Welcome to the ISCB Community News Blog

This blog collects news, announcements or other information which could be of interest to our ISCB members. We are a group ISCB members who volunteer to populate this blog on a regular basis. In case you want to become an "ISCB-News Reporter" yourself, let us know: contact ISCB
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Monday, December 27, 2010

FASEB Excellence in Science Award Call for Nominations

FASEB is seeking nominations for its 2012 Excellence in Science Award, that recognizes the significant accomplishments of women scientists. We look forward to another list of nominees that reads like a 'Who's Who' of international science, containing the names of outstanding women in science who have accomplished scientific work of lasting impact and have contributed substantially to training the next generation of scientists. The 2012 season for the FASEB Excellence in Science Award will begin January 1, 2011.

Nominations must be submitted on the FASEB award website by March 1, 2011.
URL: http://www.faseb.org/What-We-Do/Awards/Excellence-in-Science-Award.aspx

Contact Person: Linda Stricker (lstricker@faseb.org)

Friday, December 17, 2010

Introducing SWIFT MODELLER: A Java Based GUI for Molecular Modelling

Dear Colleagues,
We are very happy to inform you that we have developed a new GUI for molecular modelling.Now this is online on Modeller\'s website http://salilab.org/modeller/wiki/Links with the link swift modeller. This is freely available to all.

MODELLER is command line argument based software which requires tedious formatting of inputs and writing of Python scripts which most people are not comfortable with. The visualization of output becomes cumbersome due to verbose files. This makes the whole software protocol very complex and requires extensive study of MODELLER manuals and tutorials. Here we describe SWIFT MODELLER, a GUI that automates formatting, scripting and data extraction processes and presents it in an interactive way making MODELLER much easier to use than before.

The screens in SWIFT MODELLER are designed keeping homology modeling in mind and their flow is a depiction of its steps. It eliminates the formatting of inputs, scripting processes and analysis of verbose output files through automation and makes pasting of the target sequence as the only prerequisite. It lowers the skill level required for the software through automation of many of the steps in the original software protocol, thus saving an enormous amount of time per instance and making MODELLER very easy to work with

It would be great for me if you evaluate this tool and send the feedback, so that we can further improve this GUI.
I am waiting for the suggestions, as these are very important for us.

Thanks and Regards,
Shankaracharya
URL: http://www.bitmesra.ac.in/swift-modeller/swift.htm

Contact Person: Shankaracharya, Abhinav Mathur and Dr. A. S. Vidyarthi (shankaracharya@bitmesra.ac.in)

Thursday, December 16, 2010

Recent Science Policy News for ISCB

This page was initially set up to allow our ISCB representatives to FASEB share information with interested ISCB members on matters of science policy.
URL: http://docs.google.com/Doc?docid=0AQZYSgQ_82j7ZDNmeHhwcV8yMDRnejRic3dkYw&hl=en&authkey=CJP2t_MD

Contact Person: Barbara Bryant (barb.bryant@gmail.com)

Wednesday, December 15, 2010

Joanne Luciano joins Web Science Research group at Rensselaer

Luciano brings expertise in health care and life science research to the Tetherless World Research Constellation

Joanne Sylvia Luciano has joined Rensselaer Polytechnic Institute as research associate professor in the Tetherless World Research Constellation. Luciano's research uses computational modeling and the World Wide Web to improve health care and advance medical discovery.

Luciano is an experienced technology consultant to major hospitals, biotechnology, and pharmaceutical companies. In addition to her nearly 30 years as a consultant, she held a joint appointment with Harvard Medical School and Massachusetts General Hospital for nine years, where she served as a lecturer and research scientist using computational modeling to study human disease.

She joins an interdisciplinary research team within the Tetherless World Research Constellation at Rensselaer, dedicated to advancing science and society through understanding and utilization of the World Wide Web.

"There's a vast amount of medically relevant data sitting in databases or websites and not being utilized," Luciano said. "The focus of my research is to create technologies that make it easy to do medical research whether you are a doctor, patient, pharmaceutical company, or searching for alternative therapies or lifestyle changes."

To accomplish these aims, Luciano utilizes ontologies and advanced mathematical modeling and computer simulation to understand illness, share medical data, and advance medical discovery and patient care. She builds computer-based technologies that improve healthcare by translating discoveries made at the laboratory or computer bench to the care received at an individual patient's bedside – known as bench to bedside care.

"There is an urgent need to shorten the time it takes to bring basic life science research results to clinical practice, and to get the clinical observations back to the research lab for further analysis," she said. "To do this, technologies need to be in place that allow scientists to better represent, reuse, and communicate medical data."

Luciano has helped develop several important ontologies including BioPAX, which is an international standard used for data related to cellular processes. BioPAX enables data to be combined in ways that were not possible before, making it possible to ask and answer complex biological questions. The language enables data to be combined automatically by computers, and because the representations are true to the current understanding of biology, other technology can be used to make inferences and reason over the data.

At the MITRE Corporation, she developed InfluenzO, an ontology to support influenza research, surveillance, and outbreak monitoring. She continues to lead this collaboration with the University of Maryland, the University of Texas Southwestern Medical Center, and the Canadian government.

She helped create the World Wide Web Consortium (W3C) Health Care and Life Sciences (HCLSIG) special interest group. The HCLSIG integrates the efforts of pharmaceutical and clinical researchers, doctors, and technologists to build the next generation of medical Web-based technology standards.

She is also a co-organizer of the BioPathways Consortium (BPC), a group of scientists working to support scientific advancement in the area of biological pathways. Such research, which has been a foundation of Luciano's career, uses computation to understand cell development, genetics, drug development, and disease.

In addition to ontologies, Luciano also utilizes mathematical modeling to study the dynamics of medical treatment response, looking for patterns that will help clinicians make more informed treatment choices. Patterns of treatment response often exist in groups of individuals. This study of treatment response patterns leads to so-called "personalized medicine" in which individual response to treatment can be modeled effectively and is important because individuals may respond differently to a treatment. She began this research at McLean Hospital while at Boston University, where she earned her doctorate. The work began as a study of different treatments (drug and therapy) for major depressive disorder (MDD).

That research led to the development of patented methods to select the best treatment for individual patients and predict the expected recovery patterns of treatments.

Luciano holds bachelor's and master's degrees in computer science and a doctorate incognitive and neural systems from Boston University.

About the Tetherless World Research Constellation

The Tetherless World Research Constellation at Rensselaer Polytechnic Institute (RPI) explores the research and engineering principles that underlie the Web, to enhance the Web's reach beyond the desktop and laptop computer, and develop new technologies and languages that expand the capabilities of the Web under three themes: Future Web, Informatics, and Semantic Foundations.

The goals of the constellation include making the next-generation Web natural to use while being responsive to the growing variety of policy, educational, societal, and scientific needs. Research areas include: Web science, privacy, intellectual property, general compliance, Web-based medical and health systems, semantic eScience, data-science, semantic data frameworks, next-generation virtual observatories, semantic data and knowledge integration, ontologies, semantic rules and queries, semantic applications, data and information visualization, and knowledge provenance, trust, and explanation for science.

The faculty, staff, and students (graduate and undergraduate) use powerful scientific and mathematical techniques from many disciplines to explore the modeling of the next-generation Web from network-, data-, and information-centric views.

Published November 23, 2010 Contact: Gabrielle DeMarco
Phone: (518) 276-6542
E-mail: demarg@rpi.edu
URL: http://news.rpi.edu/update.do?artcenterkey=2796

Contact Person: Gabrielle May DeMarco (demarg@rpi.edu)

Wednesday, December 8, 2010

Bioinformatics Books Collection

Bioinformatics students, researchers and professionals may be interested in an online collection of scientific books that includes a growing number of titles related to the bioinformatics field.

The books are published by InTech, Open Access publisher of books and journals in science, technology and medicine, and are available on the reading platform www.intechopen.com. The full texts are absolutely free to read online, download in PDF format and share. No registration is required on the site.

The whole collection includes more than 270 books, and 30 new titles are due to come online by Christmas 2010. Books which may be of interest to the bioinformatics community include:

- Data Mining in Medical and Biological Research;
- Bioinspiration;
- Intelligent and Biosensors;
- Finite Element Analysis;
- Stochastic Control, and new on 8 Debember 2010:
- Data Acquisition.

You are most welcome to visit, bookmark and spread the word to your friends and colleagues who you feel may also enjoy the publications.


InTech – Open Access Publishers in Science, Technology and Medicine
Reading platform: www.intechopen.com
Corporate site: www.intechweb.org
URL: http://www.intechweb.org

Contact Person: Nataly Anderson (anderson@intechweb.org)

Wednesday, October 6, 2010

Sao Paulo School of Advanced Science Advanced Topics in Human Molecular Genetics-with associated practical course in Structural Computational Biology

São Paulo School of Advanced Science


Advanced Topics in Human Molecular Genetics (with associated practical course in Structural Computational Biology)

Universidade Estadual de Campinas
UNICAMP
Campinas – São Paulo - Brazil

From February 28th to March 4th , 2011

The main purpose of the course is to provide an update on recent research in genetic diseases involving a number of different areas of knowledge, such as genomics, cancer research, hemoglobinopathies, neurosciences, amongst others. In addition, the course will report on the development and application of new tools applied in molecular biology, encouraging the expansion of collaborative research projects among Brazilian and foreign scientists.
Professors invited to participate in offering the courses are scientists with excellent qualifications and prominence in their fields of research, including foreign scientists. Among the teachers are important names in the field of Medical Genetics that focus their research on clinical and laboratory areas, covering key issues for students in the biological and medical sciences.
Selection of students participating:
60 positions will be offered for medical doctors and graduate students in Genetic or Biomedical Sciences. Half of these positions (30) are reserved for applicants from abroad. The other half will be distributed among applicants from the São Paulo metropolitan area (15 positions) and students from other Brazilian States (15 positions).

Note: For approved participants, the organization will cover all costs with return
fares from the candidate's place of residence to São Paulo, in addition to accommodation in double apartments plus meals during the event.
URL: http://www.spschool.com.br

Contact Person: Professor Edi Lúcia Sartorato (spschool@cbmeg.unicamp.br)

Wednesday, September 29, 2010

New Healthcare Associated Infection Community

Join the community of healthcare professionals concerned with preventing Healthcare-Associated Infections (HAIs), which at any given moment seriously affect 1.4 million hospitalized patients worldwide. The HAI WATCHDOG forums are intended to provide a place for health care providers to discuss issues and best practices related to Hospital-Associated Infections (HAIs).

Kimberly-Clark is committed to helping win the battle to prevent HAIs. As part of that effort, we are pleased to sponsor this new community site for healthcare providers to discuss HAI without discussion of product-specific information.

Additionally, Kimberly-Clark has created the HAI WATCHDOG Awards in recognition of Healthcare-Associated Infection champions who are making a difference for the reduction and prevention of these infections.
URL: http://haiwatchdog.com

Contact Person: Barbara Dunn (barbara@haiwatchnews.com)

Tuesday, August 31, 2010

EMBO Global Exchange Lecture Course: Bioinformatics and Comparative Genome Analysis (Institut Pasteur Tunis, Tunisia)

Announcement and Call for Application to the EMBO Global Exchange Lecture Course on Bioinformatics and Comparative Genome Analysis ( http://cwp.embo.org/glc10-14/) that will take place in the Institut Pasteur Tunis, Tunisia, December 13-18, 2010. The course is co-sponsored by the Institut Pasteur International Network.

The main objective of this intensive course is to strengthen capacities of Phd students and young scientists from African countries, in Bioinformatics and large-scale genome data analyses skills.

The course will focus on reviews on advanced fundamental algorithms and methods used in Bioinformatics and their applications in genome studies (no practical sessions will be included in this course).

The topics that will be included in the course programme are similar to those included in previously organized courses: http://www.pasteur.fr/~tekaia/BGA_courses.html

The course is aimed at motivated Post-Graduate and Ph.D students in African Academic Institutions, with background in Mathematics, Statistics, Biology or Computer Science and who are involved in Bioinformatics and Genomes studies.

Participants selection will be based on an evaluation process involving an accepted Poster presentation (see Application form).

Detailed information are available on the course web site: http://cwp.embo.org/glc10-14/

Candidates are advised to read the indicated informations, then to complete carefully the application form, together with a one-page CV, a Poster abstract and a personal Identity Picture (Photo).

The deadline application is October 30, 2010.

The organizers:
Balkiss Bouhaouala-Zahar (Institut Pasteur Tunis, Tunisia)
Ahmed Rebai (CBS, Tunisia)
Fredj Tekaia (Institut Pasteur Paris, France)
URL: http://cwp.embo.org/glc10-14/

Contact Person: Fredj Tekaia (tekaia@pasteur.fr)

Tuesday, August 17, 2010

Evolution may have pushed humans toward greater risk for type-1 diabetes, study shows

Gene variants associated with an increased risk for type-1 diabetes and rheumatoid arthritis may confer previously unknown benefits to their human carriers, say researchers at the Stanford University School of Medicine. As a result, the human race may have been evolving in the recent past to be more susceptible, rather than less, to some complex diseases, they conclude.
URL: http://med.stanford.edu/ism/2010/august/selection.html

Contact Person: Krista Conger (kristac@stanford.edu)

Critical Assessment of Function Annotations

When: 15-SEP-2010 through 15-JAN-2011
What: Critical Assessment of Function Annotations
Why: Because we need to assess computational gene and protein function prediction programs
More: http://biofunctionprediction.org

Sequence and structure genomics have generated a wealth of data. However, extracting meaningful information from genomic data is becoming increasingly difficult. Both the number and the diversity of discovered genes is increasing. This increase means that established annotation methods, such as homology transfer, are annotating less data. In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software which is out there. We probably know the sequence of the target for next generation antibiotics or cancer treatment. We just did not recognize that target for what it is: it is currently annotated as a "domain of unknown function".
The mission of the Automated Function Prediction Special Interest Group (AFP-SIG) is to bring together computational biologists who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations.
About the CAFA experiment
The problem: There are far too many proteins in the database for which the sequence is known, but the function is not. The gap between what we know and what we do not know is growing. A major challenge in the field of bioinformatics is to predict the function of a protein from its sequence or structure. At the same time, how can we judge how well these function prediction algorithms are preforming?
The solution: The Critical Assessment of protein Function Annotation algorithms (CAFA) is an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein function. We will evaluate methods in predicting the Gene Ontology (GO) terms in the categories of Molecular Function and Biological Process. A set of protein sequences is provided by the organizers. Participants are expected to submit their predictions by the submission deadline. The predictions will be evaluated during the Automated Function Prediction (AFP) meeting, which has been approved as a Special Interest Group (SIG) meeting, at ISMB 2011 conference (Vienna, Austria).
How to participate in CAFA?
1.Register for the experiment at http://biofunctionprediction.org
2.(Recommended) Subscribe to the low-traffic announcement list http://groups.google.com/group/afp2011-announce
3.Download target proteins, available September 15, 2010
4.Submit predictions before January 15, 2011
5.Join us at the AFP-SIG at Vienna July 15-16 for the fifth protein function prediction meeting, and to hear the CAFA results, and about the latest research in computational protein function prediction
More details at: http://biofunctionprediction.org
URL: http://biofunctionprediction.org

Contact Person: Iddo Friedberg (idoerg@gmail.com)

NIH Demystifying Medicine

A DVD has been prepared by NIH/FAES of the 2009-2010 Series of presentations for the Course on "Demystifying Medicine for PhD Students, Fellows and Investigators". This successful Course bridges basic science and medicine by combining patient presentations and state of the art talks by leading clinical and basic science investigators. The topics include a wide range of diseases and research disciplines. The DVD is available on request (email) to basap@faes.od.nih.gov as long as the supply lasts. http://videocast.nih.gov/pastevents.asp?c=45
URL: http://videocast.nih.gov/pastevents.asp?c=45

Contact Person: Support (basap@faes.od.nig.gov)

Monday, August 2, 2010

Burroughs Wellcome Fund Career Awards at the Scientific Interface

Career Awards at the Scientific Interface Advancing the careers of physical, chemical or computational science researchers and engineers whose work addresses biological questions.

Preproposal Deadline: September 1, 2010

BWF's Career Awards at the Scientific Interface provide $500,000 to bridge advanced postdoctoral training and the first three years of faculty service. These awards are intended to foster the early career development of researchers with backgrounds in the physical/mathematical/computational sciences and engineers whose work addresses biological questions.

These awards are open to U.S. and Canadian citizens or permanent residents as well as to U.S. temporary residents.

In previous years, candidates for this award had to be nominated by a North American degree-granting institution. This year, eligible candidates for this award may self-nominate by submitting a preproposal by September 1, 2010.

Preproposals will be reviewed by the Interfaces in Science Advisory Committee and selected candidates will be invited to submit a full application. Full invited applications must be submitted by January 12, 2011.

For full grant details, see www.bwfund.org
URL: http://www.bwfund.org/

Contact Person: Russ Campbell (rcampbell@bwfund.org)

Friday, July 9, 2010

Free Online Access to special issue of Journal of Biomedical Informatics on Translational Bioinformatics

Since July 2009, the Journal of Biomedical Informatics (JBI) has changed its editorial policy to focus its publication of bioinformatics articles on the growing area of translational bioinformatics (see JBI editorial 2009;42(2):199-200). JBI publishes articles that introduce new methodologies and techniques that form the basis for the evolving science of biomedical informatics. While such methods often have broad generalizability, their development is typically motivated by specific applications in one of the four principal subfields of biomedical informatics (clinical informatics, public health informatics, imaging informatics, or bioinformatics). It is in the latter category that JBI has now chosen to focus specifically on articles that deal with bioinformatics innovations that are related to solving problems in human disease – its diagnosis, prognosis, prevention, and treatment. We return without review bioinformatics articles that are not translational and ask their authors to consider submitting their paper to another, more appropriate journal.

The move to translational bioinformatics (TBI) arose in part from the success and appeal of the Summit on Translational Bioinformatics that has been held each March since 2008 in San Francisco, California. The meeting, organized by the American Medical Informatics Association (AMIA) with affiliated sponsorship by the International Society for Computational Biology (ISCB), has published a well received Proceedings with top papers referred for journal publication. In honor of JBI's new emphasis on TBI, the 2009 Program Chair, Dr. Yves Lussier (University of Chicago) has served as guest editor of a special issue of JBI, composed in part of expanded papers from that year's meeting. He has been assisted by Dr. Atul Butte (Stanford University) and Dr. Lawrence Hunter (University of Colorado).

The TBI special issue has just appeared as the May-June issue in 2010 (see JBI 2010;43(3):355-357). In honor of ISMB this year, some sample copies have been made available at the Elsevier booth. In addition, JBI has arranged to provide open access to this special issue for a period of two months following the meeting (until September 15th). We invite ISMB attendees to visit the JBI site on Science Direct at:

www.tinyurl.com/JBIonScienceDirect

or go directly to the special issue at:

www.tinyurl.com/JBI-TBI-special-issue

Please familiarize yourself with JBI and consider submitting your best methodological work for possible publication in its pages.

Ted Shortliffe, Editor-in-Chief, JBI

URL: http://www.tinyurl.com/JBI-TBI-special-issue

Contact Person: Vijala Kiruvanayagam (v.kiruvanayagam@elsevier.com)

Thursday, June 10, 2010

Rare genetic variants linked to autism

The search for the genetic underpinnings of autism spectrum disorder has just yielded a new set of clues. In the largest study to date, the Autism Genome Project consortium reports that people with autism have more copy number variants – segments of DNA that have been either duplicated or deleted – in their genes.

The results, published today in Nature, could eventually be used to develop quick diagnostic tests. The consortium was also able to group some of the affected genes into biochemical pathways. These pathways – some of which are clearly linked to brain function -- may then become attractive targets for those who hope to develop drugs to treat the condition

Read more...


Tuesday, June 8, 2010

And man made life

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

We report the design, synthesis, and assembly of the 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.

Published in ScienceXpress, May 20th

Some more:

Sunday, May 30, 2010

U of T researchers crack the splicing code

The coding capacity of the vertebrate genome is greatly expanded by alternative splicing, which enables a single gene to produce more than one distinct protein. Alternative splicing shapes how genetic information controls cellular processes, and many human disease mutations affect splicing. The ability to predict expression of different alternatively spliced messenger RNAs from genomic sequence data is a long-sought goal in the field of gene expression. The Frey and Blencowe labs at the University of Toronto have combined forces to develop a 'splicing code' that accurately predicts how hundreds of RNA features work together to regulate tissue-dependent alternative splicing for thousands of exons. It has been used to predict how alternative splicing may play important roles in development and neurological processes, and has provided insights into mechanisms of splicing regulation. The code has also been incorporated into a web tool that allows researchers to scan uncharacterized exon and intron sequences to predict tissue-dependent splicing patterns.

Source: Nature Editor's Summary

Read more:

Wednesday, May 19, 2010

LifeDB Autonomous Data Integration System Trial Release


Announcement
LifeDB Autonomous Data Integration System Trial Release

It is with great excitement and anticipation that we
announce the release of LifeDB Autonomous Data Integration
system [1] for Life Sciences data management and workflow
querying. LifeDB has its own SQL-like query language
called BioFlow [2, 3] using which, most arbitrary
online deep web resources and tools can be used to develop
applications completely dynamically and on an ad hoc basis.
The goal in LifeDB is to allow application development by
end users using SQL-like declarative query language without
having to worry about schema heterogeneity and geographical
distribution of resources. LifeDB relies on two basic fully
autonomous sub-systems: FastWrap [4, 5] for wrapper
generation and table annotation, and OntoMatch [6] for
schema mapping. BioFlow supports horizontal and vertical
integration and autonomous record linkage through entity
identification and resolution. It is based on an extended
parameterized relational algebra called Integra [7] that is
capable of blurring the distinctions between web documents
and traditional SQL tables by uniformly treating both as
relations.

To support end user application development, we have also
developed a visual application development system called
VizBuilder [8] that allows writing BioFlow applications
visually without any knowledge of BioFlow. In our current
LifeDB release, VizBuilder is included as an alternate
interface.

Currently, LifeDB is in a trial phase while it undergoes
internal validation. We believe LifeDB is performing within
its design parameters. We invite interested researchers in
Databases and Life Sciences to register for LifeDB as end
users. Registered users will be able to either download
LifeDB binary for local use, or use LifeDB in our server
with limited user data space. Currently, our goal is to
compile bug reports, if any, and fix the currently unknown
bugs before its final release. Full information on LifeDB
can be found at http://integra.cs.wayne.edu:8080/lifedb.

Our laboratory is fully committed to supporting registered
users and their applications on a long term basis on our
Wayne State Server. Registered users will have their own
data space in our server to store their data, applications
and other resources. For high-end users, we will also
consider offering dedicated processors to support computation
intensive applications, resource permitting. We are
considering a novel resource sharing model and it will be
announced when we finalize our plan and acquire the needed
resource. LifeDB will be an open source system for the
community, following the release of its final version. We
are now compiling user requests for data space over the
next 3-6 months based on which we plan to acquire the needed
hardware to support our users. A request for needed space
(and dedicated processor, subject to agreement) may be made
through an e-mail to the PI at jamil@cs.wayne.edu. Please use
subject heading "LifeDB Resource Request."

Publications related to LifeDB and other projects can be found
at our Integration Informatics Lab home page at
http://integra.cs.wayne.edu. A comprehensive LifeDB user manual
is also available for end users. The user manual will include
test examples and design parameters under which LifeDB is
designed and expected to function well.

LifeDB has been funded in part by National Science Foundation
grants SEIII IIS 0612203 and MRI CNS 0521454.

References:

[1] Anupam Bhattacharjee, Aminul Islam, Mohammad Shafkat Amin,
Shahriyar Hossain, Shazzad Hosain, Hasan Jamil and Leonard Lipovich,
"On-the-fly Integration and ad hoc Querying of Life Sciences
Databases using LifeDB", 20th Database and Expert Systems
Applications, Linz, Austria, August 2009.

[2] Hasan Jamil, Bilal El-Hajj-Diab, "BioFlow: A Web-based
Declarative Workflow Language for Life Sciences", IEEE International
Workshop on Scientific Workflows, Hawaii, United States, July 2008.

[3] Hasan Jamil, Aminul Islam, "The Power of Declarative
Languages: A Comparative Exposition of Scientific Workflow Design
using BioFlow and Taverna", IEEE SCC International Workshop on
Scientific Workflows, Los Angeles, California, July 2009.

[4] Mohammad Shafkat Amin, Hasan Jamil, "FastWrap: An Efficient
Wrapper for Tabular Data Extraction from the Web", IEEE
International Conference on Information Reuse and Integration,
Las Vegas, Nevada, United States, August 2009.

[5] Mohammad Shafkat Amin, Anupam Bhattacharjee, Hasan Jamil,
"Wikipedia Driven Autonomous Label Assignment in Wrapper Induced
Tables with Missing Column Names", ACM International Symposium on
Applied Computing, Sierre, Switzerland, March 2010.

[6] Anupam Bhattacharjee, Hasan Jamil, "OntoMatch: A Monotonically
Improving Schema Matching System for Autonomous Data Integration",
IEEE International Conference on Information Reuse and Integration,
Las Vegas, Nevada, United States, August 2009.

[7] Shazzad Hosain, Hasan Jamil, "An Algebraic Language for Semantic
Data Integration on the Hidden Web", IEEE International Conference
on Semantic Computing, Berkeley, California, United States,
September 2009.

[8] Shahriyar Hosain, Hasan Jamil, "A Visual Interface for
on-the-fly Biological Database Integration and Workflow Design
using VizBuilder", International Workshop on Data Integration in
Life Sciences (DILS), Manchester, United Kingdom, July 2009.
URL: http://integra.cs.wayne.edu

Contact Person: Hasan Jamil (jamil@cs.wayne.edu)

Monday, May 10, 2010

ISCB Member Feedback Sought on (Draft) Literature Open Public Access Policy Statement

International Society for Computational Biology
ISCB (Draft) Literature Open Public Access Policy Statement
Draft approved by the ISCB board of Directors on April 8, 2010

Open for comment from the ISCB membership
and bioinformatics community

Comment period closes June 11, 2010


Preamble.
The International Society for Computational Biology (ISCB) is dedicated to advancing human knowledge at the intersection of computation and life sciences. This (draft) ISCB policy statement is intended to express strong support for open public access to the archival scientific and technical literature and to elucidate in more nuanced detail the position of ISCB on this important issue in scientific publication.

An official ISCB policy statement on the closely related topic of sharing software provides very clear support for Open Source/Open Access (http://www.iscb.org/iscb-policy-statements-/187). ISCB supports many of the principles of the “Budapest Open Access Initiative,” the “Bethesda Declaration on Open Access Publishing,” the U.S. National Academies of Sciences report on "Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences," and the European “Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities.”


Introduction.
Knowledge is the fruit of the scientific research endeavor, and the archival scientific literature is its practical expression and means of communication. Shared knowledge multiplies its utility because every new scientific discovery is built upon previous scientific knowledge. Access to knowledge is the power to solve new problems and make informed decisions. More open public access to archival scientific and technical knowledge will empower more citizens and more scientists to solve more problems and make more informed decisions.


Recommendations
.
    1. There should be free, open, online, public access to research results in the archival scientific and technical literature, with all their existing content including supplementary material and data. This access may be at an interval following publication, which interval should not exceed one year.

    2. Existing models show high impact, scientific benefit, feasibility, and acceptability:

      a. The public benefit from open access to the world’s online information via the publicly-funded Internet provides a good model of expected impact.

      b. The scientific fertilization from open access to genomic information via the publicly-funded Human Genome Project provides a good model of expected scientific benefit.

      c. Open access policies by the U.S. National Institutes of Health, the Howard Hughes Medical Institute, and the Wellcome Trust provide good models of feasibility, acceptability, and implementation.

    3. Open literature access will enable a whole new generation of innovative tools and mechanisms that will endow the literature with enriched commentary and usability and connect the literature and databases via the proper pointers. These tools are already being built by publishers, researchers, and others. The creation of the web of knowledge around publications is an important consequence of semantic enrichment of the literature.

    4. Whether publications are immediately available or delayed, the underlying data and methods must be publicly available in sufficient detail to allow replication of the results and application of other computational methods to the data.

    5. Policy details — which version, where stored, how annotated and organized, what incentives — must be considered carefully. However, it has become essential to put forward a broad policy mandate for eventual public access to research knowledge.

    6. Publishing high-quality peer-reviewed scientific literature incurs costs. We recognize that cost recovery is a serious issue that must be addressed carefully if open access is to be a mandated policy.

    7. The funding policy must:

      a. Fund activities of peer review, copy editing, and publishing.

      b. Provide fair compensation, if and where needed, to facilitate transitions and adaptations to new models for publishing and sustaining essential revenue.

      c. Be consistent with government laws, other existing regulations, and research dissemination through viable commercial mechanisms.

    8. It is undesirable to take funding from current research and thereby risk underfunding basic science, so new funding should be made available for policy implementation. However, the expected total cost for complete open literature access is only a very small percentage of the total cost for the entire international research endeavor.
Conclusion.
Scientific literature represents a substantial investment by governments, foundations, and others. One of our primary missions is the assembly of individual pieces of knowledge from this literature in ways that provide powerful new insights and ideas for next-stage research by the entire scientific community and society in general. We in the ISCB are committed to the continuous enhancement and leveraging of mankind’s knowledge resources. To achieve this goal, investment in open public access to the research literature must be made.


ISCB (Draft) Literature Open Public Access --- Appendix

A. Documents mentioned in the statement text.
1. Text of the “Budapest Open Access Initiative.”
http://www.soros.org/openaccess/read.shtml
http://en.wikipedia.org/wiki/Budapest_Open_Access_Initiative

2. Text of the “Bethesda Declaration on Open Access Publishing.”
http://www.earlham.edu/~peters/fos/bethesda.htm

3. Text of the U.S. National Academies of Sciences report on "Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences."
http://www.nap.edu/openbook.php?isbn=0309088593
http://www.nap.edu/catalog.php?record_id=10613

4. Text of the “Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities.”
http://oa.mpg.de/openaccess-berlin/berlindeclaration.html
http://en.wikipedia.org/wiki/Berlin_Declaration_on_Open_Access_to_Knowledge_in_the_Sciences_and_Humanities

5. Text of Open Access Policy from the U.S. National Institutes of Health.
http://publicaccess.nih.gov/policy.htm
http://publicaccess.nih.gov/

6. Text of Open Access Policy from the Howard Hughes Medical Institute.
http://www.hhmi.org/about/research/sc320.pdf
http://www.hhmi.org/about/research/QA_papp.pdf

7. Text of the Wellcome Trust's "Position Statement in Support of Open and Unrestricted Access to Published Research."
http://www.wellcome.ac.uk/About-us/Policy/Spotlight-issues/Open-access/Policy/index.htm

B. General Background Material.
1. Academic publishing - Wikipedia, the free encyclopedia.
http://en.wikipedia.org/wiki/Academic_publishing

2. Open access (publishing) - Wikipedia, the free encyclopedia.
http://en.wikipedia.org/wiki/Open_access_(publishing)
http://en.wikipedia.org/wiki/Open_access_%28publishing%29

3. ROARMAP (Registry of Open Access Repository Material Archiving Policies) as recommended by the Berlin Declaration.
http://www.eprints.org/openaccess/policysignup/

C. Other Statements and Materials.
1. Text of Public Library of Science "Open Letter to Scientific Publishers" (signed by ~34,000 scholars worldwide).
http://www.plos.org/about/letter.php

2. Text of Research Councils of the UK "Access to Research Outputs."
http://www.rcuk.ac.uk/cmsweb/downloads/rcuk/documents/2006statement.pdf
http://www.rcuk.ac.uk/cmsweb/downloads/rcuk/news/oareport.pdf
http://www.rcuk.ac.uk/research/outputs/access/default.htm

3. Text of European Research Advisory Board Final Report "Scientific Publication: Policy On Open Access."
http://ec.europa.eu/research/eurab/pdf/eurab_scipub_report_recomm_dec06_en.pdf

4. Text of Bulletin of the World Health Organization "Equitable access to scientific and technical information for health."
http://www.scielosp.org/scielo.php?script=sci_arttext&pid=S0042-96862003001000003

5. UNESCO EBSCO Open Science Directory.
http://www.opensciencedirectory.net/

6. Peter Suber's "Open Access Overview."
http://www.earlham.edu/~peters/fos/overview.htm
http://www.earlham.edu/~peters/fos/brief.htm








Sunday, May 2, 2010

Clinical assessment incorporating a personal genome

Clinical assessment incorporating a personal genome



In a Lancet paper Ashley et.al. undertook "an integrated analysis of a complete human genome in a clinical context." The interpretation of the results: "Although challenges remain, our results suggest that whole-genome sequencing can yield useful and clinically relevant information for individual patients."

Tuesday, March 30, 2010

Of guerillas and cafés

Here are a few citations from an EMBO report discussing how scientists are experimenting with new initiatives to talk to the people.

"We want people to engage with other real people who just happen to be scientists"

"The café idea is spreading from its grassroots origins to science festivals and even scientific meetings"

"We're trying to make science part of culture"

Read more...

Thursday, March 18, 2010

Call for Chapters: Depth Map and 3 D Imaging Applications:Algorithms and Technologies

CALL FOR CHAPTER PROPOSALS

Proposal Submission Deadline: April 15, 2010

Depth Map and 3 D Imaging Applications: Algorithms and Technologies

A book edited by Aamir Saeed Malik, Tae‐Sun Choi and Humaira Nisar

Universiti Teknologi Petronas (Malaysia), and Gwangju Institute of Science & Technology (Korea)
To be published by IGI Global: http://www.igi-global.com/requests/details.asp?ID=846


Introduction

With the advent of few 3D consumer electronics products in 2009, the importance of three dimensional(3D) imaging technology has increased significantly. 3D imaging systems offer a richer experience for the consumers and they are expected to replace the traditional systems. In 2010, the leading consumer electronics manufacturers are introducing 3D TVs, 3D cameras, 3D printers and 3D computers. Some of them are Panasonic, Samsung, LG, Sony, Olympus, Canon, JVC, Sharp, Hitachi,HP and Acer. Their technology is currently based on stereoscopic vision and displays. However, as the 3D technology matures over time, autoseteroscopic vision and displays will replace the
stereoscopic technology. It can rightly be said that the next decade is the decade for 3D imaging technology.

Objectives of the Book

This book will aim to provide the relevant theoretical frameworks and the latest esearch findings in 3D imaging. It will cover algorithms and technologies for 3D Imaging as well as discuss their various applications. It will provide the current status of the technologies and will discuss the future trends too.

Target Audience

This book will be an important resource and reference for professionals, scientists, researchers,academics and software engineers in image/video processing and computer vision. It is a multidisciplinary field, so in addition to electrical and electronics engineering, it will also be of interest to those involved in material science, robotics, astronomy, terrain mapping, mechanical engineering and medical sciences. It will be a potential resource for post graduate and senior undergraduate students too.

Recommended topics include, but are not limited to, the following:

• 3D Capture: 3D ‐visual scene capture, multi‐view and multi‐sensor image capture, calibration and synchronization of multiple cameras, stereoscopic capture, and holographic capture.
• 3D Processing: 3D ‐visual scene reconstruction techniques for static and dynamic scenes, 3D data processing, 3D tracking, depth estimation and view synthesis from multi‐view images/videos, and compact representation and compression of multi‐view images/ videos.
• 3D Visualization & Displays: Stereoscopic, auto‐stereoscopic, and holographic display & projectors, 3D projectors, volumetric displays & projectors, head‐mounted 3D displays, 2D‐3D conversion of Images, and 3D representation tools: meshes, points, and voxels.
• 3D Transmission: Source coding, channel coding, transmission, decoding and broadcasting of 3D/ multi‐view images/videos/data, 3D teleimmersion and remote collaboration.
• 3D Applications: 3D television, free viewpoint TV systems, 3D cinema, 3D printing,
educational 3D systems, guidance and advertizing systems, 3D imaging in virtual heritage and virtual archaeology, 3D games, 3D entertainment, 3D virtual studios, augmented reality and virtual environments, medical and biomedical applications, 3D content‐based retrieval and recognition, 3D watermarking, 3D computers and other applications.

Submission Procedure

Researchers and practitioners are invited to submit on or before April 15, 2010, a 2‐3 page chapter proposal clearly explaining the mission and concerns of his or her proposed chapter. Authors of accepted proposals will be notified before May 15, 2010 about the status of their proposals and sent chapter guidelines. Full chapters are expected to be submitted by September 1, 2010. All submitted chapters will be reviewed on a double‐blind review basis.

Publisher

This book is scheduled to be published by IGI Global (formerly Idea Group Inc.), publisher of the "Information Science Reference" (formerly Idea Group Reference), "Medical Information Science
Reference," "Business Science Reference," and "Engineering Science Reference" imprints. For additional information regarding the publisher, please visit www.igi‐global.com. This publication is anticipated to be released in 2011.

Important Dates

April 15, 2010: Proposal Submission Deadline
May 15, 2010: Notification of Acceptance
September 1, 2010: Full Chapter Submission
October 31, 2010: Review Results Returned
November 30, 2010 Revised Chapter Submission
December 15, 2010 Final Acceptance Notification
January 15, 2011 Final Chapter Submission

Editorial Advisory Board Members:

Fabrice Meriaudeau, University of Bourgogne, France
Naeem Azeemi, COMSATS Institute Information Technology, Pakistan
Kishore Pochiraju, Stevens Institute of Technology, USA
Martin Reczko, Biomedical Sciences Research Center \"Alexander Fleming\", Varkiza, Greece
Iftikhar Ahmad, Nokia, Finland
Nidal kamel, Universiti Teknologi Petronas, Malaysia
Umer Zeeshan Ijaz, University of Cambridge, UK
Asifullah Khan, Pakistan Institute of Engineering and Applied Sciences, Pakistan


Inquiries and submissions can be forwarded electronically or by mail to:

Aamir Saeed Malik, Ph.D.
Department of Electrical and Electronics Engineering
Universiti Teknologi Petronas
Tel.: +605‐368‐7853 • Fax: +605‐365‐7443 • GSM: +60‐16‐553‐7853
E‐mail: aamir_saeed@petronas.com.my
URL: http://www.igi-global.com/requests/details.asp?ID=846

Contact Person: Aamir Saeed Malik (aamir_saeed@petronas.com.my)

Tuesday, March 16, 2010

ALFRED P. SLOAN FOUNDATION AWARDS MORE THAN $6 MILLION;118 EARLY CAREER RESEARCHERS TO RECEIVE PRESTIGIOUS SLOAN RESEARCH FELLOWSHIPS


The Alfred P. Sloan Foundation is pleased to announce the selection of 118 outstanding early career scientists, mathematicians, and economists as Alfred P. Sloan Research Fellows. The winners are faculty members at 56 colleges and universities in the United States and Canada who are conducting research at the frontiers of physics, chemistry, computational and evolutionary molecular biology, computer science, economics, mathematics and neuroscience.

"The Sloan Research Fellowships support the work of exceptional young researchers early in their academic careers, and often at pivotal stages in their work," says Paul L. Joskow, President of the Alfred P. Sloan Foundation. "I am proud of the Foundation's rich history in providing the resources and flexibility necessary for young researchers to enhance their scholarship, and I look forward to the future achievements of the 2010 Sloan Research Fellows."

The Sloan Research Fellowships have been awarded since 1955, initially in only three scientific fields: physics, chemistry, and mathematics. Since then, 38 Sloan Research Fellows have gone on to win the Nobel Prize in their fields; 57 have received the National Medal of Science; and 14 have been awarded the Fields Medal, the top honor in mathematics. Although Sloan Research Fellowships in economics began only in 1983, Sloan Fellows have subsequently accounted for 9 of the 14 winners of the John Bates Clark Medal, generally considered the most prestigious honor for young economists.

Grants of $50,000 for a two-year period are administered by each Fellow's institution. Once chosen, Sloan Research Fellows are free to pursue whatever lines of inquiry are of most interest to them, and they are permitted to employ Fellowship funds in a wide variety of ways to further their research aims. For a complete list of winners, visit:

http://www.sloan.org/pressroom/item/458/2010-sloan-research-fellowships.

The Alfred P. Sloan Foundation is a philanthropic, not-for-profit grantmaking institution that supports original research and broad-based education in science, technology, engineering, mathematics and economic performance. For more information visit www.sloan.org.

URL: http://www.sloan.org

Contact Person: Erica Stella (Stella@sloan.org)

Monday, March 15, 2010

The John von Neumann Days and The Genome and the Computational Sciences: The Next Paradigms Symposium at Brown University May 3-7, 2010

Brown University, the Center for Computational Molecular Biology (CCMB), and the Department of Computer Science present the first in the John von Neumann Distinguished Lecture Series and the second in the symposium series "The Genome and the Computational Sciences: The Next Paradigms". This event will bring together influential entrepreneurs, leaders, and visionaries from academia and industry who will build the next paradigms in genomics and biotechnology. Each lecturer will present provocative, critical, and visionary talks on the state of the art in their academic and technological domains, and discuss the emerging paradigm changes made possible by their research and development work. All sessions will feature lively scientific dialogue and rigorous questioning by participants and audience members, including a post-lecture 'sweatbox' question-and-answer session. NSF and RECOMB travel awards are available for graduate students and postdoctoral fellows. Details about the events, which will be held from May 3-7, 2010, can be found at the Symposium webpage or email Lisa Manekofsky at ljm@cs.brown.edu

We look forward to your participation in our Symposium.

Sorin Istrail, Chair of the Symposium



Brown University CCMB Symposium, May 3-7, 2010
Co-organized with the Office of the President
Co-organized with the Department of Computer Science
Supported in part by the National Science Foundation

http://www.brown.edu/Research/CCMB/Conferences/SYMPOSIUMMAY2010/info.htm

John von Neumann Distinguished Lecture Series
organized by Leon Cooper (Physics), Stuart Geman (Applied Mathematics), Sorin Istrail (Computer Science), Roberto Serrano (Economics)

Marina von Neumann Whitman, Professor of Business Administration and Public Policy, University of Michigan

Freeman Dyson, Professor Emeritus of Physics, Institute for Advanced Study, Princeton, NJ

John Conway, John von Neumann Professor of Mathematics, Princeton University

Kenneth Arrow, Nobel Laureate, Joan Kenney Professor of Economics and Professor of Operations Research Emeritus, Stanford University

Richard Karp, University Professor, University of California, Berkeley

David Mumford, University Professor, Department of Applied Mathematics, Brown University

Leon Cooper, Nobel Laureate, Thomas J. Watson Professor of Science and Director, Institute for Brain and Neural Systems, Brown University

George Dyson, historian of science, University of Washington, Seattle


Symposium: The Genome and the Computational Sciences: The Next Paradigms

Eric H. Davidson, Norman Chandler Professor of Cell Biology, California Institute of Technology

Andrew G. Clark, Jacob Gould Schurmn Professor of Population Genetics, Department of Molecular Biology and Genetics, Cornell University

J. Craig Venter, Founder, Chairman and President, J. Craig Venter Institute (not confirmed)

Ellen V. Rothenberg, Albert Billings Ruddock Professor of Biology, California Institute of Technology

Richard Lewontin, Alexander Agassiz Research Professor, Museum of Comparative Zoology, Harvard University

David Botstein, Anthony B. Evnin Professor of Genomics and Director, Lewis-Sigler Institute, Princeton University

Martin Meier-Schellersheim, Team Leader, Computational Biology Group, National Institute of Allergy and Infectious Diseases, NIH

Sean Eddy, Group Leader, Janelia Farm, Howard Hughes Medical Institute

Martha Bulyk, Associate Professor of Medicine and Pathology (and Health Sciences and Technology), Harvard Medical School

Jonathan W. Yewdell, Chief, Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH

David Shaw, Ph.D., Chief Scientist and Founder, D.E. Shaw Research

Marcus Feldman, Ph.D., Professor of Biology, Stanford University

Sam Broder, Chief Medical Officer, Celera, Former Director of the National Cancer Institute
URL: http://www.brown.edu/Research/CCMB/Conferences/SYMPOSIUMMAY2010/info.htm

Contact Person: Lisa Manekofsky (ljm@cs.brown.edu)

Sunday, March 14, 2010

InCoB2010 - EasyChair Submission site now open

International Conference in Bioinformatics (InCoB) 2010,
Tokyo 26-28 September 2010

The Ninth International Conference on Bioinformatics, InCoB2010
(incob.apbionet.org or incob10.hgc.jp) will be held at International Conference
Center, Waseda Campus, Waseda University, Tokyo on 26-28 September 2010.

This year, InCoB is organized in collaboration with the International Immunomics
Society (IIMMS) and Chem-Bio Informatics Society (CBI). Day 3 is held in
conjunction with special CBI sessions and the 3rd Conference of Basic and
Clinical Immunogenomics and Immunomics (BCII).

InCoB, the annual conference of the Asia-Pacific Bioinformatics Network
(http://www.apbionet.org) brings together scientists working in bioinformatics
and computational biology, spanning a wide range of underpinning disciplines
including computer science, biology, biotechnology, genomics, proteomics,
transcriptomics, immunomics, mathematics and statistics.

Clyde Hutchison (J. Craig Venter Institute), Hiroaki Kitano (SONY CSL), and
Japan Academy Prize 2008 winner Yoshiyuki Nagai (RIKEN CNRID), have accepted to
present Keynotes at InCoB2010. Please see the website for the latest list of
other distinguished speakers.

We invite you to participate in the following sessions:
1. Full papers for oral presentation and publication in BMC Genomics or BMC
Bioinformatics, Immunome Research, ISPJ Transactions on Bioinformatics or
Bioinformation.
2. Abstracts for (A) Poster Sessions and (B) Technology, Tools, Methodology,
Resource, Database, Software Demonstrations or Posters.
3. Late-breaking abstracts for short oral presentations
4. Tutorial videos for virtual e-learning sessions
5. APBioNet Annual General Meeting
Submissions to InCoB2010 may cover any aspect of bioinformatics, computational
biology, chem-bioinformatics, bioinformatic-related cloud computing,
biocomputing, personalized medicine, environmental genomics (white bio),
synthetic genomes and organisms, metagenomics, pharmacogenomics, and immunomics
conveying a scientific result.

1. FULL PAPERS: SUBMISSION DEADLINE: 15 APRIL 2010 ACCEPTANCE: 31 MAY 2010
InCoB2009 will feature oral presentations shortlisted from full paper
submissions, for selection in: - BMC Genomics (IF 3.93)
http://www.biomedcentral.com/bmcgenomics/ - BMC Bioinformatics (IF 3.78)
http://www.biomedcentral.com/bioinformatics/ - Immunome Research (unofficial IF
5.33) http://www.immunome-research.com/ - ISPJ Transactions on Bioinformatics
http://www.jstage.jst.go.jp/browse/ipsjtbio or - Bioinformation
http://www.bioinformation.net/

ABBioNet was the first Asia-Pacific bioinformatics society to publish full
papers in BMC Bioinformatics and in 2009, also in BMC Genomics. Supplements from
previous conferences are below:
2009: http://www.biomedcentral.com/1471-2164/10?issue=S3 2009:
http://www.biomedcentral.com/1471-2105/10?issue=S15 2008:
http://www.biomedcentral.com/1471-2105/9?issue=S12 2007:
http://www.biomedcentral.com/1471-2105/9?issue=S1 2006:
http://www.biomedcentral.com/1471-2105/7?issue=S5

After rigorous review by the Program Committee, authors will be asked to revise
their manuscripts, prior to acceptance for publication and oral presentation at
InCoB2010, for which at least one author must register.

2. ABSTRACTS SUBMISSION DEADLINE: 07 JUNE 2010 ACCEPTANCE: 30 JUNE 2010
We solicit high-quality research abstracts for (A) Poster Sessions and (B)
Technology, Tool, Methodology, Resource, Database, Software Demonstrations or
Posters.

At least one author of each selected poster/demonstration must register for
InCoB2010. Furthermore, a single registration can cover only oral presentation
and one poster presentation or two poster presentations. Posters are intended to
convey a scientific result and are not meant to be used as advertisements for
commercial software.

3. LATE-BREAKING ABSTRACTS: SUBMISSION DEADLINE: 01 AUGUST 2010 ACCEPTANCE: 10
AUGUST 2010

We invite abstracts on peer-reviewed journal papers that have accepted for
publication or have been will be published on or after July 20, 2010 (please
provide us email acceptance or online version). A small number of short oral or
poster presentations is available and will be allocated at the discretion of
scientific Program Committee. Decision criteria are the impact of the work on
the field, the likelihood that the study would be of interest to the InCoB
audience and the relevance of the research to bioinformatics and application to
molecular and medical sciences.

4. TUTORIAL VIDEOS SUBMISSION DEADLINE: 01 JULY 2010 ACCEPTANCE: 30 JULY 2010

InCoB2010 will feature shortly before and after the conference virtual
e-learning sessions on new and emerging, cutting-edge topics. Authors for
accepted tutorials agree to be available for feedback and potential questions
fielded by e-mail in the period from Sep 20-Oct 19, 2010. For details see
Submissions/Guidelines at conference website. Tutorial providers who wish to
attend InCoB2010 are required to register.

SUBMISSION DETAILS:
All submissions will be via EasyChair at:
http://www.easychair.org/conferences/?conf=incob2010
Please contact Kenta Nakai (knakai -at- ims.u-tokyo.ac.jp) or Christian
Schoenbach (schoen -at- bio.kyutech.ac.jp) for any queries (replace -at- with @).

5. APBioNet Annual General Meeting The AGM of APBioNet will traditionally be
held in InCoB2010 during the lunch break on Sep 27, 2010.

We look forward to your active participation! Please feel free to pass on this
email to colleagues who might be interested in this meeting.

With best wishes,
Shoba Ranganathan President, APBioNet
Kenta Nakai University of Tokyo, PC Co-Chair
Christian Schoenbach, PC Co-Chair Kyushu Institute of Technology

URL: http://incob.apbiobionet.org

Contact Person: Shoba Ranganathan (shoba.ranganathan1@gmail.com)

Saturday, March 6, 2010

Bioinformatics Summer School in Erice (Italy)


SCIENTIFIC BACKGROUND AND COURSE AIMS AND DESCRIPTION
High-throughput technologies in the life-sciences, from sequencing to microarrays, continue to produce exponentially increasing amounts of data and drive the needs and inspiration for new methods in the computational sciences to efficiently manage and mine these data and provide a better understanding of life from the molecular to the population level.

Bioinformatics, computational and systems biology, and the new -omics sciences, from genomics to metabolomics, all attempt to address these needs and better understand carbon-based computing systems, using silicon-based computing systems, with slightly different perspectives and emphases. Their success is intimately related to progress in mathematics and computer science, in particular in the areas of artificial intelligence, statistical machine learning, and optimization, in order to deal with very complex, high-dimensional, and noisy data.

The aim of the School is to introduce and expose the students to some of the contemporary problems and state-of-the-art solutions at the intersection of the life- and computational- sciences. For this purpose, the School is organized into four themes, at approximately four increasing spatial scales: Chemoinformatics, Proteomics, Genomics, and Systems Biology. Each theme will comprise lectures and invited talks, as well ample time for discussion, over a period of one and a half day. Additional minicourses to cover computational methods in machine learning and optimization will be given in the afternoons.

IMPORTANT DATES
• Registrations Opens: September 15, 2009
• Registrations Closes: April 30, 2010
• Notification of acceptance: May 31, 2010

VENUE
Erice is among the oldest cities of Sicily. The town sits on top of the homonymous mount Eryx, 750 m above sea level. It was the religious center of the ancient Elimi tribes, and is famous for its temple where the Phoenicians worshipped Astarte, the equivalent of Aphrodite or Venus for the ancient Greeks or Romans. Throughout its long contentious history, Erice has fallen to the hands of different tribes and empires, each leaving its own palpable mark on the city. Today, Erice is an enchanting wonderfully-preserved medieval town with the most breathtaking views of Sicily.


DIRECTORS
Pierre Baldi (USA)
Søren Brunak (Denmark)
Raffaele Cerulli (Italy)
Roberto Tagliaferri (Italy)

Lecturers
Pierre Baldi (USA)
Søren Brunak (Denmark)
Paolo Frasconi (Italy)
Panos Pardalos (USA)
Gianluca Pollastri (Ireland)
Gunnar Raetsch (Germany)
Burkhard Rost (Germany)
Michal Rozen Zvi (Israel)
Jean-Philippe Vert (France)


Additional Invited Speakers
Elia Biganzoli (Italy)
Piero Fariselli (Italy)
Alfredo Ferro (Italy)
Salvatore Gaglio (Italy)
Irene Kouskoumvekaki (Denmark)



Local Organizing Committee
Monica Gentili (Italy)

URL: http://www.graphalgorithms.it/Erice2010

Contact Person: Pierre Baldi (pfbaldi@ics.uci.edu)

Monday, March 1, 2010

Call for DREAM5 Computational Systems Biology Modeling Challenges and Datasets

The Dialogue for Reverse Engineering Assessments and Methods (DREAM) Project is soliciting proposals for the DREAM5 Challenges. We invite your input on the design of new challenges and the contribution pre-publication data sets to assess the efficacy of the systems biology modeling community. Contact the DREAM organizers through the DREAM Project website (http://wiki.c2b2.columbia.edu/dream/).
URL: http://wiki.c2b2.columbia.edu/dream/

Contact Person: Robert Prill (rjprill@us.ibm.com)

Saturday, January 23, 2010

International Team Develops Yeast Genetic Interaction Map

A University of Toronto-led research team reported today that they have come up with a genome-wide genetic interaction map for the model organism Saccharomyces cerevisiae.

Read more...

Wednesday, January 20, 2010

Nvidia launches Tesla Bio Workbench


The NVIDIA® Tesla™ Bio Workbench enables biophysicists and computational chemists to push the boundaries of biochemical research. It turns a standard PC into a ‘computational laboratory’ capable of running complex bioscience codes, in fields such as drug discovery and DNA sequencing, more than 10-20 times faster through the use of NVIDIA Tesla GPUs. It consists of:

Bioscience applications
This community site for downloading, discussing, and viewing the results of these applications
GPU-based platforms that enable these applications to run at 1/10th the cost of CPU-only computers"



(Via http://www.nvidia.com/object/tesla_bio_workbench.html.)


EMBL-EBI Launches Open Access Drug Discovery Database

Open access drug discovery database launches with half a million compounds


Hinxton and London, 18 January 2010 – ChEMBLdb, a vast online database of information on the properties and activities of drugs and drug-like small molecules and their targets, launches today with information on over half a million compounds. The data lie at the heart of translating information from the human genome into successful new drugs in the clinic.

more.....




(Via EBI Press release.)


Friday, January 8, 2010

ISCB Exemplifies Organisations Supporting Scientific Social Networking

In Bonetta's 2009 Cell article entitled "Should You Be Tweeting?", she explains the benefits---and limitations---of using Twitter as part of a scientist's online persona. Though many of those limitations are solved with the use of FriendFeed, there was no mention of this resource in the Bonetta article. Therefore, following an interesting discussion in some of the FriendFeed Science Groups, a number of people wrote a response, where the usefulness of FriendFeed for scientists was described.

Many FriendFeed scientists contributed, and the three main authors jointly posted the response to the Bonetta article on their blogs. To view this response, please see the jointly-published posts of Björn Brembs (FriendFeed; blog post), Allyson Lister (FriendFeed; blog post) and Daniel Mietchen (FriendFeed; blog post) from 7 January 2009.

What ISCB members and attendees of ISCB conferences and workshops might find most interesting about this response is use of ISMB 2008 and 2009 as examples of how scientific organisations can actively aid scientists in dissemination of conference knowledge through social networking. Through its ISMB conferences (and the co-located conferences such as the ECCB), the ISCB has provided infrastructure, support, and encouragement to scientists wishing to make use of social networking software such as FriendFeed and Twitter during its conferences. For example, the conference organisers integrated the FriendFeed threads from each talk within the ISMB 2009 website, e.g. Keynotes pages from ISMB 2009.

And it's not just the attending scientists who make use of this resource: as can be seen with articles such as the one posted yesterday by Brembs, Lister, Mietchen and other associated FriendFeeders, scientists worldwide have taken note of the good work done by the ISCB and others like it.

Please note that the author of this blog post (Allyson Lister) was both one of the bloggers at ISMB 2009 and one of the co-authors of the January 7 post written in reply to Bonetta. You can find Allyson Lister's main blog at http://themindwobbles.wordpress.com.