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qPCR 2010 Event - Call for Abstracts

2009-11-24T04:45:24Z

qPCR 2010 Event - Call for Abstracts

www.qPCR2010-Vienna.net

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

BioEPS GmbH is organizing the qPCR 2010 Event taking place April 7th –
9th, 2010 in Vienna, Austria. Scientists from all around the world
will come to exchange ideas, share experiences, and discuss the
exciting future of the perhaps most powerful analytical technology
ever developed in the life sciences area – the quantitative real-time
polymerase chain reaction (qPCR).

We have the pleasure to announce the Call for Abstracts for the qPCR
2010 Event !

Finally we want to present 40 scientific talks from international
scientists and diagnostic companies in the qPCR field who will show
their latest research findings and newest technologies. The focus of
the qPCR 2010 Event will be “The ongoing evolution of qPCR”
representing all new and emerging techniques, applications and data
analysis methods.

Deadline is 31st January 2010 => http://submission.qPCR2010-Vienna.net

Talk topics:
--------------

MIQE and QM strategies in qPCR
The MIQE guidelines: minimum information for publication of
quantitative real-time PCR experiments. Following these guidelines
will encourage better experimental practice, allowing more reliable
and unequivocal interpretation of qPCR results. QM strategies in real-
time PCR to guarantee better and more valid results.
Keynote speaker: Prof. Stephen Bustin

High throughput quantitative PCR – digital PCR
384 well applications, new high throughput platforms, droplet PCR,
qPCR robotics, digital PCR, gene expression real-time RT-PCR arrays
(mRNA and microRNA), quantitative multiplexing, …
Keynote speaker: Prof. Mikael Kubista, Dr. Philip Day, Dr. Ken
Livak

HRM – High Resolution Melting
SNP analysis, HRM = high resolution melt applications, Epigenetics,
methylation markers, HRM platform comparison, etc …
Keynote Speaker Prof. Carl Wittwer, Prof. Claudio Orlando

Circulating nucleic acids
Analysis of circulating RNAs and DNA and microRNAs as diagnostic and
prognostic marker, …
Speaker: Dr. Pamela Pinzani, Dr. Alfred Schöller, Dr. Jim Huggett

Single–cell qPCR
single-cell sampling, pre-amplification techniques, laser micro-
dissection, sub-cellular PCR, micro-manipulation of cell clusters,
cellular micro injection, FACS spotting, single cell handling, pre-
amplification, …
Keynote speaker: Dr. Michael W. Pfaffl, Dr. Anders Stahlberg

RNAi – microRNA – siRNA Applications – miRNA normalisation
RNAi mechanism, microRNA extraction, qRT-PCR technologies to detect
microRNA, microRNA normalisation strategies, siRNA applications in
combination with qRT-PCR, microRNA targets and microRNA precursors,
new siRNA manipulation and microRNA technologies,
Keynote speaker: Prof. Jo Vandesompele, Dr. Mirco Castoldi

qPCR BioStatistics & BioInformatics
software applications, data mining, calculation of relative
expression, primer and probe design on mRNA and microRNA level, real-
time PCR efficiency determination, mathematical modelling,
multivariate expression profiling, statistics in real-time PCR, data
management, multiway expression profiling, multiple regression
analysis, 3D data visualization, ...
Speaker: Dr. Ales Tichopad, Dr. Jan Hellemans, Dr. Anders
Bergkvist

An online registration and abstract submission software CONFTOOL is
available here => http://registration.qPCR2010-Vienna.net

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

About qPCR:
Using qPCR the amount of target nucleic acid in a complex sample can
be determined with high precision, great accuracy, excellent
specificity and the ultimate sensitivity of detecting a single
molecule. The technique has revolutionized all molecular sciences and
diagnostic applications. Conference presentations will include MIQE
guidelines & QM strategies in qPCR, high performance nucleic acid
extraction, single-cell applications, Epigenetics & High-Resolution-
Melt analysis, circulating nucleic acids, and application involving
RNAi and microRNA.
Further developments of qPCR technology will be presented include
improved instrumentation, miniaturization, high throughput platforms,
cost efficacy, validity, flexibility, quality assessment and reliable
Cq calculations, expression data comparisons, and interpretation.
Today there is no field in the life sciences research, molecular
biology and diagnostics areas that has not introduced qPCR technology
for nucleic acid analysis. The combination with reverse transcription
enables determination of mRNA, microRNA and widely opens the window
for “Transcriptomics” – the first step of quantitative “Gene
Expression Profiling” and “Functional Genomics”.
An Industrial Exhibition will take place parallel to the symposium,
with 32 leading biotechnology companies presenting their latest
developments, including real-time PCR cyclers, NA extraction robots,
consumables, new fluorescence dyes, NA detection and amplification
chemistries, as well as real-time PCR data analysis software.

For more information about the qPCR 2010 event contact Dr. Martina
Reiter Martina.Reiter@...

Hope to meet you in April in Vienna!

Michael Pfaffl

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CFP ICARIS 2010 9th International Conference on Artificial Immune Systems

2009-11-23T09:29:14Z

CALL FOR PAPERS

*********************************************************************
ICARIS 2010
9th International Conference on Artificial Immune Systems
26th -- 29th July 2010, Edinburgh, UK

http://www.artificial-immune-systems.org/icaris/2010/

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

AIMS & SCOPE

Artificial immune systems (AIS) is a diverse and maturing
area of research that bridges the disciplines of immunology and
engineering. The scope of AIS ranges from modelling and simulation
of the immune system through to immune-inspired algorithms and
engineering solutions.

In recent years, algorithms inspired by theoretical
immunology have been applied to a wide variety of domains,
including computer security, fault tolerance, data-mining and
optimisation. Increasingly, theoretical insight into aspects
of artificial and real immune systems has been sought through
mathematical and computational modelling and analysis.

The 9th International Conference on AIS (ICARIS) aims to build on the
success of previous years to provide a forum for AIS researchers
in academia and industry to present and discuss their latest
advances. In addition to peer-reviewed papers, ICARIS will present
a range of plenary lectures and tutorials to inspire and facilitate
both the computer scientist and immunologist in their work.

To encourage dialogue with the theoretical and clinical immunology
communities, ICARIS 2010 will again adopt an (optional) extended
abstract submission for the immune modelling stream. Full papers are
welcome, but extended versions of abstracts will not be required.
All accepted abstracts will be published alongside full papers in
the proceedings.

STREAMS

The conference programme will be partitioned into three streams

* Theoretical Stream

This stream is for papers describing theoretical aspects of AIS,
excluding theoretical immunology. This includes (but is not limited
to) mathematical modelling of algorithms, convergence analysis,
empirical investigation into algorithm performance and complexity
analysis. To make sure the paper appeals to the widest possible
audience, the mathematics should be clearly presented, and the paper
should discuss the practical implications of any theoretical results.

* Applied Stream

This stream is for papers describing the application of AIS to
computational and engineering problems. The problem domain should
be clearly explained, detailing why it is challenging and why AIS
are a suitable methodology to use. Experiments should be carefully
explained, with the expectation that appropriate statistical analysis
of results will be used to help draw conclusions. Where possible,
the approach taken should be compared with alternative strategies.

* Immune Modelling Stream

This stream is for work detailing models and simulations of real
and artificial immune systems. Authors are asked to be mindful
of the inter-disciplinary nature of the forum when presenting
their work. Extended abstracts or full papers are invited for
submission. Both will undergo the same review process for quality
and relevance.

IMPORTANT DATES

Paper Submission 24rd March 2010
Review Rebuttal Period 13th -- 17th April
2010 Final Decision 20th April 2010
Camera Ready Copies 30th April 2010

SUBMISSIONS

Full papers should not be longer than 14 pages of LNCS, and extended
abstracts for the modelling stream not more than 3 pages. Overly
long submissions may be rejected at the reviewers discretion. All
submissions should follow the formatting guidelines detailed
by Springer

http://www.springer.com/computer/lncs

Following the reviews, a consultation period will be held, where
authors will have 1 week to respond to reviewers comments if they
wish. This is designed to increase the quality of papers, and remove
any misunderstandings that may happen as part of the review process.

See conference website for more submission details.

LOCATION

This year's ICARIS will be held in Scotland's historic capital,
Edinburgh. A city with an international reputation in cultural
events -- the ICARIS conference is squeezed between the International
Film Festival and the Fringe, the biggest arts and comedy festival
in the world.

ORGANISING COMMITTEE

General Chairs Emma Hart & Chris McEwan
Stream Leaders
Applied Stream Jon Timmis
Immune Modelling Stream Stephanie Forrest
Theoretical Stream Andy Hone
Publicity Chair Mark Read

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[ISBRA-L] ISBRA'10 Call for Workshop Proposals

2009-11-20T19:59:19Z

CALL FOR WORKSHOP PROPOSALS

6th International Symposium on Bioinformatics Research
and Applications (ISBRA'10)

May 23-26, 2010
University of Connecticut, Storrs, CT, USA
http://www.cs.gsu.edu/isbra10/

The organizers of the 2010 International Symposium on Bioinformatics
Research and Applications (ISBRA 2010) invite proposals for joint
workshops. Workshop organizers will be responsible for forming a program
committee, preparing a call for papers, reviewing submissions, and
selecting the papers to be presented at the workshop. Joint workshops will
be advertised through the ISBRA website and mailing list.

Joint workshops are expected to focus on recent research directions and
initiatives in Bioinformatics and Computational Biology, and may include
talks of a tutorial nature if appropriate. Workshop organizers should seek
submissions in one or both of the categories accepted by the main
symposium: extended abstracts of up to 12 pages in Springer LNCS format
and short abstracts of up to 4 pages. Workshop submissions must be made
electronically at https://www.easychair.org/login.cgi?conf=isbra2010 where
separate submission tracks will be set-up for each workshop. The
submission and review process of each workshop should follow the timeline
of the main symposium:

Extended Abstracts Short Abstracts
__________________ _______________

Submission January 29, 2010 April 2, 2010
Notification February 19, 2010 April 16, 2010
Final version March 5, 2010 April 23, 2010

Accepted extended abstracts will be published in the symposium proceedings
published as a volume of Springer-Verlag's Lecture Notes in Bioinformatics
series and presented orally at the symposium. Accepted short abstracts
will be published online and on CD-ROM and may be selected for either oral
or poster presentation. Workshop organizers are encouraged to make
arrangements for publishing special journal issues devoted to full
versions of the abstracts presented at the workshop.

For more information or to submit a workshop proposal please contact the
ISBRA 2010 workshop chairs:

Craig E. Nelson
University of Connecticut
Molecular & Cell Biology Dept.
354 Mansfield Road
Storrs, CT 06269-2131
Telephone: 860-486-5617
Fax: (860) 486-1936
E-Mail: Craig.Nelson@...

Yufeng Wu
University of Connecticut
Computer Science & Engineering Dept.
371 Fairfield Road
Storrs, CT 06269-2155
Telephone: 860-486-2234
Fax: 860-486-4817
Email: ywu@...

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The first Indian virtual conference on Bioinformatics 2010 (Inbix'10)

2009-11-20T00:28:02Z

Dear All,

The first Indian virtual conference on Bioinformatics 2010
(Inbix'10):
http://www.bioinformatics.org/wiki/Inbix10

Excellent opportunity to interact with leading scientists in the
world
in the area of Bioinformatics and Systems Biology!
All for just Rs 500/- or 10 USD

All the best
Prash

Prashanth Suravajhala
C-DAC-Bioinformatics Group, Pune, India
http://wiki.bioinformatics.org/prash

I 'put a fullstop' as soon as I see myself complaining and blaming.
These two habits destroy my inner power completely, because they show
I am still expecting solutions and changes from others.

Courtesy: Thought for Today

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Workshop: Modern Drug Target Crystallography and Structure Based Drug Discovery

2009-11-19T14:32:08Z

Dear All,

MolSoft LLC ( www.molsoft.com ) and q.e.d. life science discoveries,
inc., are conducting a joint two day workshop on Dec 14-15, 2009 at the
Molsoft LLC facility in La Jolla, CA USA entitled "Modern Drug Target
Crystallography and Structure Based Drug Design".

The course will be taught by two experts in the field: Dr. Bernhard
Rupp, crystallography textbook author and president of q.e.d. life
science discoveries, and Dr. Ruben Abagyan, founder of Molsoft LLC
and Professor of Pharmacology at the University of California San Diego,
Skaggs School of Pharmacy and Pharmaceutical Sciences.

The provided course materials include a copy of the new and highly
acclaimed textbook Biomolecular Crystallography: Principles, Practice,
and Applications to Structural Biology.

For more information please see:
http://www.ruppweb.org/workshops/Molsoft_2009.htm

--
Andrew Orry Ph.D.
Senior Scientist
MolSoft LLC
3366 North Torrey Pines Court
Suite 300
La Jolla, CA 92037
U S A

Phone: (858) 625-2000 (x108)
Fax: (858) 625-2888
www.molsoft.com
Latest ICM News: www.molsoft.com/news.html

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Adopting R&D Informatics Systems

2009-11-17T11:52:00Z

Part of the Informatics Channel at CHI's 17th International Molecular
Medicine Tri-Conference.

Cambridge Healthtech Institute's Second Annual
Adopting R&D Informatics Systems: Data Management, Integration & Knowledge
Management
February 3-5, 2010
Moscone North Convention Center * San Francisco, CA

Register by November 20 and Save up to $350:
http://www.tri-conference.com/ird.asp

Speaker Presentations:

Enterprise Scientific Workflow Environment Drives Innovation

Juergen Hammer, Ph.D., M.B.A., Pharma Research Scientific Informatics;
Global Head, In Silico Sciences; Center Head, Scientific Informatics, F.
Hoffmann-La Roche, Inc.

The Pistoia Alliance, Inc.-A Construct for Precompetitive Collaboration

Chris Waller, Ph.D., Senior Director, Precompetitive Collaborations,
Research, Development & Medical Informatics, Worldwide Technology, Pfizer,
Inc.

Recent Strategies with Cloud, Wikis, Ontologies and Open Source Data
Standards

Giles M. Day, Senior Director, BBC Informatics, Pfizer, Inc.

Luncheon Presentation Sponsored by Microsoft

Personalized Medicine: The Missing Pieces

Jim Karkanias, Senior Director of Applied Research & Technology, Microsoft
Health Solutions Group

Integrated Informatics Systems for R&D

John Reynders, Ph.D., CIO, Pharmaceutical Research & Development, Johnson &
Johnson

Executive Panel with Q&A

Are We Integrating the Right Data: Extending Beyond Laboratory Data to
Decisions Impacting Project Success

Moderator: David M. Sedlock, Ph.D., Senior Director, Research & Development
Systems, Millennium, The Takeda Oncology Company

Presentation Sponsored by Accelrys

Knowledge Management

David Hodgson, Ph.D., Site Head, Global Research Informatics, Roche Palo
Alto

Knowledge for Strategic Advantage: Accelerating the R&D Cycle

Thomas P. Hill, Principal, The Leverage Innovation Group; former Director,
Learning and Knowledge Management, Genentech

ASAP-Emphasizing Multidimensional Drug Discovery

W. Patrick Walters, Ph.D., Senior Research Fellow & Group Head,
Computational Drug Discovery Technologies, Vertex Pharmaceuticals, Inc.

Agile Software Development: Meeting the Rapidly Changing Needs in Drug
Discovery

Man-Ling Lee, Ph.D., Senior Program Analyst, Discovery Chemistry, Small
Molecule Drug Discovery, Genentech, Inc.

Application of Translational Informatics in Tailored Therapeutics

Susie Stephens, Director, Biomedical Informatics, Pharmaceutical Research &
Development, Johnson & Johnson

Data Integration-What's in it for Me?

Randal Chen, Ph.D., Director, Research Informatics, Amgen, South San
Francisco

Integrative Data Mining for Drug Discovery using the Semantic Web

Michael Lajiness, Ph.D., Research Scientist, Structural and Computational
Sciences, Eli Lilly & Company

Collaborative Drug Discovery Humanitarian and Commercial Researcher Network
Case Studies

Barry A. Bunin, Ph.D., Chief Executive Officer & President, Collaborative
Drug Discovery (CDD), Inc.

Panel: Drug Discovery Collaborations in 2010

Moderator: Barry A. Bunin, Ph.D., Chief Executive Officer & President,
Collaborative Drug Discovery (CDD), Inc.

Implementing a Translational Biomarker Strategy to Reduce Attrition in Drug
Development

Irina Antonijevic, M.D., Ph.D., Director, Translational Research, Biological
Research, Lundbeck Research, Inc. USA

High Content Mining of Disease Biomarkers

Jake Chen, Ph.D., Assistant Professor, Informatics & Computer Science,
Indiana University School of Informatics; Director, Indiana Center for
Systems Biology and Personalized Medicine, Indiana University-Purdue
University Indianapolis; Founder, MedeoLinx, Inc.

Profiling Patients to Drive Biomarker Development

N. R. Nirmala, Ph.D., Director, Biomarker Analysis and Informatics Unit,
Translational Sciences, Novartis Institutes of Biomedical Research

Panel: Informatics at R&D Interphases

Moderator: Pearl S. Huang, Ph.D., Integrator, Oncology Franchise, Research &
Early Development, Merck & Co.

Image Analysis Considerations for Pre-clinical, in vivo Medical Imaging

Matt Silva, Head, Imaging Sciences, Millennium, The Takeda Oncology Company

RISe Prowler: A Semantic Web Approach to Integrating External and In-house
Biology and Chemistry Information

Ajay Shah, Ph.D., MBA, PMP, Director, Research Informatics, Elan
Pharmaceuticals, Inc.

Development of a Registration System for Biologics in a Collaborative
Special Interest Group

Jeremy Packer, Ph.D., Head, Bioinformatics, Abbott

Semantic Web and Cloud Computing for Integrative Data Management and
Analysis Infrastructure

Jonas S. Almeida, Ph.D., Abell-Hanger Distinguished Professor,
Bioinformatics and Computational Biology, University of Texas, M.D. Anderson
Cancer Center

How to Register:
Telephone: 781-972-5400

Fax: 781-972-5425
Email: reg@...

To inquire about sponsorship and exhibit options, contact:
Carol Dinerstein, 781-972-5471, dinerstein@...

or Jon Stroup, 781-972-5483, jstroup@...

Posted by:

James Prudhomme

Marketing Manager

Cambridge Healthtech Institute

250 First Avenue, Suite 300

Needham, MA 02494

Direct: 781-972-5486

Fax: 781-972-5425

www.healthtech.com

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Eco allele

2009-11-17T02:32:13Z

Hello friends,

What are eco-alleles? Please answer

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2nd CFP: HiCOMB 2010 - 9th IEEE International Workshop on High Performance Computational Biology

2009-11-13T12:01:06Z

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
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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Deadline extension - FBTC 2010, From Concurrency To Biology and back

2009-11-12T10:28:48Z

[Apologies for multiple posting]

** Deadline Extension
** 3rd Workshop "From Biology To Concurrency and back" (FBTC 2010)

** New deadline for abstracts: November 29, 2009 (abstracts)
** New deadline for papers: December 8, 2009

More information below or at http://www.disi.unitn.it/~fbtc2010/

================================================================================

CALL FOR PAPERS: FBTC 2010

From Biology To Concurrency and back

(satellite event of ETAPS 2010)

March 27, 2010
Paphos, Cyprus

http://www.disi.unitn.it/~fbtc2010/

================================================================================

AIMS AND OBJECTIVES
As in its previous editions, the workshop aims at gathering researchers with
special interest at the convergence of life and
computer science, with particular
focus on the application of techniques and tools from concurrency.
We solicit the submission of unpublished results reporting on both modelling,
analysis, and validation of biological behaviours using concurrency-inspired
methods and platforms, and on bio-inspired models and tools for describing
distributed interactions.
Topics of interest include, but are not limited to:
applications of techniques from rewriting logics, process calculi, Petri Nets,
graph grammars, hybrid systems, and model checking to the representation and
testing of scenarios from life sciences.

SUBMISSION AND PUBLICATION
Submission through EasyChair,
15 pages manuscripts in EPTCS (http://www.eptcs.org/) style.

IMPORTANT DATES
Submission of title and abstract: November 29, 2009
Submission of paper: December 8, 2009
Notification: January 17, 2010
Submission of final version: February 21, 2010

PROGRAMME COMMITEE (to be confirmed)
Marco Antoniotti (University of Milan Bicocca, IT)
Chiara Bodei (University of Pisa, IT)
Luca Bortolussi (University of Udine, IT)
Luca Cardelli (Microsoft Research Cambridge, UK)
Erik de Vink (Technische Universiteit Eindhoven, NL)
Vincent Danos (CNRS and University of Edinburgh, UK)
François Fages (INRIA Paris-Rocquencourt, F)
Anthony Finkelstein (University College London, UK)
Walter Fontana (Harvard Medical School, US)
Radu Grosu (Stony Brook University, US)
Jane Hillston (University of Edinburgh, UK)
Anna Ingólfsdóttir (Reykjavik University, IS)
John Lygeros (Automatic Control Laboratory, CH)
Emanuela Merelli (University of Camerino, IT) (Co-chair)
Paola Quaglia (CoSBi and Trento University, IT) (Co-chair)
Carolyn Talcott (SRI International, US)
Adelinde Uhrmacher (University of Rostock, DE)
Cristian Versari (University of Bologna, IT)

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BICoB-2010 CFP - paper Deadline Extended: November 23, 2009

2009-11-11T15:56:52Z

Submission Deadline Extended: November 23, 2009

*** We apologize if you receive multiple copies of this CFP ***
****************************************************
BICoB-2010 - Call for Papers
http://sce.uhcl.edu/bicob10/
<http://sce.uhcl.edu/bicob10/>
2nd International Conference
on Bioinformatics and Computational Biology (BICoB)
March 24 - 26, 2010, Honolulu, Hawaii, USA

Full paper Submission Deadline:...............................November
23, 2009
Notification of Acceptance: .....................................
December 23, 2009
Pre-registration and Camera-ready paper due:...... January 15, 2010

Computational techniques have already enabled unprecedented advances in
modern
biology and medicine. This continues to be a vibrant research area with
broadening of
computational techniques and new emerging challenges. The Bioinformatics
and
Computational Biology (BICoB) conference was established by the ISCA to
promote
the advancement of computing techniques and their application to life
sciences. T

he BICoB conference will feature original unpublished research in all
areas of
bio-informatics and computational biology, and covering the entire
spectrum of
underlying computational techniques/models/paradigms. The topics of
interest include
(and are not limited to):
* Genome analysis: Genome assembly, genome and chromosome
annotation,
gene finding, alternative splicing, EST analysis and comparative
genomics.
* Sequence analysis: Multiple sequence alignment, sequence search
and clustering,
function prediction, motif discovery, functional site recognition
in protein, RNA and
DNA sequences.
* Phylogenetics: Phylogeny estimation, models of evolution,
comparative biological
methods, population genetics.
* Structural Bioinformatics: Structure matching, prediction,
analysis and comparison;
methods and tools for docking; protein design
* Analysis of high-throughput biological data: Microarrays
(nucleic acid, protein,
array CGH, genome tiling, and other arrays), EST, SAGE, MPSS,
proteomics, mass
spectrometry.
* Genetics and population analysis: Linkage analysis, association
analysis, population
simulation, haplotyping, marker discovery, genotype calling.
* Systems biology: Systems approaches to molecular biology,
multiscale modeling,
pathways,gene networks.
SUBMISSION PROCEDURES
BICoB welcomes submissions in all areas of computing with impact on life
sciences
including (but not limited to) algorithms, databases, languages,
systems, and high
performance computing. For example:
- Parallel and high-performance techniques
- Unifying computational techniques
- Data and image mining techniques
- Approximation and randomized algorithms and systems
- Computational biology on emerging architectures and hardware
accelerators
Papers will be accepted only by electronic submission (PDF only). A full
paper, including
title, author's name(s) and affiliation, mailing address, telephone, fax
and email of the
principal author, should be submitted by November 23, 2009 at the
following web site:
https://cmt.research.microsoft.com/BICOB2010/
The submitted manuscript should closely reflect the final paper as it
will appear in
the Proceedings which will be a maximum of 6 pages (+2 pages with
additional page
charge). ISCA double-column format will be used.
See http://www.isca-hq.org/sample-isca-manuscript-format.pdf .
Latex users: http://www.isca-hq.org/Latex-format.htm
If you encounter any difficulties during submission or if you require
further information,
please contact: isca@....

Authors wishing to have their papers reviewed for possible publication
in the ISCA
Journal of Computers and Applications should send by postal mail or
email expanded
versions of their papers directly to the Editor, Prof. David Jeff
Jackson.
(See Instructions to Authors at: http://www.isca-hq.org/j-authr.htm )

................................................... IMPORTANT DATES
Full paper Submission Deadline:
......................................November 23, 2009
Notification of Acceptance:
............................................... December 23, 2009
Pre-registration and Camera-ready paper due:................ January 15,
2010

CONFERENCE CHAIR

George Karypis
University of Minnesota
karypis@...

PROGRAM CHAIRS

Hisham Al-Mubaid

University of Houston-Clear Lake
hisham@...

If you would like to be removed from our distribution list,
please reply to this email with the word 'REMOVE' in the Subject line.

Mary Ann Sullivan
Executive Director, ISCA
International Society for Computers
and Their Applications
975 Walnut Street, Suite 132
Cary, NC 27511 USA
Phone: 919-467-5559
FAX: 919-467-3430
E-mail: isca@...

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Reminder - Call for GECCO 2010 workshop proposals - Deadline November 16th

2009-11-11T02:46:52Z

Our apologies if you receive multiple copies of this announcement.

CALL FOR WORKSHOP PROPOSALS
2010 GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE (GECCO-2010)

Sponsored by ACM SIGEVO
http://www.sigevo.org/GECCO-2010

The GECCO-2010 Program Committee invites proposals for workshops to be
held in conjunction with the 2010 Genetic and Evolutionary Computation
Conference (GECCO-2010) in Portland, Oregon, USA, July 7-11.

** Important Dates **
Deadline for Workshop Proposals: November 16th, 2009
Notification of Acceptance: November 30th, 2009
Information and Submissions: jqb@...

GECCO workshops provide an excellent opportunity to meet people with
similar interests, to be exposed to cutting-edge research and to
exchange ideas in an informal setting. Ideally, a GECCO workshop should
focus on a specialized research area, on an emerging research field, or
on interdisciplinary research area between the genetic and evolutionary
computation community and other research fields. GECCO workshops can be
two hours, half day, or a full day long. The format can be decided by
the organizers who are encouraged to plan interactive sessions (e.g,
debate/discussion sessions, brainstorming or problem solving sessions)
which cannot be easily accommodated in the GECCO conference program.
Proposals should be mailed to: jqb@...

Each proposal must be submitted as a plain text file and must contain
the following information:
1. A half page description of the workshop including a clear description
of the specific topics issues on which the workshop will focus should be
identified.
2. A brief (half page) discussion of why the topic is of interest to the
genetic and evolutionary computation community and about the workshop
target audience.
3. The estimated number of potential attendees, accepted papers and
submissions. If a previous edition of the workshop has already taken
place, then the previous number of submissions, accepted papers, and
attendees should be included.
4. A draft schedule of the workshop (with a duration of either 2 hours,
half day or a full day) highlighting the planned discussion sessions
(panels, Q&A, hands-on demonstrations, problem-solving sessions,
brainstorming, etc.)
5) The complete contact information of the workshop organizers (Postal
address, E-mail, phone and fax numbers, & WWW page).
6) A brief biography of the organizers.

The proposal should be accompanied by the full CVs of the organizers in
PDF format. These should include previous experience in workshop or
conference organization.

The organizers of an accepted workshop are responsible for its
coordination, for its publicity (e.g., for sending out call for papers),
for collecting and reviewing the papers, for providing a list of
accepted papers and their authors, if applicable.

Attendance at the workshops will be open to all GECCO attendees. Note
that *all* organizers, participants and presenters must register to the
GECCO-2010 conference. Organizers of a workshop *do not* qualify for a
reduction in the registration or accommodation costs at the conference.
Accepted workshop papers will be collected by Sheridan/ACM Press, and
published in a separate workshop proceedings volume. Details and
additional deadlines will be provided once it has been decided which
workshops will be accepted for GECCO-2010. All accepted Workshop Papers
must use the ACM template for papers and must follow all ACM formatting
rules. Accepted workshop papers that do not use the ACM template and/or
do not adhere to ACM formatting rules will not be published.

The deadline for the submission of workshop proposal is November 16,
2009. Proposals should be submitted as plain text files (no HTML) with
the exception of the CVs which have to be submitted as PDFs. Workshop
organizers will be notified by November 30th whether the workshop
proposal has been accepted.

GECCO is sponsored by the Association for Computing Machinery Special
Interest Group on Genetic and Evolutionary Computation (SIGEVO). SIG
Services: 2 Penn Plaza, Suite 701, New York, NY, 10121, USA,
1-800-342-6626 (USA and Canada) or +212-626-0500 (Global).

This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.

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International Speaker Line-up Announced for Pharma IQ's Next-Generation DNA Sequencing

2009-11-10T03:49:42Z

http://www.dnaevent.com/

Dear Colleague,

Today's Next-Generation DNA Sequencing systems are opening novel fields and
applications in biology studies and medical research. Beyond genomic
sequencing, of which there are now many successful results, the technology is
also allowing scientists to pursue:

- Personal genomics with detailed analysis of individual genome stretches
- Precise analysis of RNA transcripts for gene expression
- Genome-wide characterisation and profiling of mRNAs, small RNAs and
transcription factor regions
- Structure of chromatin and DNA methylation patterns
- Microbiology and metagenomics

At Pharma IQ's Next-Generation DNA Sequencing conference, January 18th - 20th
in London, you will share study and technology pilot results with peers on how
to utilise NGS systems to predict disease risk at genome level by using next-
generation systems to accurately scan and identify rare variants in genes,
short sequence repeats and CNPs.

You will also discuss with other principal investigators how they're evaluating
the right next generation approach for their research project, comparing deep
vs. wide, de novo vs. re-sequencing and conventional microarray platforms.

The international speaker panel includes:

- Dr Nicholas H. Bergman, Principal Investigator and Genomics Team Leader,
National Biodefense Analysis and Countermeasures Center
- Dr Nick Loman, Head of Bioinformatics, University of Birmingham
- Dr Daniel J. Turner, Head of Sequencing Technology Development, Wellcome
Trust Sanger Institute
- Dr Ina Vandenbroucke, Senior Scientist, Translational Genetics & Genomics,
Tibotec - Virco BVBA
- Dr Joris Veltman Department of Human Genetics, Radboud University Nijmegen
Medical Centre
- Dr Bhupinder Bhullar , Laboratory Head, Biomedical Research, Novartis
- Dr Harma Feitsma, Research Scientist Molecular Diagnostics, Philips Research
Labs
- Dr Peter Verhasselt, Principal Scientist, Translational Genomics & Genetics,
Johnson & Johnson Pharmaceutical Research & Development
- Guy Cochrane, Team Leader, European Nucleotide Archive Team, European
Bioinformatics Institute
- Roderic Guigo, Senior Group Leader, Genomic Regulations, Biomedical
Informatics, IMIM-Hospital del Mar
- Bernd Timmermmann, Next Generation Sequencing Service Group, Max Planck
Institute for Molecular Genetics

Don't miss this opportunity to hear from leading practitioners and technology
users. Download the brochure for further information about the agenda:
http://www.dnaevent.com/Event.aspx?id=234806

NGS systems are rapidly evolving. However many challenges remain, including the
development of robust protocols for generating sequencing libraries, building
effective new approaches to data-analysis and often a rethinking of
experimental design.

Sign up today for January's Next-Generation DNA Sequencing meeting to discuss
how to overcome these challenges with other practitioners.

If you sign up before 20th November 2009, you can SAVE up to 400 GBP off the
standard rates. Plus the first 10 academics to book on can take advantage of
registering for only 399 GBP (+VAT)! For further information on the savings you
could make, visit the website:
http://www.dnaevent.com/Event.aspx?id=234808

We look forward to meeting you in London in January.

Sincerely,

Courtney Becker-James
Conference Director
Pharma IQ

PS: If you know who this meeting is most relevant for, please forward it to
them so they have the opportunity to join their peers at this unique gathering!

This email was sent by:IQPC Ltd.

Anchor House 15-19 Britten Street, London, SW3 3QL, United Kingdom

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BCBGC-10 Call for papers

2009-11-08T16:05:02Z

BCBGC-10 Call for papers

The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference.

The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10.

International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10)
International Conference on Automation, Robotics and Control Systems (ARCS-10)
International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10)
International Conference on Computer Networks (CN-10)
International Conference on Enterprise Information Systems and Web Technologies (EISWT-10)
International Conference on High Performance Computing Systems (HPCS-10)
International Conference on Information Security and Privacy (ISP-10)
International Conference on Image and Video Processing and Computer Vision (IVPCV-10)
International Conference on Software Engineering Theory and Practice (SETP-10)
International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10)

We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details.

Sincerely
John Edward
Publicity committee

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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

This email was sent to comp-bio@.... You can instantly unsubscribe
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A Graph-Laplacian-Based Feature Extraction Algorithm for Neural Spike Sorting

2009-11-04T12:42:06Z

PDF:
http://lyle.smu.edu/~yghanbari/EMBC09_FinalSubmission_YasserGhanbari_0876.pdf

ABSTRACT:
Analysis of extracellular neural spike recordings is highly dependent
upon the accuracy of neural waveform classification, commonly referred
to as spike sorting. Feature extraction is an important stage of this
process because it can limit the quality of clustering which is
performed in the feature space. This paper proposes a new feature
extraction method (which we call Graph Laplacian Features, GLF) based
on minimizing the graph Laplacian and maximizing the weighted
variance. The algorithm is compared with Principal Components Analysis
(PCA, the most commonly-used feature extraction method) using
simulated neural data. The results show that the proposed algorithm
produces more compact and well-separated clusters compared to PCA. As
an added benefit, tentative cluster centers are output which can be
used to initialize a subsequent clustering stage.

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Re: Some Wavelet applications on Speech Enhancement

2009-11-04T12:37:21Z

I like this paper published in Journal of Speech Communication:
http://lyle.smu.edu/~yghanbari/Speech_Communication_2006.pdf

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Microsoft and Oracle Showcase Informatics Solutions at...

2009-11-04T12:23:09Z

CHI's 2nd Annual
Adopting R&D Informatics Systems: Data Management, Integration & Knowledge
Management

February 3-5, 2010
Moscone North Convention Center - San Francisco, CA

Register by November 20 at the Early Bird Discount!

www.tri-conference.com/ird.asp

Key Benefits of Attending this Conference:

Network with senior level informatics experts and IT professionals at
conference sessions dedicated to:

- Executive Strategies-Integrated R&D Informatics

- Data Information and Knowledge Management

- Integrative Data Management through Cloud, Wikis, Ontologies &
Semantic Web

- Translational Informatics-How Far Have We Come?

- Integrated Genomic, Biology, And Image Data

Participate in Break-out discussion groups on focused these topics:

E-Notebooks - The Power House of Integration?

Moderator: David M. Sedlock, Ph.D., Senior Director, Research & Development
Systems, Millennium, The Takeda Oncology Company

- Data Integration vs. System Integration

- Value and Pitfalls of ELN Integration

- Vendor Role (Impact of Customization)

- Alternatives to ELN System Integration

- ELN vs. LIMS vs. SDMS - How Do These Systems Achieve Maximum
Value?

Ontologies and Semantic Web
Moderator: Susie Stephens, Director, Biomedical Informatics, Pharmaceutical
Research & Development, Johnson & Johnson

- Is there a cloud in your future?

- Aggregation of key information from sources including structural
chemical and biological data along with predictions of activity

Open Source Data Standards
Moderator: Ajay Shah, Ph.D., MBA, PMP, Director, Research Informatics, Elan
Pharmaceuticals, Inc.

- Open source and public platforms

- Role of Open Source Technology in Systems Design

- Virtual Pharmaceutical collaborations

Attend our Poster session to learn about new, innovative research and
informatics techniques.

View Informatics platforms and tools presented by Technology Service
Providers in the Exhibit Hall.

Sponsorship and Exhibit Opportunities are Available!

For details on customized packages, contact Carol Dinerstein at +1
781-972-5471, dinerstein@... or Jon Stroup at +1 781-972-5483,
jstroup@...

Group Discounts are Available!

CHI will work within your company's budget to send your team to this
conference. For details, contact David Cunningham at +1 781-972-5472,
cunningham@...

View the full agenda and register at www.tri-conference.com/ird.asp

Contact for more information:

James Prudhomme

Marketing Manager

Cambridge Healthtech Institute

250 First Avenue, Suite 300

Needham, MA 02494

Tel: 781-972-5400

Fax: 781-972-5425

jprudhomme@...

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Ph.D. Position in Computational Biophysical Chemistry

2009-11-04T06:20:35Z

Ph.D. Position in Computational Biophysical Chemistry

A four year Ph.D. fellowship is available in the faculty of Chemistry at
the University of the Basque Country, San Sebastian Spain. The Ph.D.
project will make use of computational methods to investigate several
issues in epigenetics that involve DNA-protein recognition. In
particular, the driving force that governs the selectivity of
hemi-methylated DNA by the regulatory protein UHRF1, as well as, the
base flipping mechanism associated with this interaction. These studies
will utilize molecular dynamics simulations and several techniques in
free energy calculations. The candidate should have a Master (or an
equivalent) degree in chemistry, physics, biology, or a related area,
preferably from an EU country. The starting date of the position is
flexible.

For more information contact Prof. Ronen Zangi: r.zangi@...

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Reactome Pathway Database User Survey

2009-11-02T08:29:52Z

Reactome is a curated database of core pathways and reactions in human biology. Information is authored by expert biological researchers, maintained by the Reactome editorial staff and cross-referenced to several third-party databases. Reactome has an entity-level pathway viewer and data mining tools to facilitate searching and visualizing pathway data and the analysis of user-supplied data sets. Furthermore, Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species. Reactome's data content and software can all be freely used and redistributed under open source terms.

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
http://www.reactome.org
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Call for Papers: IEEE CIBCB '10

2009-11-02T04:19:06Z

Call for Papers: IEEE CIBCB 2010

2010 IEEE Symposium on Computational Intelligence in
Bioinformatics and Computational Biology
2-5 May 2010, Montreal, Canada

IMPORTANT DATES:

Special Session Proposals Due: 15 Nov. 2009
Tutorial Proposals Due: 15 Nov. 2009
Paper submission deadline: 15 Dec. 2009
Author notification: 15 Feb. 2010
Camera-ready paper deadline: 15 Mar. 2010
Conference: 2-5 May 2010

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

SCOPE:

This symposium will bring together top researchers, practitioners, and students
from around the world to discuss the latest advances in the field of
Computational Intelligence and its application to real world problems in
biology, bioinformatics, computational biology, chemical informatics,
bioengineering and related fields.

Computational Intelligence (CI) approaches includes artificial neural networks,
fuzzy logic, evolutionary algorithms, hybrid approaches and other emerging
techniques.

Topics of interest include, but are not limited to:
- high-throughput data analysis (microarrays, mass spectrometry, EST, etc.)
- molecular docking and drug design
- RNA and protein folding and structure prediction
- metabolic pathway analysis
- analysis of large biological data sets
- single nucleotide polymorphism (SNP) analysis
- immuno- and chemo-informatics
- molecular evolution and phylogenetics
- bio and medical ontologies
- microRNA gene expression analysis
- molecular sequence alignment and analysis
- systems and synthetic biology
- emergent properties in complex biological system
- computational proteomics
- motif and signal detection
- medical image analysis and pattern recognition
- in-silico optimization of biological systems

The use of computational intelligence must play a substantial role in submitted
papers. Submissions will be peer reviewed and accepted papers will be published
in the conference proceedings and will be indexed in IEEE eXplore.

SUBMISSION PROCEDURE:

Prospective authors are invited to submit papers of no more than
eight (8) pages in IEEE conference format, including results, figures and
references. Submission details can be found on the symposium web
site at: www.cibcb.org/CIBCB2010. Authors are expected to present their paper
at the symposium.

CALL FOR SPECIAL SESSIONS and TUTORIALS:

Consult the CIBCB'10 symposium web site for instructions on proposing a special
session or tutorial. Papers for special sessions must have significant
computational intelligence content.

LOCATION:

The symposium will take place at the Hotel Omni Mont-Royal located in beautiful
downtown Montreal close to the University of Montreal and McGill University

ORGANIZING COMMITTEE:

General Chair L. Gwenn Volkert
Program Chair: Dan Ashlock
Technical Co-Chairs: Francesco Masulli
Mihail Popescu
Clare Bates Congdon
Publicity Chair: Sorin Draghici
Proceedings Chair: Chengpeng (Charlie) Bi
Finance Chair: Gary Fogel

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

Direct your questions or requests for additional information to:

L. Gwenn Volkert Ð volkert@... - CIBCB 2010 General Chair
or
Daniel Ashlock - dashlock@... - CIBCB 2010 Program Chair

or visit:

http://www.cibcb.org/CIBCB10
http://www.cibcb.org/files/cibcb2010cfp.pdf

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DNA Fragmentation: The Critical First Step in Next Generation Sequencing

2009-10-30T08:49:53Z

Topic:Controlled DNA Fragmentation: The Critical First Step
in Next Generation Sequencing
When: November 11, 2009
Time: 11:00a.m. EST
Duration: Presentation: 30 Minutes
Discussion: 30 Minutes
Hosts: Introduction: Jim Laugharn, Founder and CEO
Presentation: Hamid Khoja, Ph.D., Senior Applications Scientist

Registration: To register for the online event:
1. Click here
2. Click Register
3. On the registration form, enter your information and then click Submit.
You will receive a confirmation email and an event reminder.

What You Will Learn:
The important role of Controlled DNA Fragmentation in the sample preparation process for Next Generation Sequencing.
What DNA Fragmentation methods are commercially available today for Fragment and Mate-Pair Libraries.
How the Covaris AFA process works.
Additional key applications and services.

Webinar Abstract:
DNA fragmentation is the most critical sample preparation step required by all the currently available next generation sequencing platforms. The sensitivity and broader application depth of these platforms necessitates the utilization of an efficient, easy to use, high throughput capable, and highly reproducible DNA fragmentation technology.
Although nebulization, enzymatic digestion, hydrodynamic shearing, and sonication have been used to shear DNA, they all have significant disadvantages, which cause them to be a weak point in the workflow for next generation sequencing technologies. Drawbacks include thermal and sequence specific biased shearing, thermal degradation, sample loss, automation difficulties, and user-based issues.
The Covaris AFA process stands out as the preferred method for easily and reproducibly fragmenting DNA ranging from 100bp to 5kb in length.
In this meeting we will provide details of the Covaris AFA technology, and the distinct advantages it provides when compared to other DNA shearing methodologies. We will also present data to showcase the control and reproducibility of our validated protocols when fragmenting DNA in the 100bp to 5kb size range. Also discussed will be the use of AFA technology in chromatin fragmentation for ChIP-chip, ChIP-seq, and RNA fragmentation applications.

About Covaris
At Covaris, we believe that high value samples deserve controlled preparation, prior to committing to high cost analysis. Covaris' line of high-performance focused ultra-sonicators deliver industry-leading sample processing capability directly to the benchtop. We provide workstation-based instruments capable of extremely rapid and complete DNA/RNA/Chromatin fragmentation, tissue disruption, and non-contact isothermal homogenization of cell culture, tissue, and organisms for DNA, RNA, protein, and metabolites extraction. The Covaris family of instruments provides single through 96 sample preparation with scalable acoustic energy, capable of processing a wide range of sample types and volumes.
With over 850 installations, the Covaris proprietary and patented Adaptive Focused Acoustics (AFA) technology enables numerous non-contact, isothermal sample preparation processes for use in a broad range of applications including Genomics, Proteomics, and Drug Discovery research.
For more information about Covaris and AFA, please visit us at Covarisinc.com or on KBioscience.

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Title: SWAT4LS Call for participation

2009-10-29T22:55:10Z

*** apologies for multiple postings ***

Registration is now open for SWAT4LS Semantic Web Applications and
Tools for Life Sciences

to be held in Amsterdam, Science Park, 20th November 2009

Registration: http://www.swat4ls.org/2009/rform.php#rform

------------------------------
Provisional scientific program:

Keynotes:
* Alan Ruttenberg: Semantic Web Technology to Support Studying the
Relation of HLA Structure Variation to Disease

* Barend Mons: (provisional) CWA: The meta-analysed Semantic Web ,
getting rid of ambiguity and redundancy

* Michael Schroeder: Prediction of drug-target interactions from
literature by context similarity

Accepted papers:

* OBO & OWL: Roundtrip Ontology Transformations
Syed Hamid Tirmizi, Stuart Aitken, Dilvan Moreira, Chris Mungall,
Juan Sequeda, Nigam H. Shah and Daniel P. Miranker.

* Mining Semantic Networks of Bioinformatics e-Resources from Literature
Hammad Afzal, James Eales, Robert Stevens and Goran Nenadic.

* Linking Open Drug Data to Cheminformatics and Proteochemometrics
Egon Willighagen and Jarl Wikberg.

* TIM: A Semantic Web Application for the Specification of Metadata
Items in Clinical Research
Matthias Löbe, Magnus Knuth and Roland Mücke.

* Semantics-Based Composition of EMBOSS Services with Bio-jETI
Anna-Lena Lamprecht, Stefan Naujokat, Tiziana Margaria and Bernhard
Steffen.

* Towards the Ontology-based Classification of Lymphoma Patients using
Semantic Image Annotations
Sonja Zillner.

Short communications:

* Weekend Triple Billionaire
Jerven Bolleman and Thomas Kappler.

* Towards a Logic-based Assessment of the compatibility of UMLS sources
Ernesto Jimenez-Ruiz, Bernardo Cuenca Grau, Rafael Berlanga and Ian
Horrocks.

* Using the NCBO Web Services for Concept Recognition and Ontology
Annotation of Expression Datasets
Simon Twigger, Joey Geiger and Jennifer Smith.

Demos:

* A system for repairing missing is-a structure in ontologies
Patrick Lambrix, Qiang Liu and He Tan.

* NeuroLex.org - A semantic wiki for neuroinformatics based on the NIF
Standard Ontology
Stephen Larson, Sarah Maynard, Fahim Imam and Maryann Martone.

* ContentCVS: A CVS-based Collaborative ONTology ENgineering Tool
Ernesto Jimenez-Ruiz, Bernardo Cuenca Grau, Ian Horrocks and Rafael
Berlanga.

* DC-THERA Directory, a Knowledge Management System for the support of
the European Dendritic Cell Immunology Community
Marco Brandizi, Michaela Gündel, Ciro Scognamiglio and Andrea
Splendiani.

Panel discussion:
Theme: TBD

Plus poster sessions (authors of posters are not listed in this call,
but will be listed on the website)

An updates version of the program will be available at http://www.swat4ls.org/2009/progr.php

Early registrations are very appreciated.

----------------------------------------
Registrations costs:
full registration: 50 euros
social dinner (optional): 35 euros
PhD students: free (subject to availability)

To register please visit: http://www.swat4ls.org/2009/rform.php#rform

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@...

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

We wish to thank once again the review panel that made this possible:

* 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

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Cfp: The first Indian virtual conference on Bioinformatics (Inbix '10)

2009-10-23T00:23:25Z

Dear All,
This is the first call and announce for Indian virtual conference on
Bioinformatics (Inbix '10)

For more details, please visit
http://www.bioinformatics.org/wiki/Inbix10. There are various
speakers of repute in the area of Systems Biology and Bioinformatics.

Registration starts October 15, 2009. Stay tuned for more
announcements. If you are a group of 15 or more, you can form a
virtual hub.

This is organized by Bioclues.org and Bioinformatics.org. for further
information and news, please contact the organizers.

Sincerely
Prash for Inbix'10 organizers

Prashanth Suravajhala
C-DAC-Bioinformatics Group, Pune, India
http://wiki.bioinformatics.org/prash

“If you only have a hammer, you tend to see every problem as a nail."
~Abraham Maslow

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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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Visualizing Biological Data, 3-5 March 2010: Deadline on 16 Nov 2009

2009-10-21T06:22:36Z

Dear colleagues,

We invite you to participate in the first

EMBO Workshop on Visualizing Biological Data (VizBi, http://www.vizbi.org)

3 - 5 March 2010 at the EMBL's new Advanced Training Centre in Heidelberg, Germany

The goal of the workshop is to bring together, for the first time, researchers developing and using visualization systems across all
areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including
microscopy and magnetic resonance imaging). We have assembled an authoritative list of 29 invited speakers who will present an
exciting program, reviewing the state-of-the-art and perspectives in each of these areas. The primary focus will be on visualizing
processed and annotated data in their biological context, rather than on processing of raw data.

The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give
a 'fastforward' presentation about their work (limited to 30 seconds and 1 slide).

To apply to join the workshop, please go to http://vizbi.org and submit an abstract and image related to your work. Submissions
close on 16 November 2009. Since places are limited, participants will be selected based on the relevance of their work to the
goals of the workshop. Notifications of acceptance will be sent within three weeks after the close of submissions.

We plan to award a prize for the submitted image that best conveys a strong scientific message in a visually compelling manner.

Please forward this announcement to anyone who may be interested. We hope to see you in Heidelberg next spring!

SeÃ¡n O'Donoghue, EMBL
Jim Procter, University of Dundee
Nils Gehlenborg, European Bioinformatics Institute
Reinhard Schneider, EMBL

If you have any questions about the registration process please contact:

Adela Valceanu

Conference Officer
European Molecular Biology Laboratory
Meyerhofstr. 1
D-69117 Heidelberg
Tel: +49-6221-387 8625
Fax: +49-6221-387 8158
Email: valceanu@...

For full event listings please visit our website: www.embl.org/events or sign up for our newsletter www.embl.de/events/newsletter

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ACS/IEEE'10 (Hammamet, Tunisia May 16-19, 2010) - Extended Deadline

2009-10-14T20:14:55Z

Dear all,

The deadline for the submission of abstracts to AICCSA'10 <http://www2.lifl.fr/AICCSA2010/> has been extended to October 27, 2009.

Best regards,
Mourad Elloumi.
______________________________________________________

Mobile :+216 98 46 88 59
E.Mail:Mourad.Elloumi@...
URL :www.esstt.rnu.tn/utic/english/memb_elloumi.html
______________________________________________________

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7th Georgia Tech - ORNL Conference on Bioinformatics

2009-10-08T17:27:18Z

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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Adopting R&D Informatics Systems

2009-10-01T12:08:11Z

Part of the Diagnostics Channel at CHI's 17th International Molecular
Medicine Tri-Conference.

Cambridge Healthtech Institute's Second Annual
Adopting R&D Informatics Systems: Data Management, Integration & Knowledge
Management
February 3-5, 2010
Moscone North Convention Center * San Francisco, CA

Register by October 9 and Save up to $350:
http://www.tri-conference.com/ird.asp

Speaker Presentations:

Enterprise Scientific Workflow Environment Drives Innovation

Juergen Hammer, Ph.D., M.B.A., Pharma Research Scientific Informatics;
Global Head, In Silico Sciences; Center Head, Scientific Informatics, F.
Hoffmann-La Roche, Inc.

The Pistoia Alliance, Inc.-A Construct for Precompetitive Collaboration

Chris Waller, Ph.D., Senior Director, Precompetitive Collaborations,
Research, Development & Medical Informatics, Worldwide Technology, Pfizer,
Inc.

Recent Strategies with Cloud, Wikis, Ontologies and Open Source Data
Standards

Giles M. Day, Senior Director, BBC Informatics, Pfizer, Inc.

Luncheon Presentation Sponsored by Microsoft

Personalized Medicine: The Missing Pieces

Jim Karkanias, Senior Director of Applied Research & Technology, Microsoft
Health Solutions Group

Integrated Informatics Systems for R&D

John Reynders, Ph.D., CIO, Pharmaceutical Research & Development, Johnson &
Johnson

Executive Panel with Q&A

Are We Integrating the Right Data: Extending Beyond Laboratory Data to
Decisions Impacting Project Success

Moderator: David M. Sedlock, Ph.D., Senior Director, Research & Development
Systems, Millennium, The Takeda Oncology Company

Presentation Sponsored by Accelrys

Knowledge Management

David Hodgson, Ph.D., Site Head, Global Research Informatics, Roche Palo
Alto

Knowledge for Strategic Advantage: Accelerating the R&D Cycle

Thomas P. Hill, Principal, The Leverage Innovation Group; former Director,
Learning and Knowledge Management, Genentech

ASAP-Emphasizing Multidimensional Drug Discovery

W. Patrick Walters, Ph.D., Senior Research Fellow & Group Head,
Computational Drug Discovery Technologies, Vertex Pharmaceuticals, Inc.

Agile Software Development: Meeting the Rapidly Changing Needs in Drug
Discovery

Man-Ling Lee, Ph.D., Senior Program Analyst, Discovery Chemistry, Small
Molecule Drug Discovery, Genentech, Inc.

Application of Translational Informatics in Tailored Therapeutics

Susie Stephens, Director, Biomedical Informatics, Pharmaceutical Research &
Development, Johnson & Johnson

Data Integration-What's in it for Me?

Randal Chen, Ph.D., Director, Research Informatics, Amgen, South San
Francisco

Integrative Data Mining for Drug Discovery using the Semantic Web

Michael Lajiness, Ph.D., Research Scientist, Structural and Computational
Sciences, Eli Lilly & Company

Collaborative Drug Discovery Humanitarian and Commercial Researcher Network
Case Studies

Barry A. Bunin, Ph.D., Chief Executive Officer & President, Collaborative
Drug Discovery (CDD), Inc.

Panel: Drug Discovery Collaborations in 2010

Moderator: Barry A. Bunin, Ph.D., Chief Executive Officer & President,
Collaborative Drug Discovery (CDD), Inc.

Implementing a Translational Biomarker Strategy to Reduce Attrition in Drug
Development

Irina Antonijevic, M.D., Ph.D., Director, Translational Research, Biological
Research, Lundbeck Research, Inc. USA

High Content Mining of Disease Biomarkers

Jake Chen, Ph.D., Assistant Professor, Informatics & Computer Science,
Indiana University School of Informatics; Director, Indiana Center for
Systems Biology and Personalized Medicine, Indiana University-Purdue
University Indianapolis; Founder, MedeoLinx, Inc.

Profiling Patients to Drive Biomarker Development

N. R. Nirmala, Ph.D., Director, Biomarker Analysis and Informatics Unit,
Translational Sciences, Novartis Institutes of Biomedical Research

Panel: Informatics at R&D Interphases

Moderator: Pearl S. Huang, Ph.D., Integrator, Oncology Franchise, Research &
Early Development, Merck & Co.

Image Analysis Considerations for Pre-clinical, in vivo Medical Imaging

Matt Silva, Head, Imaging Sciences, Millennium, The Takeda Oncology Company

RISe Prowler: A Semantic Web Approach to Integrating External and In-house
Biology and Chemistry Information

Ajay Shah, Ph.D., MBA, PMP, Director, Research Informatics, Elan
Pharmaceuticals, Inc.

Development of a Registration System for Biologics in a Collaborative
Special Interest Group

Jeremy Packer, Ph.D., Head, Bioinformatics, Abbott

Semantic Web and Cloud Computing for Integrative Data Management and
Analysis Infrastructure

Jonas S. Almeida, Ph.D., Abell-Hanger Distinguished Professor,
Bioinformatics and Computational Biology, University of Texas, M.D. Anderson
Cancer Center

How to Register:
Telephone: 781-972-5400

Fax: 781-972-5425
Email: reg@...

To inquire about sponsorship and exhibit options, contact:
Carol Dinerstein, 781-972-5471, dinerstein@...

or Jon Stroup, 781-972-5483, jstroup@...

Posted by:

James Prudhomme

Marketing Manager

Cambridge Healthtech Institute

250 First Avenue, Suite 300

Needham, MA 02494

Direct: 781-972-5486

Fax: 781-972-5425

www.healthtech.com

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BICoB-2010 CFP - Submission Deadline: October 23, 2009

2009-09-30T14:07:48Z

*** We apologize if you receive multiple copies of this CFP ***

BICoB-2010 - Call for Papers
http://sce.uhcl.edu/bicob10/
<http://sce.uhcl.edu/bicob10/>
2nd International Conference
on Bioinformatics and Computational Biology (BICoB)
March 24 - 26, 2010, Honolulu, Hawaii, USA

Full paper Submission Deadline:
........................................October 23, 2009
Notification of Acceptance:
............................................... December 11, 2009
Pre-registration and Camera-ready paper due:................ January 8,
2010

Computational techniques have already enabled unprecedented advances in
modern
biology and medicine. This continues to be a vibrant research area with
broadening of
computational techniques and new emerging challenges. The Bioinformatics
and
Computational Biology (BICoB) conference was established by the ISCA to
promote
the advancement of computing techniques and their application to life
sciences. T

he BICoB conference will feature original unpublished research in all
areas of
bio-informatics and computational biology, and covering the entire
spectrum of
underlying computational techniques/models/paradigms. The topics of
interest include
(and are not limited to):

* Genome analysis: Genome assembly, genome and chromosome
annotation,
gene finding, alternative splicing, EST analysis and comparative
genomics.

* Sequence analysis: Multiple sequence alignment, sequence search
and clustering,
function prediction, motif discovery, functional site recognition
in protein, RNA and
DNA sequences.

* Phylogenetics: Phylogeny estimation, models of evolution,
comparative biological
methods, population genetics.

* Structural Bioinformatics: Structure matching, prediction,
analysis and comparison;
methods and tools for docking; protein design

* Analysis of high-throughput biological data: Microarrays (nucleic
acid, protein,
array CGH, genome tiling, and other arrays), EST, SAGE, MPSS,
proteomics, mass
spectrometry.

* Genetics and population analysis: Linkage analysis, association
analysis, population
simulation, haplotyping, marker discovery, genotype calling.

* Systems biology: Systems approaches to molecular biology,
multiscale modeling,
pathways,gene networks.

SUBMISSION PROCEDURES

BICoB welcomes submissions in all areas of computing with impact on life
sciences
including (but not limited to) algorithms, databases, languages,
systems, and high
performance computing. For example:

- Parallel and high-performance techniques

- Unifying computational techniques

- Data and image mining techniques

- Approximation and randomized algorithms and systems

- Computational biology on emerging architectures and hardware
accelerators

Papers will be accepted only by electronic submission (PDF only). A full
paper, including
title, author's name(s) and affiliation, mailing address, telephone, fax
and email of the
principal author, should be submitted by October 23, 2009 at the
following web site:

https://cmt.research.microsoft.com/BICOB2010/

The submitted manuscript should closely reflect the final paper as it
will appear in
the Proceedings which will be a maximum of 6 pages (+2 pages with
additional page
charge). ISCA double-column format will be used.

See:See http://www.isca-hq.org/sample-isca-manuscript-format.pdf .

If you encounter any difficulties during submission or if you require
further information,
please contact: isca@....

Authors wishing to have their papers reviewed for possible publication
in the ISCA
Journal of Computers and Applications should send by postal mail or
email expanded
versions of their papers directly to the Editor, Prof. David Jeff
Jackson.

(See Instructions to Authors at: http://www.isca-hq.org/j-authr.htm )

................................................... IMPORTANT DATES

Full paper Submission Deadline:
..........................................October 23, 2009
Notification of Acceptance:
............................................... December 11, 2009
Pre-registration and Camera-ready paper due:.....................
January 8, 2010

CONFERENCE CHAIR

George Karypis
University of Minnesota
karypis@...

PROGRAM CO-CHAIRS

Hisham Al-Mubaid

University of Houston-Clear Lake
hisham@...

If you would like to be removed from our distribution list,
please reply to this email with the word 'REMOVE' in the Subject line.

Mary Ann Sullivan
Executive Director, ISCA
International Society for Computers
and Their Applications
975 Walnut Street, Suite 132
Cary, NC 27511 USA
Phone: 919-467-5559
FAX: 919-467-3430
E-mail: isca@...

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RE: Perl script in miRanda microRNA data output

2009-09-29T11:06:57Z

It's also easy and sometimes faster to do with sed:

sed -e '/no hits/d' output.txt

Lyle Wiedeman
UC Irvine

-----Original Message-----
From: comp-bio-bounces@...
[mailto:comp-bio-bounces@...] On Behalf Of Morris, Chris
(STFC,DL,CSE)
Sent: Tuesday, September 29, 2009 3:44 AM
To: kennerqq; comp-bio@...
Subject: RE: [Computational-biology] Perl script in miRanda microRNA data
output

You don't even need per perl. Just do:
grep -v 'no hits' output.txt

____________________________________________
Chris Morris
chris.morris@...
Tel: +44 1925 603689 Fax: +44 1925 603825
Mobile: 07921-717915
http://pims.instruct-fp7.eu/
STFC, Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD

> -----Original Message-----
> From: comp-bio-bounces@... [mailto:comp-bio-
> bounces@...] On Behalf Of kennerqq
> Sent: 28 September 2009 19:53
> To: comp-bio@...
> Subject: [Computational-biology] Perl script in miRanda microRNA data
output
>
> Hi all,
>
> I used miRanda software to predict the microRNA target from 3'UTR.
It come
> up with a large file which includes those "hits" and "no hits" lines.
Since
> it is too big to handle, i want to remove the "no hits" lines. I heard
that
> using a simple Perl Script can easily get rid of "no hits" lines in
the
> document. Unfortunately, I do not know how to use it. Does anybody
have a
> clue?
>
> Thanks a lot,
>
> Ken
> _______________________________________________
> Comp-bio mailing list
> Comp-bio@...
> http://www.bio.net/biomail/listinfo/comp-bio
--
Scanned by iCritical.

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RE: Perl script in miRanda microRNA data output

2009-09-29T03:44:00Z

You don't even need per perl. Just do:
grep -v 'no hits' output.txt

____________________________________________
Chris Morris
chris.morris@...
Tel: +44 1925 603689 Fax: +44 1925 603825
Mobile: 07921-717915
http://pims.instruct-fp7.eu/
STFC, Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD

> -----Original Message-----
> From: comp-bio-bounces@... [mailto:comp-bio-
> bounces@...] On Behalf Of kennerqq
> Sent: 28 September 2009 19:53
> To: comp-bio@...
> Subject: [Computational-biology] Perl script in miRanda microRNA data
output
>
> Hi all,
>
> I used miRanda software to predict the microRNA target from 3'UTR.
It come
> up with a large file which includes those "hits" and "no hits" lines.
Since
> it is too big to handle, i want to remove the "no hits" lines. I heard
that
> using a simple Perl Script can easily get rid of "no hits" lines in
the
> document. Unfortunately, I do not know how to use it. Does anybody
have a
> clue?
>
> Thanks a lot,
>
> Ken
> _______________________________________________
> Comp-bio mailing list
> Comp-bio@...
> http://www.bio.net/biomail/listinfo/comp-bio
--
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Perl script in miRanda microRNA data output

2009-09-28T11:53:14Z

Hi all,

I used miRanda software to predict the microRNA target from 3'UTR. It come
up with a large file which includes those "hits" and "no hits" lines. Since
it is too big to handle, i want to remove the "no hits" lines. I heard that
using a simple Perl Script can easily get rid of "no hits" lines in the
document. Unfortunately, I do not know how to use it. Does anybody have a
clue?

Thanks a lot,

Ken
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CALL FOR ABSTRACTS - Plant & Animal Genome XVIII Conference

2009-09-28T02:21:53Z

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

2009-09-25T16:21:26Z

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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Cfp FBTC 2010, From Concurrency To Biology and back

2009-09-24T11:46:55Z

_Apologies for multiple posting_

================================================================

CALL FOR PAPERS

FBTC 2010
3rd Int. Workshop "From Biology To Concurrency and back"

March 27, 2010, Paphos, Cyprus
Satellite event of ETAPS 2010, http://www.etaps10.cs.ucy.ac.cy/

http://www.disi.unitn.it/~fbtc2010/

================================================================

AIM:

As in its previous editions, the workshop aims at gathering researchers with
special interest at the convergence of life and computer science, with
particular
focus on the application of techniques and tools from concurrency.
We solicit the submission of unpublished results reporting on both modelling,
analysis, and validation of biological behaviours using concurrency-inspired
methods and platforms, and on bio-inspired models and tools for describing
distributed interactions.
Topics of interest include, but are not limited to: applications of techniques
from rewriting logics, process calculi, Petri Nets, graph grammars, hybrid
systems,
and model checking to the representation and testing of scenarios from life
sciences.

IMPORTANT DATES:

Title and abstract submission: Sunday, November 8, 2009
Paper submission: Sunday November 15, 2009
Author notification: Sunday January 17, 2010
Camera-ready papers: Friday February 12, 2010

SUBMISSION:

We solicit the submission of unpublished papers reporting on original research
on the topics of interest to FBTC.
Authors will have to submit their papers via EasyChair (https://www.easychair.
org/login.cgi?conf=fbtc2010).
Papers should take the form of a pdf file in
EPTCS style (http://www.eptcs.org/),
and should not exceed 15 pages.
If necessary, detailed proofs or other additional material can be added in a
clearly-labelled section "Applendix for referees".
Referees might review it at their discretion.

PUBLICATION:

The proceedings will be a volume of the open-access journal EPTCS.
A soft-copy of the proceedings will be distributed at the workshop.
Full versions of selected papers may later on be invited for an archival
journal special issue dedicated to FBTC 2010.

PROGRAM COMMITTEE:

Marco Antoniotti (University of Milan Bicocca, IT)
Chiara Bodei (University of Pisa, IT)
Luca Bortolussi (University of Trieste, IT)
Luca Cardelli (Microsoft Research Cambridge, UK)
Erik de Vink (Technische Universiteit Eindhoven, NL)
François Fages (INRIA Paris-Rocquencourt, F)
Anthony Finkelstein (University College London, UK)
Radu Grosu (Stony Brook University, US)
Jane Hillston (University of Edinburgh, UK)
Anna Ingólfsdóttir (Reykjavik University, IS)
Emanuela Merelli (University of Camerino, IT) (Co-chair)
Paola Quaglia (CoSBi and Trento University, IT) (Co-chair)
Carolyn Talcott (SRI International, US)
Adelinde Uhrmacher (University of Rostock, DE)
Cristian Versari (University of Bologna, IT)

INVITED SPEAKER:

Alberto Policriti (University of Udine, IT)

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