bejerano,
Stanford University, Stanford, CA, USA

Genomics and the Evolution of Human-Specific Traits Dr. King
Jordan, Georgia Tech, Atlanta, GA, USA

MIR Elements Provide Chromatin Boundaries to the Human Genome
Dr. Vineet Bafna, University of California at San Diego, USA

Proteogenomics Conference ends at 9pm, November 14 Visit the
Website [http://www2.isye.gatech.edu/binf2009] Questions?
Contact Megan McDevitt, Event Manager

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International Conference - Genome Biology and Bioinformatics

2009-10-22T09:31:23Z

Dear Colleagues,

The 7th Georgia Tech - ORNL Conference -
"Genome Biology and Bioinformatics"
to be held on November 12-14, 2009
is now less than a month away:
http://www2.isye.gatech.edu/binf2009/

The program of the conference features
talks of many leading experts in the field
http://www2.isye.gatech.edu/binf2009/speakers_2009.php

Thanks to financial support from a larger group of sponsors
we are happy to announce that the registration fee is reduced to:

$20 student/postdoc
$50 - academic
$100 - industry

Deadline for poster abstract submission is extended to
November 1

We hope to see you soon in the
Georgia Tech Ferst Center for the Arts

_____________________________________

Invited Speakers

Margaret O. Dayhoff Lecture
David Lipman, NCBI/NIH, Bethesda, MD, USA
Margaret Dayhoff and Molecular Evolution in the 21st Century

Vineet Bafna, University of California at San Diego, USA
Proteogenomics

Gill Bejerano, Stanford University, Stanford, CA, USA
Genomics and the Evolution of Human-Specific Traits

Jeffrey Bennetzen, University of Georgia, Athens, GA, USA
The Hyperevolution of Artifacts and Realities in the Structure and Function of Higher Plant Genomes

Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA
Gene Finding in the Era of Next Generation Sequencing

Nick Grishin, Howard Hughes Medical Institute, University of Texas, Dallas, TX, USA
Evolutionary Classification of Protein Structures

Curtis Huttenhower, Harvard University, Boston, MA, USA
Large Scale Genomic Data Mining

King Jordan, Georgia Tech, Atlanta, GA, USA
MIR Elements Provide Chromatin Boundaries to the Human Genome

Igor Jouline, University of Tennessee - Oak Ridge National Laboratory, Oak Ridge, TN, USA Molecular Evolution of a Complex Signal Transduction System in Prokaryotes

Eugene Koonin, NCBI/NIH, Bethesda, MD, USA
Systems Biology and the Prospects of a Post-Modern Evolutionary Synthesis

Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA
The Future of Microbial Genomics

Boris Lenhard, University of Bergen, Norway
Long-, Short- and Mid-Range Gene Regulation: Lessons from Genome-Wide Patterns of Sequence Conservation and Transcription Factor Binding

Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA
Unraveling the Ancestral Mammalian Genome Yields Insights into the Human Genome

Yael Mandel-Gutfreund, Technion, Israel Institute of Technology, Haifa, Israel
Deciphering the Role of Alternative Splicing in Modulating the Human Gene Regulatory Network

Joanna Masel, University of Arizona, Tucson, AZ, USA
The Origin of New Coding Sequences

Andrey Mironov, Moscow State University, Russia
Conserved Intronic RNA Secondary Structures

Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA
Studies of The Human Microbiome

Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA
Integrated Genomic Reconstruction of Metabolic and Regulatory Networks in Bacteria

Natasa Przulj, Imperial College London, UK
>From Network Topology to Biological Function and Disease

John Reinitz, State University of New York at Stony Brook, NY, USA
When Two Plus Two Doesn't Equal Four: Modeling Non-Modular Enhancer
Behavior in the Eve Promoter

Pierre Rouze, Gent University, Gent, Belgium
>From Protists to Plants, Fungi and Animals: Eukaryote Genomes Are
Not Born Equal

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Announcement: GenPept 174.0 available

2009-10-22T08:12:33Z

This is to announce the availability of release 174.0 of the GenPept(R)
(GenBank Gene Products) Database. GenPept is provided in a format similar
to that formerly distributed by GenBank(R) under the administration of
Intelligenetics Inc. This GenPept release IS _NOT_ AN OFFICIAL RELEASE FROM
THE NCBI-GENBANK, but an attempt to provide a data file format compatible
with existing software products.

This data format is suitable as an input data file for the GCG program
genbanktogcg -genpept. Compatibility with other software has not been tested.

Site: ftp.ncifcrf.gov

Directory: pub/genpept
Files: gprel.txt.gz, gpdat.seq.gz, gpdat.fasta.gz

Directory: pub/genpept/divisions
Files: 1 file for each GenBank file

Directory: pub/genpept/updates (daily, cumulative)
Files: gpseq_updates.dat.gz

Rel. Date: 20-Oct-2009

If you have questions or comments concerning this data, or you experience any
difficulty in downloading the data via ftp, please contact:

Gary Smythers smytherg@... 301-846-5778

================================================================
GenPept (R) and GenBank (R) are registered trademarks of the U.S. Department
of Health and Human Services for the GenBank Gene Products and the GenBank
Genetic Sequence Data Banks.

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7th Georgia Tech - ORNL Conference on Bioinformatics

2009-10-08T17:23:20Z

Call for Paper Abstracts is extened

---------------------------------
Dear Colleagues

The 7th Georgia Tech - ORNL Conference on Bioinformatics -
In silico Biology: Genome Biology and Bioinformatics
will be held in Atlanta, Georgia, November 12-14, 2009
http://www2.isye.gatech.edu/binf2009/

Georgia Tech continues the tradition of organizing biennial
International Conference on Bioinformatics, bringing together leading
researchers in genomics, bioinformatics and genome biology to present
recent advances in the field and to discuss open problems.

Important Dates

Deadline for poster abstract subsmission: October 11, 2009
Notification of acceptance of abstracts: October 20, 2009
Deadline for early registration: October 23, 2009

We invite papers submissions in the following areas
* genomics
* transcriptomics
* proteomics
* reconstruction and modeling of gene networks
* evolutionary biology

SPEAKERS

Margaret O. Dayhoff lecture:

David Lipman, NCBI/NIH, Bethesda, MD, USA

Plenary Speakers:

Vineet Bafna, University of California at San Diego, USA
Gill Bejerano, Stanford University, Stanford, CA, USA
Jeffrey Bennetzen, University of Georgia, Athens, GA, USA
Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA
Nick Grishin, University of Texas, Dallas, TX, USA
Curtis Huttenhower, Harvard University, Boston, MA, USA
King Jordan, Georgia Tech, Atlanta, GA, USA
Igor Jouline (Zhulin), University of Tennessee - ORNL, Oak Ridge, TN, USA
Eugene Koonin, NCBI/NIH, Bethesda, MD, USA
Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA
Boris Lenhard, University of Bergen, Norway
Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA
Yael Mandel-Gutfreund, Technion, Israel Insitute of Technology, Haifa, Israel
Joanna Masel, University of Arizona, Tucson, AZ, USA
Andrey Mironov, Moscow State University, Russia
Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA
Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA
Natasa Przulj, Imperial College London, UK
John Reinitz, State Uiversity of New York at Stony Brook, NY, USA
Pierre Rouze, Gent University, Gent, Belgium

CONFERENCE CHAIRS
Mark Borodovsky, Georgia Tech and Emory University
Eva K. Lee, Georgia Tech and Emory University

PROGRAM COMMITTEE
Nicholas Bergman, Georgia Tech
Dmitrij Frishman, Technische Universitaet Muenchen, Germany
Andrey Gorin, Oak Ridge National Laboratory
Andrzej M. Kierzek, University of Surrey, UK.
Eileen Kraemer, University of Georgia
Jun Liu, Harvard University
Hannah Margalit, Hebrew University
Andrey Rzhetsky, University of Chicago
Andre Rogatko, Samuel Oschin Comprehensive Cancer Institute
Gary Stormo, Washington University
Lance Waller, Emory University
Ying Xu, University of Georgia and Oak Ridge National Laboratory
Soojin Yi, Georgia Tech
Igor Zhulin, Oak Ridge National Laboratory and University of Tennessee

ADMINISTRATION
Harry Sharp, Georgia Tech

CONFERENCE LOCATION

The Georgia Tech Ferst Center for the Arts.

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CFP: HiCOMB 2010 - 9th IEEE International Workshop on High Performance Computational Biology

2009-10-06T15:56:54Z

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Call For Papers

HiCOMB 2010
9th IEEE International Workshop on High Performance Computational Biology
http://www.hicomb.org/

held in conjunction with the
International Parallel and Distributed Processing Symposium
http://www.ipdps.org/

Monday, April 19, 2010

Atlanta, Georgia
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

Computational Biology are related disciplines are fast emerging as an
important area for academic research and industrial application.
The large size of biological data sets, inherent complexity of biological
problems and the ability to deal with error-prone data all result in large
run-time and memory requirements. The goal of this workshop is to provide a
forum for discussion of latest research in developing high-performance
computing solutions to problems arising from molecular biology and related
life sciences areas. We are especially interested in parallel algorithms,
memory-efficient algorithms, large scale data mining techniques, and design
of high-performance software. The workshop will feature contributed
papers as well as invited talks from reputed researchers in the field.
Topics of interest include but are not limited to:

* Bioinformatic databases
* Computational genomics
* Computational proteomics
* DNA assembly, clustering and mapping
* Gene expression and microarrays
* Gene identification and annotation
* Parallel algorithms for biological analysis
* Parallel architectures for biological applications
* Molecular evolution
* Molecular sequence analysis
* Phylogeny reconstruction algorithms
* Protein structure prediction and modeling
* String data structures and algorithms
* Parallel algorithms in chemical genetics and chemical informatics

Submission Guidelines:
----------------------

Papers reporting original research (both theoretical and experimental)
in all areas of bioinformatics and computational biology are sought.
Surveys of important recent results and directions are also welcome.
To submit a paper, upload a postscript or PDF copy of the paper from
the workshop web page (http://www.hicomb.org/). The paper should not
exceed 12 single-spaced pages (US Letter or A4 size) in 11pt font or
larger. All papers will be reviewed. IEEE CS Press will publish the
IPDPS symposium and workshop abstracts as a printed volume. The
complete symposium and workshop proceedings will also be published by
IEEE CS Press on CD-ROM and will also be available in the IEEE Digital
Library.

Important Dates:
----------------
November 30, 2009 Workshop Submissions Due
December 25, 2009 Author Notification
February 1, 2009 Camera-ready Paper Due

Workshop Co-Chairs:
-------------------

David A. Bader
College of Computing
Georgia Institute of Technology
Atlanta, GA 30332 USA
Phone: +1.404.894.3152
http://www.cc.gatech.edu/~bader

Srinivas Aluru
Dept. of Electrical & Computer Engg.
Iowa State University
3227 Coover Hall
Ames, IA 50011 USA
Phone: +1.515.294.3539
Email: aluru@...

Program Chair:
--------------

George Karypis
Dept. of Computer Science & Engineering
University of Minnesota
Minneapolis, MN 55455
Email: karypis@...
http://www.cs.umn.edu/~karypis

Program Committee:
------------------

Pratul K. Agarwal, Oak Ridge National Laboratory, USA
Inanc Birol, Genome Sciences Centre, British Columbia, Canada
Georg Fuellen, University of Rostock, Rostock, Germany
Ananth Grama, Purdue University, Indiana, USA
Mark Miller, San Diego Supercomputer Center, California, USA
Sandeep Patel, University of Delaware, USA
Andrew Rau-Chaplin, Dalhousie University, Nova Scotia, Canada
Huzefa Rangwala, George Mason University, Virginia, USA
Jared Simpson, Wellcome Trust Sanger Institute, Cambridge, UK
Alexandros Stamatakis, Technische Universität Munchen, Munich, Germany
John Stone, University of Illinois at Urbana-Champaign, USA
Evripidis Sotiriadis, Tech. Univ. of Crete, Greece
Denis Trystram, LIG, France
Chau-Wen Tseng, University of Maryland, College Park, USA
Ian Watson, Lilly, Indiana, USA
Tiffani Williams, Texas A&M University, Texas, USA
Ying Zhao, Tsinghua University, Beijing, China
Albert Zomaya, University of Sydney, Sydney, Australia

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CALL FOR ABSTRACTS - Plant & Animal Genome XVIII Conference

2009-09-28T01:16:50Z

Dear Colleague:

You are invited to attend the Plant & Animal Genome XVIII Conference
(PAG-XVIII), January 9-13, 2010 taking place at the Town & Country
Convention Center in San Diego, California.

To view the pre-registration brochure please download the PDF file:

http://www.scherago.com/pag/RegBrochure.pdf

The meeting will again offer the satellite sessions and workshops which
took place at Plant & Animal Genome XVII. The meeting draft for
PAG-XVIII and abstracts from PG-I through PAG-XVII are available on the
PAG website listed below. The exhibits and posters will now take place
in the Grand Exhibit Hall, adjacent to the California room. We are no
longer using the lower level parking facility.

We are requesting that all abstracts be submitted electronically. The
abstract deadline is MONDAY, November 2, 2009; extended to allow for
the new registration process. The abstract submission website is now open.

All attendees looking to submit an abstract will be required to pay the
registration fee PRIOR to submitting their abstract. You will be
assigned an attendee ID# which will be issued once you complete the
on-line registration process. You can look up your ID# on the PAG
website at:

http://intl-pag.org

You will be required to provide your attendee ID# to complete the
on-line abstract submission process.

Due to severe delays in getting VISAs to enter the United States, we
recommend that you plan ahead and do NOT wait for your abstract
acceptance to begin the process. DO NOT WAIT.

All researchers presenting posters must pre-register for the meeting to
have their abstract printed in the final meeting program. Tha abstract
deadline is MONDAY, November 2, 2009. Registration is available via the
Internet using our secure on-line registration form listed below.

https://www.pagregistration.com/pag18reg.shtml

Full Conference (Univ/Non-Profit/Govt) Registration for ALL attendees:
Pre-Registration (deadline November 2, 2009): $550
Late Registration (after November 2, 2009): $650
On-site Registration: $750

Full Conference (Industry) Registration for ALL attendees:
Pre-Registration (deadline November 2, 2009): $775
Late Registration (after November 2, 2009): $875
On-site Registration: $975

Weekend Only (Univ/Non-Profit/Govt) Registration (Fri/Sat/Sun) for ALL attendees:
Pre-Registration (deadline November 2, 2009): $400
Late Registration (after November 2, 2009): $450
On-site Registration: $500

Weekend Only (Industry) Registration (Fri/Sat/Sun) for ALL attendees:
Pre-Registration (deadline November 2, 2009): $500
Late Registration (after November 2, 2009): $550
On-site Registration: $600

Student Registration (proof required):
Pre-Registration (deadline November 1, 2009): $375
Late Registration (after November 1, 2009): $425
On-site Registration: $475

All questions regarding Plant & Animal Genome XVIII should be directed
to Scherago Int'l at Tel: 201-653-4777 ext. 20, Fax: 201-653-5705 or
or Email: pag@....

Sincerely,

Darrin Scherago - VP, Meeting Manager
Scherago International, Inc.
525 Washington Blvd., Suite 3310, Jersy City, NJ 07310
--------------------------------------------------------------------------
Plant & Animal Genome XVIII Conference ---------------- January 9-13, 2010
--------------------------------------------------------------------------

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7th Georgia Tech - ORNL Conference on Bioinformatics

2009-09-25T16:17:22Z

The 7th Georgia Tech - ORNL Conference on Bioinformatics -
In silico Biology: Genome Biology and Bioinformatics
will be held in Atlanta, Georgia, November 12-14, 2009
http://www2.isye.gatech.edu/binf2009/

Georgia Tech continues the tradition of organizing bi-annual
International Conference on Bioinformatics, bringing together leading
researchers in genomics, bioinformatics and genome biology to present
recent advances in the field and to discuss open problems.

Important Dates

Deadline for early registration: October 15, 2009
Deadline for poster abstract subsmission: October 1, 2009
Notification of acceptance of abstracts: October 11, 2009

We invite papers submissions in the following areas
* genomics
* transcriptomics
* proteomics
* reconstruction and modeling of gene networks
* evolutionary biology

SPEAKERS

Margaret O. Dayhoff lecture:

David Lipman , NCBI/NIH, Bethesda, MD, USA

Plenary Speakers:

Vineet Bafna, University of California at San Diego, USA
Gill Bejerano, Stanford University, Stanford, CA, USA
Jeffrey Bennetzen, University of Georgia, Athens, GA, USA
Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA
Nick Grishin, University of Texas, Dallas, TX, USA
Curtis Huttenhower, Harvard University, Boston, MA, USA
King Jordan, Georgia Tech, Atlanta, GA, USA
Igor Jouline (Zhulin), University of Tennessee - ORNL, Oak Ridge, TN, USA
Eugene Koonin, NCBI/NIH, Bethesda, MD, USA
Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA
Boris Lenhard, University of Bergen, Norway
Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA
Yael Mandel-Gutfreund, Technion, Israel Insitute of Technology, Haifa, Israel
Joanna Masel, University of Arizona, Tucson, AZ, USA
Andrey Mironov, Moscow State University, Russia
Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA
Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA
Natasa Przulj, University of California at Irvine, CA, USA
John Reinitz, State Uiversity of New York at Stony Brook, NY, USA
Pierre Rouze, Gent University, Gent, Belgium

CONFERENCE CHAIRS
Mark Borodovsky, Georgia Tech and Emory University
Eva K. Lee, Georgia Tech and Emory University

PROGRAM COMMITTEE
Nicholas Bergman, Georgia Tech
Dmitrij Frishman, Technische Universitaet Muenchen, Germany
Andrey Gorin, Oak Ridge National Laboratory
Andrzej M. Kierzek, University of Surrey, UK.
Eileen Kraemer, University of Georgia
Jun Liu, Harvard University
Hannah Margalit, Hebrew University
Andrey Rzhetsky, University of Chicago
Andre Rogatko, Samuel Oschin Comprehensive Cancer Institute
Gary Stormo, Washington University
Lance Waller, Emory University
Ying Xu, University of Georgia and Oak Ridge National Laboratory
Soojin Yi, Georgia Tech
Igor Zhulin, Oak Ridge National Laboratory and University of Tennessee

ADMINISTRATION
Harry Sharp, Georgia Tech

CONFERENCE LOCATION

The Georgia Tech Ferst Center for the Arts. The Georgia Tech campus
is located in Midtown Atlanta near the center of the 1996 Olympic
development, close to the Fox Theatre and Margaret Mitchell house.

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Reactome Pathway Database User Survey

2009-09-25T08:07:11Z

Reactome is committed to providing access to high-quality pathway
information and helpful data analysis tools. With this in mind, we
are actively soliciting comments from the research community in order
to assess community needs. We are interested to hear about your
experience with Reactome, and would like to know a bit about your
background and research interests so that we can continue to improve
the Reactome site and tools.

You can access the survey at: http://tinyurl.com/l48zzq

Thank you for taking part.

Robin Haw
Manager of Reactome Outreach
Outreach [at] reactome.org
http://www.reactome.org

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Practical Course in Biomolecular Modelling

2009-09-25T05:50:23Z

Dear colleagues,

please be informed that online applications are still accepted for the
following course until October 16, 2009:

8TH NCCR PRACTICAL COURSE IN BIOMOLECULAR MODELLING

January 10 - 15, 2010
Kandersteg, Switzerland
http://www.structuralbiology.uzh.ch/course2010.asp

Course topics include
Simulation techniques, force-field development, conformational search,
computation of free energy and entropy, treatment of electrostatic
forces, simulation of folding, comparison of simulation with experiment

This course is primarily directed to PhD students and postdocs from
experimental structural biology groups wishing to learn more on
biomolecular modelling. The course format will include morning lectures
and late-afternoon/early evening tutorials, and provide ample
opportunities for discussions with experts and fellow participants.
Participants will be invited to bring own problems for tutorials and/or
discussion. The course will be organized as a winter retreat in the
Swiss Alps offering a stimulating learning atmosphere with the
afternoons available for informal participation in discussions, reading
and self-study or recreational activities in the area.

Interested candidates are encouraged to apply online on
http://www.structuralbiology.uzh.ch/course2010_application.asp.
Application deadline will be October 16, 2010. We will be able to accept
20 participants to this course.

Best regards,
Patrick Sticher

--
_________________________________
Visit the NCCR on the Internet
www.structuralbiology.uzh.ch

Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
Mail sticher@...

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InnovationWell 2009 Meeting; Philadelphia Oct 09: Program available

2009-09-23T06:05:23Z

The InnovationWell 2009 community of practice meeting program with
abstracts is now complete and available at http://innovationwell.com/comty_conferencesprog09

The InnovationWell program will cover discussion of topics on
Collaboration in Discovery and Development, Translational
Bioinformatics, Systems Biology, Biomarkers, Blood-Brain Barrier
Modeling and Predictive Toxicology.
More detailed program below.

This annual community of practice meeting is taking place for the
fifth time and brings together a unique combination of pharmaceutical
and healthcare industry experts, principal investigators and
researchers from the academic and government sectors, and leaders from
innovative enterprises. The smaller and more intimate meeting format
pursued has fostered the type of collaboration not always found at
large conferences.

Registration fees include food (lunch, dinner, breaks and evening
refreshments) for the days attended. Furthermore, arrangements have
been made for some affordable accommodations (preferred rates), making
the meeting economical to attend. We now have a great deal of
information on preferred rates and travel directions available at
http://innovationwell.com/comty_conferencelocation

Innovation in Life Science & Healthcare R&D
InnovationWell 2009 InterAction Meeting
October 13-16, 2009
Bryn Mawr College, Bryn Mawr, Philadelphia, USA

Format: Seminars, Roundtables, Presentations, Panel Q&As, Discussions,
Break-out Workshops, Web-supported. Evening Poster sessions,
networking, social activities.

This meeting will take place concurrently with the eCheminfo 2009 drug
discovery community of practice meeting:
http://echeminfo.com/comty_conferencesprog09

Call for Abstracts:
If you wish to submit a poster abstract for the meeting which will be
placed on the program, please send to Barry Hardy (barry.hardy –(at)-
douglasconnect.com) for review. Attractive poster prizes will be
awarded for best posters at the meeting (subject to peer review).

A special peer-reviewed issue of Future Medicinal Chemistry with a
focus on collaboration in discovery and development is being published
from the meeting. Accepted poster and presentation abstracts are
eligible for consideration. Please contact Barry Hardy if interested
in submitting a paper for review.

Pre-Conference Workshop, October 12
Forum on Collaboration in Discovery and Development
To register for the meeting right now, please visit:
http://InnovationWell-BM09.eventsbot.com
To download a pdf of the program including the registration form:
http://barryhardy.blogs.com/files/innovationwell-bm09-90812.pdf

InnovationWell 2009 Program Summary

MONDAY, OCTOBER 12
Forum on Collaboration in Discovery and Development, Co-chaired by
Peter Gates (Johnson & Johnson PR&D) and Barry Hardy (Douglas
Connect). Speakers include Barry Hardy (Douglas Connect), Shree Nath
(Pointcross), Simson Alex (Johnson & Johnson), Chris Waller
(Pfizer), Michael Liebman (Strategic Medicine), Jeff Spitzner
(Rescentris), and Bob O’Hara (ResultWorks).

TUESDAY, OCTOBER 13
Translational Bioinformatics: Bridging Bioinformatics and Biomedical
Informatics in Translational Medicine, Chaired by Jake Chen (Indiana
University). Speakers include Jessica Tenenbaum (Duke Translational
Medicine Institute, Duke University), Steve Naylor (Predictive
Physiology and Medicine, Inc.), Javed Mostafa (University of North
Carolina), Jay Zhang (Myriad Genetics), Maricel Kann (University of
Maryland), Iya Khalil (Gene Network Sciences), Hai Hu (Windber
Research Institute), Jake Chen (Indiana University – Purdue
University), and Susan Stephens (Johnson & Johnson).

WEDNESDAY, OCTOBER 14
Systems Biology and Biomarkers, Chaired by Darius Dziuda (Central
Connecticut State University). Speakers include Anamika Sarkar
(Novartis), Darius Dziuda (Central Connecticut State University),
Frank Tobin (Tobin Consulting LLC), Andreas Matern (Thomson Reuters
Healthcare and Science), and Usha Reddy (Merck).

Modeling of the Blood–Brain Barrier in Drug Discovery and Development,
Chaired by Roméo Cecchelli (Université d'Artois, France). Speakers
include Stefan Lundquist (AstraZeneca), Reinhard Gabathuler
(AngioChem), Maxime Culot (University of Lille), Damir Janigro
(Cleveland Clinic), Marie-Pierre Dehouck (University of Lille), Pierre-
Olivier Couraud (Institut Cochin), and Anna Seelig (University of
Basel).

THURSDAY, OCTOBER 15
Predictive Toxicology: Combining in vitro and in silico Techniques in
Predictive Toxicology Applications, Co-chaired by Richard Judson (US
EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of
Russian Academy of Medical Sciences). Speakers include Richard Judson
(US EPA), Ellen Berg (BioSeek), Jonathan Dordick (Rensselaer
Polytechnic Institute), Barry Hardy (Douglas Connect), Sanji Bhal (ACD/
Labs), Christodoulos Floudas (Princeton University), Robert
Fraczkiewicz (Simulations Plus), Kyoung Tai No (Yonsei University),
and Stephen Bryant (NIH).

FRIDAY, OCTOBER 15
Predictive Toxicology: Combining in vitro and in silico Techniques in
Predictive Toxicology Applications, Co-chaired by Richard Judson (US
EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of
Russian Academy of Medical Sciences). Speakers include Vladimir
Poroikov (Institute of Biomedical Chemistry of Russian Academy of
Medical Sciences), Fangping Mu (Los Alamos National Laboratory), Katya
Tsaioun (Apredica), Grace Patlewicz (DuPont), Michael Pelekis
(Simulations Plus), and Anil Aswani (University of California at
Berkeley).

Contact:
Program: Dr. Barry Hardy, InnovationWell Community of Practice,
Douglas
Connect. Tel: +41 61 851 0170. email: innovationwell -[at]-
douglasconnect.com
Blog: http://barryhardy.blogs.com/

Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg
14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. innovationwell -
[at]- douglasconnect.com

Meeting Support: Rob Reedijk, eCheminfo Community of Practice,
Douglas
Connect. email: rob.reedijk -[at]- douglasconnect.com

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Unipro UGENE v1.5.2 released

2009-09-22T04:08:13Z

Our team is glad to announce UGENE 1.5.2 - a feature-oriented minor release,
which brings several unique possibilities to its users.

A new version adds 2 new plugins and brings numerous improvements and
bug fixes.

New plugins:
MUSCLE 4 - a port of the newest tool for multiple sequence alignment by
Robert C. Edgar;
CUDA Support - an utility plugin which makes possible using NVIDIA graphical
processing units for accelerating computational algorithms (only for
Windows).

New features and bug fixes:
CUDA-accelerated Smith-Waterman algorithm is ready to use for Windows users;

The one of the most awaited features: sequence editing has been added;
Exporting annotation tables to CSV has been provided;
HMM2 models support has been added to HMM3;

The complete list of changes can be found here:
http://ugene.unipro.ru/changelist.html

Project web site: http://ugene.unipro.ru/

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Bionet Arthropods news/discussion list request for comments

2009-09-21T09:48:49Z

There is interest among biologists who study various Arthropods
for a shared public news and discussion group. Please comment if
you would like to see a new Arthropod mailing list.

Values of sharing biology discussion and news among those who
study insects and crustaceans has been noted at recent venues,
including the Arthropod Genomics Symposia
(http://www.k-state.edu/agc/), Entomological Society meetings
(e.g. http://www.entsoc.org/), and recent arthropod genome projects.

BIOSCI/Bionet (www.bio.net) continues to serve such bioscience
community news needs, as it has since its inception 20
years ago by Michael Ashburner and others. Community group
lists at Bionet include DROSOPHILA, ARABIDOPSIS, MAIZE,
Medicago, CELEGANS, CHLAMYDOMONAS, Mycology, YEAST, and ZBRAFISH.
Bionet currently is maintained at Indiana University by Don
Gilbert, a genome informatician specializing in arthropods.

There are related mailing lists (see below). The uses and content of
this proposed list would presumably be similar. Please comment
whether you believe existing lists cover this need or prefer
a new one. Comment also on proposed charter and areas. Perhaps
this group should focus on one area such as genomics of arthropods.

Send your comments to bioforum@... for public discussion
or biosci-help@... (private to Don Gilbert).

---------------------------------------------------------------------

Proposal for ARTHROPOD/bionet.arthropod (moderated)

One line Description: Arthropod Biology

Status: Moderated
Moderators: to be named

Proposed mailing list name: arthropod @ net.bio.net
bionet-arthropod @ net.bio.net (alias)
Proposed USENET name: bionet.arthropod

Charter:

The purpose of the ARTHROPOD newsgroup is to provide a public
forum for scientific discussion, communication and collaboration
of shared biology interests among scientists studying species of
Arthropoda, including insects and crustaceans. Topics may include
evolutionary biology, ecology and enviroment, genomics, molecular
and organismal biology, methods and biotechnology, informatics
and databases, and any other aspect touching on shared biology of
arthropods.

---------------------------------------------------------------------

Related public mailing lists:

Arthropod Genomics Announcements
http://listserv.ksu.edu/archives/arthropodnews.html

Bionet Drosophila
http://www.bio.net/biomail/listinfo/dros

Vectorbase (mosquitoes, other human vectors)
http://www.vectorbase.org/Help/Mailing_lists

Aphid genomics
http://www.eco.princeton.edu/mailman/listinfo/aphidgenomics

Canadian Arthropods electronic mailing list
http://www.biology.ualberta.ca/bsc/english/mailinglist.html

List of various insect and arthropod mailing lists
http://www.ent.iastate.edu/List/directory/94/vid/4

---------------------------------------------------------------------

Topics of Discussion:
-- please suggest areas of special interest

In addition this newsgroup will provide:
A forum for the exchange of information about future meetings
of interest to those studying insects, crustaceans and other
arthropods.

A venue for help and sharing of methods and techniques in areas
such as Biological resources; Evolutionary and phylogenetic
techniques; Genome analysis techniques; etc.

Proposed discussion leaders/moderators:
-- to be named

The suggested list name is ARTHROPOD or bionet.arthropod
Alternate spellings, ARTHROPODA or ARTHROPODS, can be considered
or other names.

Sincerely,

Don Gilbert
BIOSCI/bionet Manager
biosci-help at net.bio.net

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SWAT4LS Cfp updates: new deadlines and journal supplement

2009-09-17T08:28:05Z

SWAT4LS Semantic Web Applications and Tools for Life Sciences

*** apologies for multiple postings ***

--- updates ---

We are glad to announce that there will be a special issue of the BMC
Journal of Biomedical Semantics dedicated to the SWAT4LS workshop.
This is a new open access journal published by BMC and we are
confident that the supplement will benefit from the additional
exposure and promotion associated with its launch (more information on
this journal can be found at http://www.jbiomedsem.com/).

The call for this special issue will be open to all the contributors
to the SWAT4LS workshop (accepted papers, posters and demos). Authors
will be invited to submit an extended version of their work,
elaborated in the light of the discussion held at the workshop.
Workshop proceedings will be published on CEUR.

In order to facilitate submissions, we have extended submission
deadlines as follows:

intention to submit (abstract only): October 5th
submission of papers: October 12
submission of posters and demos: October 15
communication of acceptance: October 28
camera ready: November 13

Due to the limited time for reviews, we would ask you to submit an
abstract of your paper by October 5th, in order to facilitate
assignment of reviews.

The lenght of contributions to the workshop as been revised to offer
more flexibility:
* Submissions for Oral communications should be between 8 and 15
pages.
* Posters submissions should be between 2 and 4 pages.
* Software demo proposals should also be between 2 and 4 pages.

Finally, we would like to announce that the special issue BMC
Bioinformatics dedicated to SWAT4LS-2008 will be published on October
1st (BMC Bioinformatics, Vol 10, Supp 10)

--- call for papers ---

***Location and date
Amsterdam, Science Park, November 20th 2009
(http://swat4ls.org/2009/)

***Rationale

The adoption of semantic-enabled applications and collaborative social
environments is ever more common in the Life Sciences. The Semantic
Web provides a set of technologies and standards that are key to
support semantic markup, ontology development, distributed information
resources and collaborative social environments. Altogether the
adoption of the Semantic Web in the Life Sciences has potential impact
on the future of publishing, biological research and medecine. This
workshop will provide a venue to present and discuss benefits and
limits of the adoption of these technologies and tools in biomedical
informatics and computational biology. It will showcase experiences,
information resources, tools development and applications. It will
bring together researchers, both developers and users, from the
various fields of Biology, Bioinformatics and Computer Science, to
discuss goals, current limits and some real use cases for Semantic Web
technologies in Life Sciences.

***Topics

Topics of interest include, but are not limited to:

* Standards, Technologies, Tools for the Semantic Web
o Semantic Web standards and new proposals (RDF, OWL,
SKOS,... )
o Biomedical Ontologies and related tools
o Formal approaches to large biomedical knowledge bases
* Systems for a Semantic Web for Bioinformatics
o RDF stores, Reasoners, query and visualization systems
for life sciences
o Semantic biomedical Web Services
o Semantics aware Biological Data Integration Systems
* Existing and prospective applications of the Semantic Web for
Bioinformatics
o Semantics aware application tools
o Semantic collaborative research environments
o Case studies, use cases, and scenarios

***Scientific Program

The workshop will be interactive and include keynotes, oral
presentations, panel discussion and a poster and demo session.

The keynote speakers of this edition will be:
* Barend Mons (http://www.biosemantics.org/index.php?page=barend-mons
)
* Michael Schroeder (http://www.biotec.tu-dresden.de/schroeder)
* Alan Ruttenberg (http://sciencecommons.org/about/whoweare/ruttenberg/
)

***Scientific Committee (committed so far:)

* Christopher J. O. Baker, Department of Computer Science and
Applied Statistics, University of Brunswick, Canada
* Pedro Barahona, Department of Informatics, New University of
Lisboa, Lisboa, Portugal
* Liliana Barrio-Alvers, Transinsight GmbH, Dresden, Germany
* Olivier Bodenreider, National Library of Medicine, Bethesda,
MD, United States of America
* Matt-Mouley Bouamrane, School of Computer Science, University
of Machester, manchester, United Kingdom
* Werner Ceusters, NY CoE in Bioinformatics and Life Sciences,
University at Buffalo, Buffalo, NY, United States of America
* Kei Cheung, Center for Medical Informatics, Yale University
School of Medicine, New Haven, United States of America
* Tim Clark, Massachusetts General Hospital and Harvard Medical
School, Boston MA, United States of America
* Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France
* Olivier Dameron, INSERM U936, University of Rennes 1, France
* Michel Dumontier, Carleton University, Ottawa, Ontario, Canada
* Huajun Chen, Zhejiang University, China
* Duncan Hull, School of Chemistry, University of Manchester, UK
* C. Maria Keet, Faculty of Computer Science, Free University of
Bozen-Bolzano, Bolzano, Italy
* Graham Kemp, Chalmers University of Technology, Sweden
* Jacob Tilman Koehler, Department of Molecular Biotechnology,
Institute of Medical Biology, University of Tromsö, Tromsö, Norway
* Michael Krauthammer, Department of Pathology, Yale University
School of Medicine, United States of America
* Martin Kuiper, Department of Pathology, Systems Biology group,
Department of Biology, Norwegian University of Science and Technology,
Trondheim, Norway
* Patrick Lambrix, Department of Computer and Information
Science, Linköping University, Linköping, Sweden
* Phillip Lord, School of Computing Science, Newcastle
University, Newcastle-upon-Tyne, United Kingdom
* M. Scott Marshall, Leiden University Medical Center /
University of Amsterdam, The Netherlands
* Chris Mungall, Lawrence Berkeley National Laboratories, United
States of America
* Stephan Philippi, Institute for Software Technology,
University of Koblenz-Landau, Koblenz, Germany
* Marco Roos, Instituut voor Informatica, University of
Amsterdam, Netherlands
* Alan Ruttenberg, Science Commons, Cambridge, MA, United States
of America
* Matthias Samwald, DERI, Galway, Ireland, and Konrad Lorenz
Institute for Evolution and Cognition Research, Altenberg, Austria
* Nigam Shah, Center for Biomedical Informatics Research,
Stanford, United States of America
* Michael Schröder, Biotechnology Centre, TU Dresden, Dresden,
Germany
* Robert Stevens, School of Computer Science, University of
Manchester, Manchester, United Kingdom
* Tetsuro Toyoda, Genomic Sciences Center, RIKEN, Yokohama, Japan
* Mark D. Wilkinson, iCAPTURE Center, St. Paul Hospital,
Vancouver, Canada

and the organizers

***Type of contributions

The following possible contributions are sought:

* Oral communications (regular papers)
* Posters
* Software demos

***Proceedings

All accepted oral communications and posters will be published with
the CEUR-WS.org Workshop Proceedings service (see http://ceur-ws.org/).
We are finalizing the agreement to have a dedicated special issue on
the 2009 edition of swat4ls in an international scientific journal of
the BMC group (open access, pubmed indexed).
To this end, a special Call will be launched shortly after the
workshop, for extended and revised versions of contributions submitted
to the workshop and accepted either as oral communication or poster.

***New Deadlines

* Intention to submit (abstract only): October 5th
* Submission of papers: October 12
* Submission of posters and demos: October 15
* Communication of acceptance: October 28
* Camera ready: November 13

***Instructions

All papers and posters must be in English and must be submitted
through the EasyChair review system at
http://www.easychair.org/conferences/?conf=swat4ls-09 .
Please upload all submissions as PDF files in LNCS format (http://www.springer.de/comp/lncs/authors.html
).
To ensure high quality, submitted papers will be carefully peer-
reviewed by at least three members of the Scientific Committee.
* Submissions for Oral communications should be between 8 and 15
pages.
* Posters submissions should be between 2 and 4 pages.
* Software demo proposals should also be between 2 and 4 pages.

***Organization

* M. Scott Marshall, Leiden University Medical Center /
University of Amsterdam, The Netherlands
* Albert Burger, School of Mathematical and Computer Sciences,
Heriot-Watt University, and Human Genetics Unit, Medical Research
Council, Edinburgh, Scotland, United Kingdom
* Adrian Paschke, Corporate Semantic Web, Freie Universitaet
Berlin, Germany
* Paolo Romano, Bioinformatics, National Cancer Research
Institute, Genova, Italy
* Andrea Splendiani, Biomathematics and Bioinformatics dept.,
Rothamsted Research, UK

***More information
* http://www.swat4ls.org/2009/
* http://swat4ls.blogspot.com
* info@...
---
Andrea Splendiani
Senior Bioinformatics Scientist
Rothamsted Research, Harpenden, UK
andrea.splendiani@...
+44(0)1582 763133 ext 2004

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New distance courses in bioinformatics and computational biology

2009-09-15T01:49:43Z

At the University of Manchester, UK, we have over 10 years experience in
running a range of online courses in computational biology. These
courses are designed to enable biologists and computer scientists to
update their skills while remaining in the workplace. They are also
very suitable for home study, helping you to keep in touch with a
research environment while taking a career break.

The courses beginning on 5 October 2009 include:

Introduction to Bioinformatics
Bioinformatics for Systems Biology

For those people interested in computational systems biology, these
courses could be followed by our new course, 'Mathematics for metabolic
modelling'.

You will find further information, including fees and a link to the
online application form, here:
http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any
questions, or need advice on the module options, please contact
Heather.Vincent@...

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Announcement: GenPept 173.0 available

2009-08-28T08:00:29Z

This is to announce the availability of release 173.0 of the GenPept(R)
(GenBank Gene Products) Database. GenPept is provided in a format similar
to that formerly distributed by GenBank(R) under the administration of
Intelligenetics Inc. This GenPept release IS _NOT_ AN OFFICIAL RELEASE FROM
THE NCBI-GENBANK, but an attempt to provide a data file format compatible
with existing software products.

This data format is suitable as an input data file for the GCG program
genbanktogcg -genpept. Compatibility with other software has not been tested.

Site: ftp.ncifcrf.gov

Directory: pub/genpept
Files: gprel.txt.gz, gpdat.seq.gz, gpdat.fasta.gz

Directory: pub/genpept/divisions
Files: 1 file for each GenBank file

Directory: pub/genpept/updates (daily, cumulative)
Files: gpseq_updates.dat.gz

Rel. Date: 27-Aug-2009

If you have questions or comments concerning this data, or you experience any
difficulty in downloading the data via ftp, please contact:

Gary Smythers smytherg@... 301-846-5778

================================================================
GenPept (R) and GenBank (R) are registered trademarks of the U.S. Department
of Health and Human Services for the GenBank Gene Products and the GenBank
Genetic Sequence Data Banks.

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7th Georgia Tech - ORNL Conference on Bioinformatics

2009-08-26T11:38:13Z

--------------------------------------------
CALL FOR PAPERS

Dear Colleagues

The 7th Georgia Tech - ORNL Conference on Bioinformatics -
In silico Biology: Genome Biology and Bioinformatics
will be held in
Atlanta, Georgia, November 12-14, 2009
http://www2.isye.gatech.edu/binf2009/

Georgia Tech continues the tradition of organizing bi-annual
International Conference on Bioinformatics, bringing together leading
researchers in genomics, bioinformatics and genome biology to present recent
advances in the field and to discuss open problems.

Important Dates
Deadline for early registration: October 15, 2009
Deadline for poster abstract subsmission: October 1, 2009
Notification of acceptance of abstracts: October 11, 2009

We invite papers submissions in the following areas
* genomics;
* transcriptomics;
* proteomics;
* reconstruction and modeling of gene networks;
* evolutionary biology;

SPEAKERS

Margaret O. Dayhoff lecture
David Lipman , NCBI/NIH, Bethesda, MD, USA

Plenary Speakers:
Vineet Bafna, University of California at San Diego, USA
Gill Bejerano, Stanford University, Stanford, CA, USA
Jeffrey Bennetzen, University of Georgia, Athens, GA, USA
Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA
Nick Grishin, University of Texas, Dallas, TX, USA
Curtis Huttenhower, Harvard University, Boston, MA, USA
King Jordan, Georgia Tech, Atlanta, GA, USA
Igor Jouline (Zhulin), University of Tennessee - ORNL, Oak Ridge, TN, USA
Eugene Koonin, NCBI/NIH, Bethesda, MD, USA
Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA
Boris Lenhard, University of Bergen, Norway
Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA
Yael Mandel-Gutfreund, Technion, Israel Insitute of Technology, Haifa, Israel
Joanna Masel, University of Arizona, Tucson, AZ, USA
Andrey Mironov, Moscow State University, Russia
Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA
Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA
Natasa Przulj, University of California at Irvine, CA, USA
John Reinitz, State Uiversity of New York at Stony Brook, NY, USA
Pierre Rouze, Gent University, Gent, Belgium

CONFERENCE CHAIRS
Mark Borodovsky, Georgia Tech and Emory University
Eva K. Lee, Georgia Tech and Emory University

PROGRAM COMMITTEE
Nicholas Bergman, Georgia Tech
Dmitrij Frishman, Munich Polytechnic University, Germany
Andrey Gorin, Oak Ridge National Laboratory
Andrzej M. Kierzek, University of Surrey, UK.
Eileen Kraemer, University of Georgia
Jun Liu, Harvard University
Andrey Rzhetsky, University of Chicago
Andre Rogatko, Samuel Oschin Comprehensive Cancer Institute
Gary Stormo, Washington University
Ying Xu, University of Georgia and Oak Ridge National Laboratory
Soojin Yi, Georgia Tech
Igor Zhulin, Oak Ridge National Laboratory and University of Tennessee

ADMINISTRATION
Harry Sharp, Georgia Tech

CONFERENCE LOCATION
The Georgia Tech Ferst Center for the Arts. The Georgia Tech campus is located in Midtown Atlanta near the center of the 1996 Olympic development, close to the Fox Theatre and Margaret
Mitchell house.

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InnovationWell 2009 Meeting; Philadelphia Oct 09: Program available

2009-08-16T13:48:45Z

The InnovationWell program will cover discussion of topics on
Collaboration in Discovery and Development, Translational
Bioinformatics, Systems Biology, Biomarkers, Blood-Brain Barrier
Modeling and Predictive Toxicology.
More detailed program below.

This annual community of practice meeting is taking place for the
fifth time and brings together a unique combination of pharmaceutical
and healthcare industry experts, principal investigators and
researchers from the academic and government sectors, and leaders from
innovative enterprises. The smaller and more intimate meeting format
pursued has fostered the type of collaboration not always found at
large conferences.

Innovation in Life Science & Healthcare R&D
InnovationWell 2009 InterAction Meeting
October 13-16, 2009
Bryn Mawr College, Bryn Mawr, Philadelphia, USA

Conference program available:
http://innovationwell.com/comty_conferencesprog09

Format: Seminars, Roundtables, Presentations, Panel Q&As, Discussions,
Break-out Workshops, Web-supported. Evening Poster sessions,
networking, social activities.

This meeting will take place concurrently with the eCheminfo 2009
Meeting.
http://echeminfo.com/comty_conferencesprog09

Call for Abstracts:
If you wish to submit a poster abstract for the meeting which will be
placed on the program, please send to Barry Hardy (barry.hardy –(at)-
douglasconnect.com) for review. Attractive poster prizes will be
awarded for best posters at the meeting (subject to peer review).

A special peer-reviewed issue of Future Medicinal Chemistry with a
focus on collaboration in discovery and development is being published
from the meeting. Accepted poster and presentation abstracts are
eligible for consideration. Please contact Barry Hardy if interested
in submitting a paper for review.

Pre-Conference Workshop, October 12
Forum on Collaboration in Discovery and Development
To register for the meeting right now, please visit:
http://InnovationWell-BM09.eventsbot.com
To download a pdf of the program including the registration form:
http://barryhardy.blogs.com/files/innovationwell-bm09-90812.pdf

InnovationWell 2009 Program Summary

MONDAY, OCTOBER 12
Forum on Collaboration in Discovery and Development, Co-chaired by
Peter Gates (Johnson & Johnson PR&D) and Barry Hardy (Douglas
Connect). Speakers include Barry Hardy (Douglas Connect), Shree Nath
(Pointcross), Alex Simson (Johnson & Johnson), Chris Waller
(Pfizer), Michael Liebman (Strategic Medicine), Jeff Spitzner
(Rescentris), and Bob O’Hara (ResultWorks).

TUESDAY, OCTOBER 13
Translational Bioinformatics: Bridging Bioinformatics and Biomedical
Informatics in Translational Medicine, Chaired by Jake Chen (Indiana
University). Speakers include Jessica Tenenbaum (Duke Translational
Medicine Institute, Duke University), Steve Naylor (Predictive
Physiology and Medicine, Inc.), Javed Mostafa (University of North
Carolina), Jay Zhang (Myriad Genetics), Maricel Kann (University of
Maryland), Iya Khalil (Gene Network Sciences), Hai Hu (Windber
Research Institute), Jake Chen (Indiana University – Purdue
University), and Susan Stephens (Johnson & Johnson).

WEDNESDAY, OCTOBER 14
Systems Biology and Biomarkers, Chaired by Darius Dziuda (Central
Connecticut State University). Speakers include Anamika Sarkar
(Novartis), Darius Dziuda (Central Connecticut State University),
Frank Tobin (Tobin Consulting LLC), Andreas Matern (Thomson Reuters
Healthcare and Science), and Usha Reddy (Merck).

Modeling of the Blood–Brain Barrier in Drug Discovery and Development,
Chaired by Roméo Cecchelli (Université d'Artois, France). Speakers
include Stefan Lundquist (AstraZeneca), Reinhard Gabathuler
(AngioChem), Maxime Culot (University of Lille), Damir Janigro
(Cleveland Clinic), Marie-Pierre Dehouck (University of Lille), Pierre-
Olivier Couraud (Institut Cochin), and Anna Seelig (University of
Basel).

THURSDAY, OCTOBER 15
Predictive Toxicology: Combining in vitro and in silico Techniques in
Predictive Toxicology Applications, Co-chaired by Richard Judson (US
EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of
Russian Academy of Medical Sciences). Speakers include Richard Judson
(US EPA), Ellen Berg (BioSeek), Jonathan Dordick (Rensselaer
Polytechnic Institute), Barry Hardy (Douglas Connect), Sanji Bhal (ACD/
Labs), Christodoulos Floudas (Princeton University), Robert
Fraczkiewicz (Simulations Plus), Kyoung Tai No (Yonsei University),
and Stephen Bryant (NIH).

FRIDAY, OCTOBER 15
Predictive Toxicology: Combining in vitro and in silico Techniques in
Predictive Toxicology Applications, Co-chaired by Richard Judson (US
EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of
Russian Academy of Medical Sciences). Speakers include Vladimir
Poroikov (Institute of Biomedical Chemistry of Russian Academy of
Medical Sciences), Fangping Mu (Los Alamos National Laboratory), Katya
Tsaioun (Apredica), Grace Patlewicz (DuPont), Michael Pelekis
(Simulations Plus), and Anil Aswani (University of California at
Berkeley).

Contact:
Program: Dr. Barry Hardy, InnovationWell Community of Practice,
Douglas
Connect. Tel: +41 61 851 0170. email: innovationwell -[at]-
douglasconnect.com
Blog: http://barryhardy.blogs.com/

Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg
14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. innovationwell -
[at]- douglasconnect.com

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Practical Course in Biomolecular Modelling

2009-08-14T07:33:33Z

Dear colleagues,

please be informed that online applications are accepted for the
following course:

8TH NCCR PRACTICAL COURSE IN BIOMOLECULAR MODELLING

January 10 - 15, 2010
Kandersteg, Switzerland
http://www.structuralbiology.uzh.ch/course2010.asp

Course topics include
Simulation techniques, force-field development, conformational search,
computation of free energy and entropy, treatment of electrostatic
forces, simulation of folding, comparison of simulation with experiment

This course is primarily directed to PhD students and postdocs from
experimental structural biology groups wishing to learn more on
biomolecular modelling. The course format will include morning lectures
and late-afternoon/early evening tutorials, and provide ample
opportunities for discussions with experts and fellow participants.
Participants will be invited to bring own problems for tutorials and/or
discussion. The course will be organized as a winter retreat in the
Swiss Alps offering a stimulating learning atmosphere with the
afternoons available for informal participation in discussions, reading
and self-study or recreational activities in the area.

Interested candidates are encouraged to apply online on
http://www.structuralbiology.uzh.ch/course2010_application.asp.
Application deadline will be October 16, 2010. We will be able to accept
20 participants to this course.

Best regards,
Patrick Sticher

--
_________________________________
Visit the NCCR on the Internet
www.structuralbiology.uzh.ch

Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
Mail sticher@...

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New Release of Survey of Informatics Programs in the US

2009-08-10T11:52:41Z

We have compiled an updated listing of academic programs in
informatics in the US. This is the 6th revision (compiled in
November/December 2008). It includes programs in bioinformatics,
dental informatics, health informatics, medical and biomedical
informatics, nursing informatics, pharmacy informatics,
chemoinformatics.

We maintain this survey information and try to keep it as accurate
as possible. We welcome your sending information about programs we
do not have listed, or corrections to existing listing.

The survey is freely available on the web at
http://ils.unc.edu/informatics_programs/

It contains summary presentations (html) and detailed listings
(Excel) of each program.

Sincerely,
Brad Hemminger

Bradley Hemminger Ph.D.
Associate Professor
School of Information and Library Science
206A Manning Hall
University of North Carolina
Chapel Hill, North Carolina 27599-3360

(919) 966-2998
(919) 962-8071 (fax)
bmh@...

Joint Appointment in the Carolina Center for Genome Sciences
http://genomics.unc.edu

Adjunct Associate Professor, Dept of Radiology, School of Medicine

Bioinformatics at School of Information and Library Science
http://ils.unc.edu/bioinfo

Digital Libraries at UNC-CH
http://ils.unc.edu/cradle

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Conference, Comparative Genomics, University of St Andrews

2009-08-04T09:13:18Z

Dear bionet.announce,

* * * * * * * * * * * * * * *

Comparative Genomics One-day International Conference
Date: 18th August 2009, 9:30 am
Location: Bute Building, University of St Andrews, UK

* * * * * * * * * * * * * * *

This is a one day event - A day of exciting talks on comparative
genomics from an array of international speakers.

Thousands of genome sequences are now available, and the amount of data
on genomes continues to increase. This presents enormous opportunities
to make discoveries of biological and medical interest, but also
requires new approaches.

Confirmed speakers:

o Prof MARK BLAXTER, University of Edinburgh. "Comparative Nematode
Genomics".
o Prof GEOFF BARTON, University of Dundee. "A tale of three small RNAs".
o Prof DANNIE DURAND, Carnegie Mellon University. "The Evolution of
Multidomain Families".
o Prof NEIL HALL, University of Liverpool. "Fast forward Genetics using
second generation sequencing".
o Dr MATTHEW HEGARTY, Aberystwyth University. "Genomic mergers: the
consequences of hybridisation and polyploidy in Senecio".
o Prof IAN KORF, University of California Davis Genome Center. "Intron
mediated enhancement".
o Prof ALAN ARCHIBALD FRSE, Roslin Institute. "Comparative farm animal
genomics - from synteny to synergy".
o Dr ZEMIN NING, Wellcome Trust Sanger Institute. "Cancer genome
assemblies and variation detection between normal and tumor human cells".
o Prof ZIHENG YANG FRS, University College London. "Population genomics
and human-chimpanzee speciation".
o Prof ANDY WATERS, University of Glasgow, "Translation of Translation:
Comparative genomics yields practical insights into sexual development
in malaria parasites".

More information can be found at http://www.sbforum.org/events.php?e_id=70

Registration details:

Early registration is encouraged. Registration fees are GBP 40; students
can register for a reduced fee of GBP 20.

** Please register on-line at: http://www.sbforum.org/eregister.php?e_id=70

The event is preceded by a conference dinner, at a subsidized price for
conference delegates. Please book in advance.
http://www.sbforum.org/events.php?e_id=76

The conference itself is followed by a networking buffet dinner,
included in the registration fee.

Poster submission:

Delegates are welcome to submit an abstract on any aspect of comparative
genomics. The poster abstract deadline has been extended to Thursday
13th August.

* * * * * * * * * * * * * * *

We look forward to seeing you on Tuesday 18th August.

Best regards,

Daniel

--
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland :
No SC013532

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Professional development in bioinformatics and systems biology

2009-08-03T00:21:26Z

Evidence of continuing professional development is increasingly
important to scientists planning a career move, whether this is to be a
promotion or a change in direction. However, work and family
commitments can make it difficult for many people to take time away to
gain the new skills that they need.

Online courses can provide a solution. At the University of Manchester
we have over 10 years experience in running interactive online courses
specifically designed for biologists needing to update their skills
while remaining in the workplace
(http://octette.cs.man.ac.uk/bioinformatics/students/index.html). The
courses are also very suitable for those interested home study, helping
you to keep in touch with a research environment during a career break.

The courses running next semester, starting in October 2009, include:

Introduction to Bioinformatics
Bioinformatics for Systems Biology
Introduction to software development in Java
Theory and Applications in Bioinformatics

You will find further information, including fees and a link to the
online application form, here :
http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any
questions, or need advice on the module options, please contact
Heather.Vincent@...

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GMOD Community Meeting, 6-7 August, 2009, Oxford UK

2009-07-17T21:02:31Z

There will be a GMOD Community Meeting, 6-7 August, 2009 at the University
of Oxford, in Oxford, UK.

GMOD (http://gmod.org) is a collection of interoperable, open-source
software components for managing, visualizing, annotating, and sharing
biological data. GMOD is also a community of users and developers
addressing common challenges with their biological data. The popularity of
next generation sequencing and other high-throughput methods has made this
GMOD meeting particularly timely.

GMOD meetings are an excellent opportunity to learn best practices from
other researchers, to meet GMOD users and developers, and to learn and
affect what is coming in the project. As with previous meetings, there will
be a mixture of project talks, component-focused talks, and user talks.

Registration for the meeting is now open and space is available on a first
come, first served basis. Attendance is limited to the first 55 people to
register. The meeting cost is £50.

See http://gmod.org/wiki/August_2009_GMOD_Meeting to register for more.

Please join us in Oxford this August.

Cheers,

Dave Clements
GMOD Help Desk

--
Register now for the August GMOD Meeting:
http://gmod.org/wiki/August_2009_GMOD_Meeting
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NCCR Symposium on New Trends in Structural Biology / NCCR Practical Course on Biomolecular Modelling

2009-07-17T06:50:51Z

Dear colleagues,

we have two announcements to make:
_____________________________________________________________

7th International NCCR Symposium on New Trends in Structural Biology
7 + 8 September 2009, ETH Zürich, Lecture Hall HG E7, Zürich, Switzerland
www.structuralbiology.uzh.ch/symposium2009

The lecture program is available online at:
http://www.structuralbiology.uzh.ch/symposium2009/program.asp

Plenary lecturers:
Frédéric Allain, Pietro de Camilli, Raimund Dutzler, Arthur L. Horwich,
Brian Kobilka, Harry Noller,
Anna Marie Pyle, Ben Schuler, David Wemmer, Masasuke Yoshida

Online registration to this event is still possible through the
symposium homepage or directly at:
http://www.structuralbiology.uzh.ch/symposium2009/registration09.asp
_____________________________________________________________

8th NCCR Practical Course and 2nd Winter School
Biomolecular Modelling

The 8th NCCR Practical Course will cover key topics in the area of
computational structural biology. The course format includes morning
lectures by experts in the field that alternate with later afternoon to
evening tutorials and discussions. The course will be organized as a
winter retreat in the Swiss alps offering participants the opportunity
to learn in a stimulating atmosphere, enjoy winter activities in the
swiss alps during course breaks, and network and exchange ideas on an
informal basis with fellow participants, tutors, and lecturers.

More information at http://www.structuralbiology.uzh.ch/course2010.asp
Online Application will be possible as of July 31, 2009
_____________________________________________________________

Please do not hesitate to contact me anytime if you need further
information (sticher@...).

With best regards,
Patrick Sticher

The NCCR Structural Biology is a research initiative of the Swiss
Science Foundation. Its research encompasses the fields of recombinant
protein technologies, macromolecular structure determination and
computational biomolecular sciences with a special focus on membrane
proteins and supramolecular assemblies/interactions. 13 research groups
from Swiss Universities and Research Institutions participate in this
network. www.structuralbiology.uzh.ch/

--
_________________________________
Visit the NCCR on the Internet
www.structuralbiology.uzh.ch

Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
Mail sticher@...

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Unipro UGENE v1.5 released

2009-07-12T22:36:05Z

After several months of work our team is glad to announce a long-
awaited
version of free and open-source UGENE bioinformatics suite.

Version 1.5 adds 4 new plugins and brings numerous improvements and
bug fixes.

New plugins:
HMM3 - profile HMM tool based on Eddy's HMMER 3.0b2,
Primer3 - integrated primer3 tool for PCR primers design,
Gor4 and Psipred - secondary structure prediction algorithms.

Major improvements were done in PDB and MMDB files viewer and
annotations editor.
Added functionality for loading remote files from PDB, Uniprot,
Swissprot.

The complete list of changes can be found here: http://ugene.unipro.ru/changelist.html

Project web site: http://ugene.unipro.ru/

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Program Available - Latest Advances in Drug Discovery Informatics: eCheminfo 2009 InterAction Meeting; Philadelphia Oct 09

2009-06-26T07:10:44Z

The program with abstracts for the Autumn eCheminfo Community of
Practice meeting on Latest Advances in Drug Discovery Informatics is
now almost complete and available at http://echeminfo.com/comty_conferencesprog09
and will be updated there as remaining abstracts are received.
The meeting will take place October 13-16, 2009 at Bryn Mawr College,
Philadelphia.

The topics addressed this year will include Structure-based Drug
Design Applications and Methods, Macromolecular Interactions and
Networks, Chemical Biological Data Analysis and Visualisation, PDB
Ligands, and Combining in vitro and in silico Techniques in Predictive
Toxicology Applications.

This meeting will take place concurrently with the InnovationWell 2009
meeting addressing the topics of Collaboration in Discovery and
Development, Translational Bioinformatics, Systems Biology and
Biomarkers, Blood Brain Barrier modeling and Predictive Toxicology.

A pre-conference best practices workshop on Predicting Binding Energy
Affinities will take place October 12, 2009 and is open to all
conference registrants.

To download a pdf of the program:
http://barryhardy.blogs.com/files/echeminfoprogrambrynmawr09.pdf

To register for the meeting, please visit:
http://echeminfo-bm910.eventsbot.com/

Contact:
Program: Dr. Barry Hardy, eCheminfo Community of Practice, Douglas
Connect. Tel: +41 61 851 0170. email: barry.hardy -[at]-
douglasconnect.com

Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg
14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. echeminfo -
[at]-
douglasconnect.com

Meeting Support: Rob Reedijk, eCheminfo Community of Practice,
Douglas
Connect. email: rob.reedijk -[at]- douglasconnect.com

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Announcement: GenPept 172.0 available

2009-06-16T07:25:43Z

This is to announce the availability of release 172.0 of the GenPept(R)
(GenBank Gene Products) Database. GenPept is provided in a format similar
to that formerly distributed by GenBank(R) under the administration of
Intelligenetics Inc. This GenPept release IS _NOT_ AN OFFICIAL RELEASE FROM
THE NCBI-GENBANK, but an attempt to provide a data file format compatible
with existing software products.

This data format is suitable as an input data file for the GCG program
genbanktogcg -genpept. Compatibility with other software has not been tested.

Site: ftp.ncifcrf.gov

Directory: pub/genpept
Files: gprel.txt.gz, gpdat.seq.gz, gpdat.fasta.gz

Directory: pub/genpept/divisions
Files: 1 file for each GenBank file

Directory: pub/genpept/updates (daily, cumulative)
Files: gpseq_updates.dat.gz

Rel. Date: 15-Jun-2009

If you have questions or comments concerning this data, or you experience any
difficulty in downloading the data via ftp, please contact:

Gary Smythers gws@... 301-846-5778
or
Bob Stephens bobs@...

================================================================
GenPept (R) and GenBank (R) are registered trademarks of the U.S. Department
of Health and Human Services for the GenBank Gene Products and the GenBank
Genetic Sequence Data Banks.

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Conservation genetics data analysis course

2009-05-14T11:57:26Z

4th ConGen- Population Genetics Data Analysis Course
Recent Approaches for Estimation of Population Size, Structure, Gene
flow, Selection Detection focusing on conservation and beyond
31-Aug/4-Sep 2009, Flathead Lake Biological Station, Montana, USA

Applications for 2009 are open!

Objective: To provide training in conceptual and practical aspects of
data analysis for the conservation genetics of natural and managed
populations. Emphasis will be on interpretation of output from recent
novel statistical approaches and software programs. The course also
will allow daily discussions among young researchers and
top-researchers to help develop the next generation of conservation
geneticists, and to identify developments needed to improve data
analysis approaches. This course will cover analysis methods including
the coalescent, Bayesian, approximate Bayesian, and likelihood-based
approaches.

Who should apply: Ph.D. students, post-docs, and population biologists
with a background of at least one semester university-level course in
population genetics and a course in population ecology. Applicants
must have a basic background in population genetic data analysis,
including testing for Hardy-Weinberg proportions and gametic
disequilibrium.

Participation will be limited to 20 people allowing efficient
instruction with hands-on computer exercises during the course.
Priority will be given to persons with their own data to analyze (for
example graduate students at the end of their degree program).

Deadline for application is 30 June, 2009

Course/Workshop Format: For each subject, we provide 30-45 minutes of
background, theory, discussion and introduction to concepts.
Immediately following, we will conduct data analyses together for
30-60 minutes using relevant software programs and real data sets.
Evening hands-on computer sessions and housing together of instructors
and students in the same location will allow for extensive exchange
and facilitate learning.

For detailed information see http://popgen.eu/congen2009/

congen@...

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Conference, Comparative Genomics, University of St Andrews

2009-05-14T04:37:18Z

Dear bionet.announce,

I would like to draw your attention to these events in St Andrews this
August:

- One day conference, "Comparative Genomics"
- Summer school, "Bioinformatics and Comparative Genomics"
- Workshop, "The Role of Behaviour in Speciation"

Details are below.

*****************************************************************
Comparative Genomics one-day international conference

Date: 18th August 2009
Location: Bute Building, University of St Andrews, UK
*****************************************************************

The Scottish Bioinformatics Forum and the University of St Andrews are
pleased to announce a one-day international conference, "Comparative
Genomics", with nine invited speakers and an open poster session.

Confirmed speakers:

- Prof MARK BLAXTER, University of Edinburgh. "Comparative nematode
genomics".
- Prof GEOFF BARTON, University of Dundee. "A tale of three small RNAs".
- Prof DANNIE DURAND, Carnegie Mellon University. "The evolution of
multidomain families".
- Prof NEIL HALL, University of Liverpool. "Fast forward genetics using
second generation sequencing".
- Dr MATTHEW HEGARTY, Aberystwyth University. "Genomic mergers: the
consequences of hybridisation and polyploidy in Senecio".
- Prof IAN KORF, University of California Davis Genome Center. "Intron
mediated enhancement".
- Dr DAVID MARTIN, University of Dundee. "Predicting protein function".
- Dr ZEMIN NING, Wellcome Trust Sanger Institute. "Cancer genome
assemblies and variation detection between normal and tumor human cells".
- Prof ZIHENG YANG FRS, University College London. "Population genomics
and human-chimpanzee speciation".

For more information on the conference, including registration and
poster abstract submission, please see:

http://www.sbforum.org/events.php?e_id=70

*****************************************************************
Summer School - Bioinformatics and Comparative Genomics

Start Date: 15th August 2009, 9:00 am
End Date: 18th August 2009 (including one-day conference)
Location: University of St Andrews, UK
*****************************************************************

The Scottish Bioinformatics Forum and the University of St Andrews are
pleased to announce the first Summer School on Bioinformatics and
Comparative Genomics. The summer school will address practical
bioinformatics for sequence analysis and comparative genomics, for use
in biological and biomedical research.

The summer school will be held in St Andrews on 15th-17th August 2009.
Registration for the summer school also includes attendance at the
one-day conference on Comparative Genomics on 18 August (see above).

Confirmed tutors:

- Prof ZIHENG YANG FRS, University College London
- Dr ZEMIN NING, Wellcome Trust Sanger Institute
- Dr DAVID MARTIN, University of Dundee
- Prof IAN KORF, University of California Davis Genome Center
- Dr CHRIS JANSSEN, SBF and University of Glasgow
- Prof NEIL HALL and Dr ALISTAIR DARBY, University of Liverpool
- Dr DAVID FERRIER, University of St Andrews
- Prof DANNIE DURAND, Carnegie Mellon University
- Prof GEOFF BARTON and Dr JIM PROCTER, University of Dundee
- Dr DANIEL BARKER, University of St Andrews

For more information on the summer school and registration details,
please see:

http://www.genome-bioinformatics.org/index.html

*****************************************************************
Workshop - The Role of Behaviour in Speciation

Start Date: 19th August 2009
End Date: 22nd August 2009
Location: University of St Andrews, UK
*****************************************************************

This is a separate workshop at St Andrews, arranged by the EU Marie
Curie Initial Training Network "SPECIATION". Details of this workshop
are available from Prof Mike Ritchie:

http://biology.st-andrews.ac.uk/staff/mgr.htm

and will appear at:

http://speciation.group.shef.ac.uk

Looking forward to seeing you in St Andrews!

Kind Regards

Daniel Barker

--
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland :
No SC013532

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{Disarmed} Systems Biology Symposium 25 - 26 June at Brunel University

2009-04-27T06:32:55Z

Symposium on Biological and Chemical Informatics for Health:

Foundations for Systems Biology

Brunel University, West London, UK

25-26 June 2009

Find out more and register for this free event here
http://bcih-sb.brunel.ac.uk

Integration of biological and chemical informatics presents a real
opportunity to address some of the most exciting and challenging issues
posed by systems biology. These diverse disciplines, and their interaction,
play a crucial role in addressing key issues in drug design and discovery,
environmental sustainability, health and disease processes, and disease
prevention, diagnosis and treatment.

Join us for a two day symposium sponsored by the BBSRC and Brunel
University, where influential leaders in bioinformatics, chemoinformatics,
systems biology and health, will present the latest developments that are
helping to shape this interdisciplinary field. This symposium is open to
those working in the field, including academics, researchers, students and
industry and will provide an excellent environment for delegates to
participate in networking activities and developing collaborative,
interdisciplinary research partnerships.

We are delighted that the following have already agreed to speak at the
event:

Bioinformatics

Janet Thornton, Director of the European Bioinformatics Institute

Marco Ramoni, Director of Biomedical Cybernetics Laboratory, Harvard Medical
School

Christine Orengo, Professor of Bioinformatics, University College London

Health

Sally Davies, Director General of Research and Development and Chief
Scientific Adviser for the Department of Health and NHS

Chemoinformatics

Peter Willett, Professor of Information Science, Sheffield University

Robert Glen, Director of Unilever Centre for Molecular Science Informatics,
Cambridge University

Peter Johnson, Professor of Computational Chemistry, Leeds University

Systems Biology

Tom Kirkwood, Director of the Newcastle Centre for Integrated Systems
Biology of Ageing and Nutrition

Simon Gaskell, Vice-President for Research, Manchester University

Chris Rawlings, Head of Department of Biomathematics and Bioinformatics,
Rothamsted Research, BBSRC

David Gilbert, Head of School of Information Systems, Computing and
Mathematics, Brunel University

Colin Miles, Head of Systems Biology, BBSRC

Stephen Muggleton, Director of Modelling, Centre for Integrative Systems
Biology at Imperial College

Peter Bramley, Head of School of Biological Sciences, Royal Holloway London

For more details and free registration see: http://bcih-sb.brunel.ac.uk
<https://owa1.brunel.ac.uk/exchweb/bin/redir.asp?URL=http://bcih-sb.brunel.a
c.uk/>

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