From tirza at biomodel.os.biu.ac.il  Tue Mar  1 04:05:14 2011
From: tirza at biomodel.os.biu.ac.il (Tirza Doniger)
Date: Tue, 1 Mar 2011 11:05:14 +0200
Subject: [BiO BB] List of transpliced genes in C. elegans
Message-ID: <AANLkTimhbi1T837ciBKVoeacV=ncoBCmigVdUjK1FbkR@mail.gmail.com>

Hi,

Are there any lists of genes in C. elegans that are transpliced? I tried to
look for one using wormbase/worm mart and I was unsuccessful. I also tried
via modencode and was not able to. Any ideas?


Much thanks,
Tirza Doniger
-- 
Tirza Doniger, Ph.D.
Bioinformatics Unit
The Mina and Everard Faculty of Life Sciences
Bar Ilan University
Phone: +972 3 531 8124
======================


From jprudhomme at healthtech.com  Thu Mar  3 12:14:29 2011
From: jprudhomme at healthtech.com (Jim Prudhomme)
Date: Thu, 3 Mar 2011 12:14:29 -0500
Subject: [BiO BB] Identification of Druggable Sites for Protein-Protein
	Interaction Targets
Message-ID: <03b201cbd9c6$74842380$5d8c6a80$@com>

Cambridge Healthtech Institute & Bio-IT World Announce Upcoming Short
Course: 

Identification of Druggable Sites for Protein-Protein Interaction Targets
June 8, 2011 (6:00 - 9:00 p.m.)

Royal Sonesta Hotel Boston, Cambridge, MA

Register at https://chidb.com/register/2011/sbd/reg.asp

On June 8, 2011, a dinner short course (6:00 - 9:00 p.m.) will take place at
the conclusion of day one of CHI's Eleventh Annual Structure-Based Drug
Design 
conference. Delegates attending CHI's Structure-Based Drug Design conference
are invited to attend, as well as others from the local area.

 

About the course:

Despite the growing number of examples of small molecule inhibitors that
disrupt protein-protein interactions (PPIs), the origin of druggability 
is poorly understood. This course is designed to demonstrate the use of
computational methods to determine the most likely structure of the 
complex formed by interacting proteins, identify potentially druggable sites
in the interface, determine whether the target is druggable, and
provide information on potential ligands. Participants will study a number
of targets using web-based software (including PIPER and ClusPro, 
currently the best protein docking tools available) on their laptops. A
light dinner will be served.

 

Course Instructors:

Sandor Vajda, Ph.D., Professor, Departments of Biomedical Engineering and
Chemistry, Boston University

Dima Kozakov, Ph.D., Research Assistant Professor, Departments of Biomedical
Engineering, Boston University

 

The problem of disrupting protein-protein interactions 

Predicting the structure of protein-protein complexes using fragment-based
identification of binding hot spots 

Druggability of binding sites determined by the hot spots 

Identification of functional groups with preferential binding to hot spots 

Comparison of computational and experimental approaches. 

 

Additional information and registration details for this course and
conference is available at http://www.healthtech.com/sbd
or call CHI at 781-972-5400.

A separate registration is required to attend the Structure-Based Drug
Design conference that is scheduled for June 6-8, 2011. 

If you would like to also attend the Structure-Based Drug Design conference,
you can save up to $350 if you register by
Friday, March 11.

 

Contact:

James Prudhomme

Cambridge Healthtech Institute

250 First Avenue, Suite 300

Needham, MA 02494

Phone: 781-972-5400

Fax: 781-972-5425

www.healthtech.com

 

 



From dan.bolser at gmail.com  Thu Mar 10 05:30:05 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Thu, 10 Mar 2011 10:30:05 +0000
Subject: [BiO BB] Fwd: [SMW-devel] Plans for Google Summer of Code
In-Reply-To: <4D76ADFD.4020005@semantic-mediawiki.org>
References: <4D76ADFD.4020005@semantic-mediawiki.org>
Message-ID: <AANLkTinXO3qZSELs4dbnLyzWX02xKX9GfpJTPKeNSvTG@mail.gmail.com>

---------- Forwarded message ----------
From: Markus Kr?tzsch <markus at semantic-mediawiki.org>
Date: 8 March 2011 22:30
Subject: [SMW-devel] Plans for Google Summer of Code
To: semediawiki-user at lists.sourceforge.net
Cc: Semantic MediaWiki developers <semediawiki-devel at lists.sourceforge.net>


Dear all,

SMW is planning to participate in Google Summer of Code this year (in
previous years, we did this under the umbrella of the Wikimedia
Foundation). This is a great opportunity for young hackers from around
the world to make key contributions to SMW-related projects while
earning both money and experience. Semantic Maps and RDFIO are examples
of projects that came out of earlier GSoCs.

As the name suggests, actual work will happen in summer, but it is not
too early to make a mental note, or to get in touch with the people you
would like to work with. I forward below an email from Sumana, the GSoC
coordinator for the Wikimedia Foundation, which contains many helpful
hints for students. The initial project page for SMW is at

http://semantic-mediawiki.org/wiki/GSoC_2011

Students (and interested users) can also propose their own projects --
the best place to do this is is on the SMW developers list (CCed) or on
the SMW IRC channel. In principle, we can host all projects which are
related to SMW extensions and to MediaWiki in general, as long as SMW
users will clearly benefit from them.

Cheers,

Markus


-------- Original Message --------
Subject: [Wikitech-l] Recruiting students to apply for Google Summer of Code
Date: Mon, 07 Mar 2011 18:57:47 -0500
From: Sumana Harihareswara <sumanah at panix.com>
Reply-To: Wikimedia developers <wikitech-l at lists.wikimedia.org>
To: wikitech-l at lists.wikimedia.org


? ? ?I'll be administering MediaWiki's participation in Google Summer of
Code this year, so I'd like to recruit bright students to consider applying.

? ? ?Google Summer of Code (GSoC) is a program where you get paid to
hack an open source project during the summer. ?It's never too early to
start thinking about summer internships! There's a good explanation of
the program here:

http://www.booki.cc/gsocstudentguide/_v/1.0/what-is-google-summer-of-code/

? ? ?Community college, university, and graduate students around the
world are eligible. ?You don't need to be a Computer Science or IT major:

http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs#who

? ? ?If you'd like to participate, check out the timeline. ?Make sure
you are available full-time from 23 May till 22 August this summer, and
have a little free time from 25 April till 23 May for ramp-up.

http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/timeline

? ? ?Then sign up on our wiki page and start talking with us in
#wikimedia-dev about a possible project!

http://www.mediawiki.org/wiki/Summer_of_Code_2011


Good luck,
Sumana Harihareswara
interim Wikimedia volunteer/community development coordinator

_______________________________________________
Wikitech-l mailing list
Wikitech-l at lists.wikimedia.org
https://lists.wikimedia.org/mailman/listinfo/wikitech-l


------------------------------------------------------------------------------
What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
_______________________________________________
Semediawiki-devel mailing list
Semediawiki-devel at lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/semediawiki-devel



From pandey.gaurav at gmail.com  Thu Mar 10 19:56:42 2011
From: pandey.gaurav at gmail.com (Gaurav Pandey)
Date: Thu, 10 Mar 2011 16:56:42 -0800
Subject: [BiO BB] Simultaneous visualization of multiple GO terms
Message-ID: <AANLkTin4+VR_L-9MVwk23OEjyRFBswKcrnq-G5xb8dem@mail.gmail.com>

Hi all,

I need to simultaneously visualize multiple terms in the same Gene Ontology
category. Could anybody inform me about a nice online tool to do this?

Thanks,

Gaurav

-- 
Gaurav Pandey                                  Email:
gaurav at compbio.berkeley.edu
Plant & Molecular Biology Department      Webpage:
compbio.berkeley.edu/people/gaurav
University of California, Berkeley                    Tel: 612-701-2494


From skhadar at gmail.com  Mon Mar 14 15:54:05 2011
From: skhadar at gmail.com (Khader Shameer)
Date: Mon, 14 Mar 2011 14:54:05 -0500
Subject: [BiO BB] Simultaneous visualization of multiple GO terms
In-Reply-To: <AANLkTin4+VR_L-9MVwk23OEjyRFBswKcrnq-G5xb8dem@mail.gmail.com>
References: <AANLkTin4+VR_L-9MVwk23OEjyRFBswKcrnq-G5xb8dem@mail.gmail.com>
Message-ID: <AANLkTinz7Xf-7nTBSo5AVpw9WVBPbvMjXRWcpKLzvQH2@mail.gmail.com>

Hi Gaurav,

You could try REVIGO:  for visualization of GO terms in a tree map.
http://revigo.irb.hr/

Best.
Khader Shameer

On Thu, Mar 10, 2011 at 6:56 PM, Gaurav Pandey <pandey.gaurav at gmail.com>wrote:

> Hi all,
>
> I need to simultaneously visualize multiple terms in the same Gene Ontology
> category. Could anybody inform me about a nice online tool to do this?
>
> Thanks,
>
> Gaurav
>
> --
> Gaurav Pandey                                  Email:
> gaurav at compbio.berkeley.edu
> Plant & Molecular Biology Department      Webpage:
> compbio.berkeley.edu/people/gaurav
> University of California, Berkeley                    Tel: 612-701-2494
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>


From hlapp at gmx.net  Tue Mar 15 17:52:01 2011
From: hlapp at gmx.net (Hilmar Lapp)
Date: Tue, 15 Mar 2011 17:52:01 -0400
Subject: [BiO BB] Deadline extension for full talk abstracts for Conference
	on Informatics for Phylogenetics, Evolution,
	and Biodiversity (iEvoBio)
Message-ID: <AC6BF017-5E28-4FBB-84AB-7F8C4ED566D3@gmx.net>

The deadline for submitting abstracts for full talks to the inaugural  
conference on Informatics for Phylogenetics, Evolution, and  
Biodiversity (iEvoBio) has been extended by one week to Friday, March  
25, 2011. We hope that this will give those interested in contributing  
sufficient time to do so.

Please see http://bit.ly/iEvoBio2011_CfA for the full Call for  
Abstracts and author instructions. We still expect to be able to  
notify accepted talks in time for the early registration deadline of  
iEvoBio (and Evolution).

More details about the program and guidelines for contributing content  
are available at http://ievobio.org.  You can also find continuous  
updates on the conference's Twitter feed at http://twitter.com/ 
iEvoBio, and there is a Google group you can join at http://groups.google.com/group/ievobio-announce 
  to receive announcements.

iEvoBio is sponsored by the US National Evolutionary Synthesis Center  
(NESCent) in partnership with the Society for the Study of Ecolution  
(SSE) and the Society of Systematic Biologists (SSB). Additional  
support has been provided by the Encyclopedia of Life (EOL).

The iEvoBio 2011 Organizing Committee:
Rob Guralnick (University of Colorado at Boulder) (Co-chair)
Cynthia Parr (Encyclopedia of Life) (Co-chair)
Dawn Field (UK National Environmental Research Center)
Mark Holder (University of Kansas)
Hilmar Lapp (NESCent)
Rod Page (University of Glasgow)




From hlapp at gmx.net  Tue Mar 15 15:14:49 2011
From: hlapp at gmx.net (Hilmar Lapp)
Date: Tue, 15 Mar 2011 15:14:49 -0400
Subject: [BiO BB] DataONE Summer Internship Opportunity
Message-ID: <FA500598-4E92-49E8-B86A-CD8A92131C2F@gmx.net>

The Data Observation Network for Earth (DataONE) is a virtual  
organization dedicated to providing open, persistent, robust, and  
secure access to biodiversity and environmental data, supported by the  
U.S. National Science Foundation. DataONE is pleased to announce the  
availability of summer research internships for undergraduates,  
graduate students and recent postgraduates.

Program Structure

Up to eight interns will be accepted in 2011, each paired with one  
primary mentor and, in some cases, secondary mentors. Interns need not  
necessarily be at the same location or institution as their mentor(s).  
Interns and mentors are expected to have a face-to-face meeting at the  
beginning of the summer, and interns are encouraged to attend the  
DataONE All-Hands Meeting in the fall to present the results of their  
work. DataONE will pay all necessary travel expenses.

Schedule

March 15 - Application period opens
April 8 - Deadline for receipt of applications at midnight Pacific time
April 15 - Notification of acceptance. Scheduling of face-to-face  
kickoff meetings based on availability of interns and mentors
May 23 - Program begins*
June 27 - Midterm evaluations
July 29 - Program concludes
October 18-20 - DataONE All-Hands-Meeting, New Mexico (attendance  
encouraged)
* Allowance will be made for students who are unavailable during these  
date due to their school calendar.

Eligibility

The program is open to all undergraduate students, graduate students,  
and postgraduates who have received their masters or doctorate within  
the past five years. Given the broad range of projects, there are no  
restrictions on academic backgrounds or field of study. Interns must  
be at least 18 years of age by the program start date, must be  
currently enrolled or employed at a university or other research  
institution and must currently reside in, and be eligible to work in,  
the United States. Interns are expected to be available approximately  
40 hours/week during the internship period (noted below) with  
significant availability during the normal business hours. Interns  
from previous years are eligible to participate.

Financial Support

Interns will receive a stipend of $4,500 for participation, paid in  
two installments (one at the midterm and one at the conclusion of the  
program). In addition, required travel expenses will be borne by  
DataONE. Participation in the program after the mid-term is contingent  
on satisfactory performance. The University of New Mexico will  
administer funds. Interns will need to supply their own computing  
equipment and Internet connection. For students who are not US  
citizens or permanent residents, complete visa information will be  
required, and it may be necessary for the funds to be paid through the  
student?s  university or research institution. In such cases, the  
student will need to provide the necessary contact information for  
their organization.

Project Ideas

Projects cover a range of topic areas and vary in the extent and type  
of prior background required of the intern. The interests and  
expertise of the applicants will, in part, determine which projects  
will be selected for the program. Off-list projects are also eligible,  
in which case potential applicants are strongly encouraged to contact  
the organizers and/or potential mentors with their ideas prior to  
applying. The titles of this year?s projects (see below for more  
detailed descriptions) are:

DATA MANAGEMENT: Best practices of data management for public  
participation in science and research
DATA MANAGEMENT: Online learning modules related to best practices  
throughout the data lifecycle
EDUCATION: Accessing and analyzing environmental data in the classroom
SOCIOLOGY OF SCIENCE: Understanding how scientists analyze data
DATA SCIENCE: How much ecological data is out there?
DATA SCIENCE: Tracking the reuse of 1000 datasets
PROGRAMMING: Subsetting and publishing ?dynamic? scientific datasets
PROGRAMMING: Scientific workflow provenance repository and publishing  
toolkit
PROGRAMMING: Integrating loosely structured data into the Linked Open  
Data cloud
SCIENCE COMMUNICATION: Developing video animations for DataONE  
community engagement
To Apply

Application materials should be sent to internship at dataone.org by  
11:59 PM (Pacific time) on April 8th, and should include a cover  
letter, resume and letter of reference all in PDF format. The  
applicant should send the cover letter and resume, while  the letter  
of reference should be sent directly by its author.

The cover letter should address the following questions:
What DataONE Summer Internship projects are you most interested in and  
why?
What contributions do you expect to be able to make to the project(s)?
What background do you have which is relevant to the project(s)?
What do you expect to learn and/or achieve by participating?
What are your thoughts and ideas about the project, including  
particular suggestions for ways of achieving the project objectives?
How will participation in this program help you achieve your  
educational and career objectives?
Are there any factors that would affect your ability to participate,  
including other summer employment, university schedules, and other  
commitments?
The resume should include the applicant?s educational history, current  
position, any publications or honors, and full contact information  
(including phone number, e-mail address, and mailing address).
The letter of reference should be sent directly to internship at dataone.org 
  and should be from a professor, supervisor, or mentor.
Evaluation of applications

Applications will be judged by the following criteria:

The academic and technical qualifications of the applicant.
Evidence of strong written and oral communication skills.
The extent to which the applicant can provide substantive  
contributions to one or more projects, including the applicant?s ideas  
for project implementation.
The extent to which the internship would be of value to the career  
development of the applicant
The availability of the applicant during the period of the internship.
Intellectual Property

DataONE is predicated on openness and universal access. Software is  
developed under one of several open source licenses, and copyrightable  
content produced during the course of the project will made available  
under a Creative Commons (CC-BY 3.0) license. Where appropriate,  
projects may result in published articles and conference  
presentations,  on which the intern is expected to make a substantive  
contribution, and receive credit for that contribution.

Funding acknowledgement

The Summer Internships are supported by The National Science  
Foundation: "INTEROP: Creation of an International Virtual Data Center  
for the Biodiversity, Ecological and Environmental Sciences" (NSF  
Award 0753138) and "DataNet Full Proposal: DataNetONE (Observation  
Network for Earth)" (NSF Award 0830944).

For more information

If you have questions or problems about the application process or  
internship program in general, please send e-mail to internship at dataone.org 
.

Project Ideas

Best practices of data management for public participation in science  
and research
Description: The DataONE Citizen Science Working Group (CSWG) is  
working to organize and develop best practices for management of data  
and information for the increasing number of local, regional and  
national projects that focus on ?Public Participation in Science and  
Research (PPSR),? also called Citizen Science projects. The 2011 CSWG  
intern will assist in the inventory and description of data practices  
for PPSR projects, based on the response from an earlier survey  
conducted as part of the CSWG. The goals of the intern project are to  
develop a metadata description for key aspects of the data held by  
each group, and make this information available back to the CSWG as a  
small database. The intern will then help identify and document best  
practices for data management by PPSR projects, assist in vetting the  
best practice documents across the PPSR community, and work with CSWG  
to make the best practices available via the DataONE website as well  
as other outlets. Products will include a suite of best practices for  
data management by PPSR projects; in addition, the intern will be  
encouraged to give a formal presentation at a scientific, data  
management or PPSR conference or meeting. Local work preferred, at  
Tucson or Ithaca, though remote work would be possible for outstanding  
candidates (though one trip for an organization meeting would be  
required).
Qualifications needed: Undergraduate or graduate student or  
equivalent; simple database management (e.g., MS Access) skills  
preferred; public engagement; writing; organization; small project  
management
Skills to be learned: Metadata management; best practices template;  
database management; communications and outreach; project management
Primary mentor: Jake Weltzin (USA National Phenology Network)
Secondary mentor: Rick Bonney (Cornell Laboratory of Ornithology)

Developing online learning modules related to the best practices  
throughout the data lifecycle
Description: DataONE is developing online learning modules designed to  
educate DataONE users in various aspects of the data lifecycle. This  
project involves: 1) researching and acquiring software that can  
produce high quality online learning; 2) developing online learning  
modules using pre-prepared power point slides produced by the DataONE  
Community Engagement and Education Working Group; 3) adding content  
about data management 4) participating in a workshop hosted by DataONE  
to refine and add additional content to educational modules (July,  
2011).
Qualifications needed: A science data management background;  
Familiarity with aspects of the data lifecycle; Ability to quickly  
learn new software; Some work in development of educational materials  
helpful
Skills to be learned: Creative ways to educate a varied audience on  
data lifecycle; familiarity in use of chosen software used to develop  
online learning modules; collaboration techniques with dispersed  
working group.
Primary mentor: Viv Hutchison (USGS NBII)
Secondary mentors: Stephanie Hampton (National Center for Ecological  
Analysis and Synthesis), Carly Strasser (National Center for  
Ecological Analysis and Synthesis)

Understanding how scientists analyze data
Description: Scientists use a wide variety of tools and techniques to  
manage and analyze data. However, to our knowledge no one has taken a  
systematic look at how scientists do their work. In this project, we  
will examine a large number of the scientific workflows that have been  
constructed. We will develop a way of categorizing workflows based on  
their complexity, types of processing steps employed, and other  
factors. The goal is to develop new and significant understanding of  
the scientific process and how it is being enabled by science workflows.
Qualifications needed: Self-starter, determined, enthusiastic, willing  
to keep a research notebook up-to-date openly online. Experience with  
a modern programming language, statistics and data analysis, and R  
would be helpful.
Skills to be learned: Kepler and Taverna workflow languages, research  
methods, research analysis, keeping an open science research notebook,  
communicating research results. A peer-reviewed publication is  
envisioned.
Primary mentor: William Michener (University New Mexico)
Secondary mentors: Rebecca Koskela (University of New Mexico), Bertram  
Ludaescher (University of California Davis)

Accessing and analyzing environmental data in the classroom
Description: A graduate student intern will create an educational  
module for use in undergraduate classrooms ? the module will be  
designed to teach basic principles in ecology or environmental science  
using data that are publicly available through the DataONE network.  
The student will work with mentors to choose appropriate data sets,  
questions and analyses, and create a simple program to access and  
analyze the data in R. The student will create documentation that  
accompanies the exercise, potentially in multimedia formats, to train  
instructors to use the exercise in classrooms.
Qualifications needed: Basic background in ecology or environmental  
science, and statistics is necessary. Experience implementing  
statistics in a scripted statistical package such as R, Matlab or SAS  
is necessary. Experience with online training materials and multimedia  
presentation ? e.g., screencasts - is useful.
Skills to be learned: The student will hone skills in statistical  
analysis, programming in R, working with large data sets, and creating  
teaching materials. The student will gain a well-rounded perspective  
on the importance of all aspects of the data life cycle in  
environmental sciences, and build a diverse professional network with  
leaders in environmental informatics and data-driven environmental  
science research.
Primary mentor: Stephanie Hampton (National Center for Ecological  
Analysis and Synthesis)
Secondary mentors: Carly Strasser (National Center for Ecological  
Analysis and Synthesis), Amber Budden (University of New Mexico)

How much ecological data is out there?
Description: No one is certain how much ecological data exists, or how  
this amount compares to the volume of data currently housed in  
repositories such as Knowledge Network for Biocomplexity (KNB). It  
would be useful to determine this for designing infrastructure, but  
also as a call to arms for ecologists to start sharing this ?dark  
data?. For this project, we will develop a method for estimating the  
amount of ecological data being generated, with a focus on ?small  
science? projects. Initially this project will involve brainstorming  
about the best way to estimate such a complex figure, and the intern  
will then be tasked with producing the estimate using the decided upon  
methods. Potential methods for estimation may include sampling  
publications, surveying scientists, or exploring existing databases.  
We foresee that results from this project will be highly cited since  
such an estimate is useful for discussions about data sharing, data  
reuse, and repository development in Ecology.
Qualifications needed: Applicants should be graduate students, have a  
strong background in the field of ecology or environmental science,  
and have statistics experience. Experience using computer scripts for  
data retrieval would be helpful, along with programming experience in  
R and/or MATLAB. The intern will need to be creative and excited about  
tackling complex problems.
Skills to be learned: The student will be exposed to topics in data  
management, reuse, and archiving, and will learn to work with  
ecological databases. They will learn to work collaboratively on  
complex problems with several members of the DataONE team, and have  
the opportunity to write a peer-reviewed publication with the  
potential for high citation rates. Particular skills related to  
computer scripting, statistics, and data mining will be specific to  
the methods determined by the student and mentors.
Primary mentor: Carly Strasser (National Center for Ecological  
Analysis and Synthesis)
Secondary mentor: Stephanie Hampton (National Center for Ecological  
Analysis and Synthesis)

Tracking the reuse of 1000 datasets
Description: We believe that openly archiving raw data facilitates  
valuable reuse. Can we measure this? What contribution does data reuse  
make to the published literature? Who reanalyzes data? For what? Does  
this vary across disciplines and repositories? These questions are the  
focus of an exploratory study, "Tracking data reuse: Following one  
thousand datasets from public repositories into the published  
literature." In this internship you'll work directly with Heather to  
collect, extract, annotate, and analyze data to explore these  
important questions. See http://bit.ly/cPsek0 for more info on the  
project.
Qualifications needed: Self-starter, determined, enthusiastic, willing  
to keep a research notebook up-to-date openly online. Experience with  
statistics, the academic literature, PubMed, ISI Web of Science,  
Python, R, and blogging would be helpful.
Skills to be learned:Research methods, research data collection, text  
extraction from the scientific literature, keeping an open science  
research notebook, communicating research results
Primary mentor: Heather Piwowar (National Evolutionary Synthesis Center)
Secondary mentor: Todd Vision (University of North Carolina Chapel  
Hill/National Evolutionary Synthesis Center)

Subsetting and publishing ?dynamic? scientific datasets
Description: The Avian Knowledge Network (AKN) is a federation of bird  
monitoring datasets, the largest and most dynamic of which is eBird.  
Datasets such as these, that are constantly being edited and expanded,  
are challenging to incorporate into the DataONE framework because of  
the way they are currently published. This project involves  
researching issues around dataset subsetting and duplication to  
recommend a publishing approach that works for ?dynamic? datasets.  
Expected outcomes: (1) Implement that strategy by migrating the AKN  
repository to a DataONE?integrated Metacat deployment, making AKN into  
a DataONE Member Node; (2) Produce a case-study article that captures  
the implementation process that could act as a guide to future Member  
Nodes making similar efforts.
Qualifications needed: metadata mapping; high level programming  
language (e.g., Perl, Java); SQL; shell scripting
Skills to be learned: data repository implementation; scientific data  
organization and publishing
Primary mentor: Paul Allen (Cornell Laboratory of Ornithology)
Secondary mentors: Kevin Webb (Cornell Laboratory of Ornithology)

Scientific workflow provenance repository and publishing toolkit
Description: Scientific workflow systems are increasingly used to  
automate scientific computations and data analysis and visualization  
pipelines. An important feature of scientific workflow systems is  
their ability to record and subsequently query and visualize  
provenance information. Provenance includes the processing history and  
lineage of data, and can be used, e.g., to validate/invalidate  
outputs, debug workflows, document authorship and attribution chains,  
etc. and thus facilitate ?reproducible science?. We aim to develop (1)  
a provenance repository system for publishing and sharing data  
provenance collected from runs of a number of scientific workflow  
systems (Kepler, Taverna, Vistrails), together with (2) a provenance  
trace publication system that allows scientists to interactively and  
graphically select relevant fragments of a provenance trace for  
publishing. The selection may be driven by the need to protect private  
information, thus including hiding, abstracting, or anonymizing  
irrelevant or sensitive parts. Part (1) will be based on a DataONE- 
extension of the Open Provenance Model (D1-OPM) and leverage an  
earlier Summer of Code project. In particular, the provenance toolkit  
includes an API for managing workflow provenance (i.e., uploading into  
and retrieving from a data storage back-end). Part (2) will implement  
a new policy-aware approach to publishing provenance, which aims at  
reconciling a user?s (selective) provenance publication requests, with  
agreed upon provenance integrity constraints. For an existing rule- 
based backend, a graphical user environment needs to be developed that  
lets users select, abstract, hide, and anonymize provenance graph  
fragments prior to their publication.
Qualifications needed: For Part 1, applicants should have experience  
in SQL and Java or a scripting language (e.g., Python or Perl). For  
Part 2, programming of GUIs with Rich Internet Application (RIA)  
technologies (e.g., GWT) is a plus.
Skills to be learned: : Collaborative open source software development  
using state-of-the-art languages and tools (databases, workflow  
systems, interactive information visualization).
Primary mentor: Bertram Ludaescher (University of California Davis)
Secondary mentor: Paolo Missier (Newcastle University)

Integrating loosely structured data into the Linked Open Data cloud
Description: The Linked Data conventions describe four principles that  
allow data of any kind and from any online source to form a global  
interconnected web of data: i) name every "thing" that has some data  
or information associated with it; ii) use HTTP URIs to do so; iii)  
provide useful information or data in Resource Description Framework  
(RDF) format to someone looking up such URIs; and iv) within  
information provided this way, link to other common "things", such as  
points or axes of reference, and use common vocabularies to attach  
meaning to links wherever possible. These seemingly simple principles  
have nonetheless been highly effective in facilitating the creation of  
large, globally distributed, and constantly growing aggregations of  
Linked Open Data (LOD), a unversally applicable framework for machines  
and users alike to integrate, navigate, and discover data by following  
links that are semantically of interest. Trying to apply the Linked  
Data principles to data holdings of non-specialized digital  
repositories, such as DataONE and many of its member nodes, is  
challenging. These data are often highly heterogenous, and not  
natively expressed in RDF, or a format structured enough that would  
lend itself to automatic conversion to RDF. Instead, they are  
typically represented in formats that are either loosely structured in  
an ad-hoc manner (such as spreadsheets), or according to one of a  
myriad of formats output by instruments or analysis programs. It is  
thus not clear what the universe of "things" to name is, what are  
common points or axes of reference, what kinds (semantics) of links  
are needed, and how data archived in this way can be exposed in RDF  
such that the conversion can be automated, yet is still useful for  
science-motivated discovery and integration. The idea of this project  
is to develop an exploratory prototype, and practical recommendations  
resulting from it, for how the heterogeneous and loosely structured  
data held in non-specialized DataONE member nodes can be exposed to  
the Linked (Open) Data cloud. The approach would consist of obtaining  
a sufficiently representative sample of data sets from DataONE's  
initial 3 member nodes (Dryad, KNB, and ORNL-DAAC), and using them as  
instance data for which to define the RDF predicate vocabularies,  
domain ontologies, resource URIs, and conversion mechanisms that are  
necessary to create a LOD representation of these data. This  
representation can then be uploaded to, navigated, and queried in  
either one of the web-based LOD browsers (such as URIburner), or for  
example in a local installation of OpenLink Virtuoso.
Qualifications needed: Knowledge of RDF and one of its widely used  
serializations (XML, N3). Familiarity with either C or Java  
programming, or a scripting language that has good support for RDF and  
OWL, will be needed. Familiarity with Linked Data, and experience with  
metadata vocabularies and domain ontologies in RDF and OWL will be  
very helpful.
Skills to be learned: Designing and executing an exploratory study  
through all phases. Identifying and communicating alternatives and  
their advantages and drawbacks. Developing practical semantic web  
resources for existing instance data.
Primary Mentor: Hilmar Lapp (National Evolutionary Synthesis Center)

Developing video animations for DataONE community engagement
Description: DataONE wishes to develop a set of video animations to  
help explain DataONE's value and capabilities to a range of audiences.  
Several topics have been identified for these short animations, a  
couple of storyboards have been developed, and one animation created.  
The intern will work with the mentors to continue building this set of  
animations according to the principles of ?universal design?.
Qualifications needed: Applicants should have strong visual design  
skills and a high level of expertise in development of digital  
animation. Expertise in communicating scientific information to a  
variety of audiences is desirable.
Skills to be learned: Video / animation development; science  
communications.
Primary mentor: Paul Allen (Cornell Laboratory of Ornithology)
Secondary mentors: Amber Budden (University of New Mexico), Will  
Morris (Cornell Laboratory of Ornithology)
This information is also available at: http://www.dataone.org/content/2011-summer-internship-program
Rebecca Koskela
Executive Director, DataONE
University of New Mexico
1312 Basehart SE
Albuquerque, NM 87106

Email: rkoskela at unm.edu
Office (M,W,F): (505) 814-1111
Cell & Office (T,Th):  (505) 382-0890
Fax: (505) 246-6007




From drgzli at gmail.com  Tue Mar 15 23:16:11 2011
From: drgzli at gmail.com (Guo-Zheng Li)
Date: Wed, 16 Mar 2011 11:16:11 +0800
Subject: [BiO BB] CFP IEEE-BIBM due July 15
Message-ID: <AANLkTinskxOV5hTn2qNz8Mo71FpxBdGTH2dCFMYpQQgc@mail.gmail.com>

Call for Papers



2011 IEEE International Conference on Bioinformatics and Biomedicine
(BIBM11)



Atlanta, Georgia,  USA, Nov. 12-15, 2011



http://www.cs.gsu.edu/BIBM2011/



IEEE BIBM 2011 provides a general forum for disseminating the latest
research in bioinformatics and health informatics. It brings together
academic and industrial scientists from computer science, biology,
chemistry, medicine, mathematics and statistics. Hong Kong is a vibrant
business city with many attractions and a distinctive culture.



* Journal special issues: IEEE BIBM has a tradition to publish selected
papers as special issues in highly respected SCI indexed journals. So far we
have confirmed the special issues publications with IEEE Transactions on
NanoBiosceiences, International Journal of Data Mining and Bioinformatics,
BMC Bioinformatics, Proteomics. (In the past BIBM conference, the number of
special issues is: BIBM 2010?7 special issues, BIBM 2009?4 special issue;
BIBM 2008?4 special issues)



* Student Travel Award: BIBM 2011 will offer as many student travel awards
as possible  to student authors (BIBM 2010--22 student travel awards,  BIBM
2009?16 student travel awards )



We solicit high-quality original research papers (including significant
work-in-progress) in any aspect of bioinformatics and biomedicine. New
computational techniques and methods in machine learning; data mining; text
analysis; pattern recognition; knowledge representation; databases; data
modeling; combinatorics; stochastic modeling; string and graph algorithms;
linguistic methods; robotics; constraint satisfaction; data visualization;
parallel computation; data integration; modeling and simulation and heir
application in life science domain are especially encouraged Relevant topics
include but are not limited to:



1. Genomics and Molecular Structure, Function and Evolution

a. Next-Gen Sequencing and Metagenomics

b. Evolution, Phylogeny, Comparative  Genomics

c. SNPs and haplotype analysis, GWAS

d. Protein/RNA Structure, Function and Interactions



2. Computational Systems Biology

a. Transcriptomics - Microarray Data Analysis

b. Gene Regulation, Alternative Splicing, Network/Pathway Analysis

c. Proteomics, PTMs, Metabolomics

d. Epigenomics, non-coding RNA analysis, DNA methylation analysis



3. Medical Informatics and Translational Bioinformatics

a. Biomedical Intelligence, Clinical Data Analysis, and Electronic Health
Record

b. Biomedical Signal/Image Analysis

c. Genome-Phenome Analysis

d. Biomarker Discovery



4. Cross-Cutting Computational Methods and Bioinformatics Infrastructure

a. Biomedical Text Mining and Ontologies

b. Biological Data Mining and Visualization

c. Computational Modeling and Data Integration

d. High Performance Computing





INDUSTRIAL Track

The Industrial Track solicits papers describing implementations of
Bioinformatics and Biomedicine solutions relevant to industrial settings.
The focus of industry track is on papers that address the practical,
applied, or pragmatic or new research challenge issues related to the use of
bioinformatics and biomedicine technologies in industry.



Conference Co-Chairs:

Prof. Yi Pan

Georgia State University, USA

pan at cs.gsu.edu



Prof. Stephen Wong

The Methodist Hospital Research Institute, USA

stwong at tmhs.org



Program Co-Chairs:

Prof. Shinichi Morishita

University of Tokyo, Japan

moris at cb.k.u-tokyo.ac.jp



Prof. Fangxiang Wu

University of Saskatchewan, Canada

Faw341 at mail.usask.ca



Prof. Mohammed Zaki

Rensselaer Polytechnic Institute, USA

zaki at cs.rpi.edu



Industry Program Committee Chair

Dr. Anastasia Christianson

AstraZeneca, USA



BIBM Steering Committee Chair:

Prof. Xiaohua Tony Hu

Drexel University, USA

thu at cis.drexel.edu





Paper Submission:

Please submit a full-length paper (8 page IEEE 2-column format) through the
online submission system (you can download the format instruction here (
http://wi-lab.com/cyberchair/2011/bibm11/cbc_index.html) for Latex or word).
Electronic submissions (in PDF or Postscript format) are required. Selected
participants will be asked to submit their revised papers in a format to be
specified at the time of acceptance.



Online Submission:

http://wi-lab.com/cyberchair/2011/bibm11/cbc_index.html



Important Dates:



Electronic submission of full papers: July 15, 2011

Notification of paper acceptance: September 5, 2011

Camera-ready of accepted papers: October 1, 2011

Conference: November 12-15, 2011





Workshop proposal: June 20, 2011

Tutorial proposal submission: Aug 20, 2011

Poster submission: October  5, 2011


From drgzli at gmail.com  Tue Mar 15 23:20:04 2011
From: drgzli at gmail.com (Guo-Zheng Li)
Date: Wed, 16 Mar 2011 11:20:04 +0800
Subject: [BiO BB] CFP ACM-BCB due March 21
Message-ID: <AANLkTinZTwe-EUyhB1PrQ5fCZu26NuO49fr0fCxODXbo@mail.gmail.com>

Call for Papers
-= DEADLINE EXTENDED =-

2011 ACM Conference on Bioinformatics,
Computational Biology and Biomedicine (ACM BCB 11)

August 1-3, 2011, Chicago, Illinois

www.acmbcb.org

The ACM Conference on Bioinformatics, Computational Biology and Biomedicine
(ACM BCB)
is the main conference of the newly formed ACM SIG Bioinformatics.

This is the second year of the ACM BCB Conference.  Over 200 people attended
ACM BCB 10,
which took in Niagara Falls, NY on August 2-4, 2010.

ACM BCB 11 will be held in Chicago at the Hilton Suites Chicago ?
Magnificent Mile from August 1-3.
The conference welcomes high quality, original research papers. Papers
should contain new
algorithms or novel computational approaches in the broad areas of
bioinformatics,
computational biology and biomedicine.  Papers that use existing
computational techniques
in new and interesting ways leading to novel biological discoveries are also
welcome.
Topics of interest include but are not limited to:

* Genomics: Structural, Functional, and Comparative
* Molecular Networks: Proteomics, Transcriptomics & Metabolomics
* Phylogenetics at Gene and Genome Levels
* Computational Systems Biology
* Immunoinformatics and Computational Immunology
* Computational Epidemiology
* Biomedical and Translational Informatics
* Databases, Knowledgebases & Ontologies for Bioinformatics
* Machine Learning, Image Analysis, Knowledge Representation and Inference
* Integration of Biomedical Data
* Text Mining and Natural Language Processing in Biomedicine
* Hardware and Software Infrastructure for Biomedicine

The best of the accepted papers will be published in special issues of four
journals.
See the web site for details.

Important dates: (http://acmbcb.org/important-dates/)
Electronic submission of full papers: March 21, 2011 (New deadline)
Notification of acceptance: April 25, 2011
Camera-ready submission of accepted papers: May 10, 2011
Conference dates: August 1-3, 2011

Workshop proposal submission: February 1, 2011
Tutorial proposal submission: March 21, 2011
Poster submission: April 30, 2011

General Chairs
Robert Grossman, University of Chicago
Andrey Rzhetsky, University of Chicago

Program Chairs
Sun Kim, Indiana University Bloomington
Wei Wang, University of North Carolina at Chapel Hill


From manjulathimma at yahoo.com  Sat Mar 19 05:25:51 2011
From: manjulathimma at yahoo.com (manju la)
Date: Sat, 19 Mar 2011 02:25:51 -0700 (PDT)
Subject: [BiO BB] Gene and upstream downstream sequence retrieval
Message-ID: <469626.22986.qm@web55602.mail.re4.yahoo.com>

Dear All,

I have a set of 300 gene names (for ex LCK, CD247 etc). I wanted to extract DNA 
sequences of these genes along with 15-20kbp both upstream and downstream of 
these genes. If you know any programmatic way of achieving this, that would be 
great.

Regards
Thimma



      

From ws1.sadiservices at gmail.com  Mon Mar 21 10:42:54 2011
From: ws1.sadiservices at gmail.com (UNBSJ cbrass)
Date: Mon, 21 Mar 2011 11:42:54 -0300
Subject: [BiO BB] Web Publishing of Scientific Data and Services Training
	Course - remind
Message-ID: <AANLkTi=MRM8u3MEodP2Xf2VPXUPX1bL+zkVUXfGT9uFW@mail.gmail.com>

Dear Colleague,

This e-mail is a reminder regarding to important dates for the Web
Publishing of Scientific Data and Services Training Courses -  Fredericton,
NB on May 19-20th, 2011
http://sadiframework.org/training/

Early Registration - Until April 1st, 2011 ( 275 CAN$, student rate 225
CAN$)
Late Registration - April 1st - May 18th, 2011 (375 CAN$, student rate 325
CAN$)
Workshop - May 19 - 20th, 2011 (on site registration - 500 CAN$, student
rate 450 CAN$)


 Themes
===========
Semantic Web
Knowledge Representation and Reasoning
Web Services
SADI Semantic Web Services
http://sadiframework.org/training/CFP.html

Any further questions can be sent to ws1.sadiservices at gmail.com



Following Event:
================

Web Publishing of Scientific Data and Services Training Courses  -
Vancouver, BC in August 2011 (date do be determined)



Best regards,
Silvane Paixao, Ph. D.
Trainer Coordinator & Instructional Design
Dept. Computer Science and Applied Statistics
University of New Brunswick, Canada
http://ca.linkedin.com/pub/silvane-paix%C3%A3o/1a/682/707


From tirza at biomodel.os.biu.ac.il  Tue Mar 22 05:11:51 2011
From: tirza at biomodel.os.biu.ac.il (Tirza Doniger)
Date: Tue, 22 Mar 2011 11:11:51 +0200
Subject: [BiO BB] Gene and upstream downstream sequence retrieval
In-Reply-To: <469626.22986.qm@web55602.mail.re4.yahoo.com>
References: <469626.22986.qm@web55602.mail.re4.yahoo.com>
Message-ID: <AANLkTikNYqgwzBSrt634W5hN5uH6Mrb4_r4R6h6NtzCu@mail.gmail.com>

Hi Thimma,

You don't mention from which organism these genes come from?

In the  UCSC genome browser - choose "tables"- you can enter a list of genes
as long as the names are in a format that is recognized.

Choose output "sequences"-> "genomic"-> then you can specify which part of
the gene you want and how much upstream/downstream
flanking.

Best,
Tirza
 --
Tirza Doniger, Ph.D.
Bioinformatics Unit
The Mina and Everard Faculty of Life Sciences
Bar Ilan University
Phone: +972 3 531 8124
======================
 Life is like riding a bicycle. To keep your balance you must keep moving.
-----Albert Einstein
On Sat, Mar 19, 2011 at 11:25 AM, manju la <manjulathimma at yahoo.com> wrote:

> Dear All,
>
> I have a set of 300 gene names (for ex LCK, CD247 etc). I wanted to extract
> DNA
> sequences of these genes along with 15-20kbp both upstream and downstream
> of
> these genes. If you know any programmatic way of achieving this, that would
> be
> great.
>
> Regards
> Thimma
>
>
>
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>


From hlapp at gmx.net  Wed Mar 23 22:55:42 2011
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed, 23 Mar 2011 22:55:42 -0400
Subject: [BiO BB] Reminder: Deadline for full talk abstracts for Conference
	on Informatics for Phylogenetics, Evolution,
	and Biodiversity (iEvoBio)
Message-ID: <EC31D9A5-33BB-42E3-BA96-F28083775A30@gmx.net>

This is a reminder that the deadline for submitting abstracts for full  
talks to the 2011 conference on Informatics for Phylogenetics,  
Evolution, and Biodiversity (iEvoBio) is Friday, March 25, 2011, which  
is just two days away. Please see http://bit.ly/iEvoBio2011_CfA for  
the full Call for Abstracts and author instructions.

As another reminder, full talks are only 1 of 5 kinds of contributed  
content that iEvoBio will feature. The other 4 are: 1) Lightning talks  
(5 mins long), 2) Challenge entries, 3) Software bazaar  
demonstrations, and 4) Birds-of-a-Feather gatherings. The Call for  
Challenge entries is also open (see http://ievobio.org/ 
challenge.html). Tentative submission deadlines are listed on the  
conference website (http://ievobio.org/program.html#dates).

More details about the program and guidelines for contributing content  
are available at http://ievobio.org.  You can also find continuous  
updates on the conference's Twitter feed at http://twitter.com/ 
iEvoBio, and there is an announcement-only Google group at http://groups.google.com/group/ievobio-announce 
. You can use the group's RSS feed (linked from its URL), or join the  
group to receive announcements by email.

iEvoBio is sponsored by the US National Evolutionary Synthesis Center  
(NESCent) in partnership with the Society for the Study of Ecolution  
(SSE) and the Society of Systematic Biologists (SSB). Additional  
support has been provided by the Encyclopedia of Life (EOL).

The iEvoBio 2011 Organizing Committee:
Rob Guralnick (University of Colorado at Boulder) (Co-chair)
Cynthia Parr (Encyclopedia of Life) (Co-chair)
Dawn Field (UK National Environmental Research Center)
Mark Holder (University of Kansas)
Hilmar Lapp (NESCent)
Rod Page (University of Glasgow)




From hlapp at gmx.net  Sat Mar 26 16:29:49 2011
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 26 Mar 2011 16:29:49 -0400
Subject: [BiO BB] Phyloinformatics Summer of Code 2011 - Call for student
	applications
Message-ID: <5F897013-F6C5-49FD-843E-0D5292C51709@gmx.net>

*** Please disseminate widely at your local institutions, ***
*** including posting to message and job boards, so that  ***
*** we reach as many interested students as possible.     ***

PHYLOINFORMATICS SUMMER OF CODE 2011

http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011

The Phyloinformatics Summer of Code program provides a unique  
opportunity for undergraduate, masters, and PhD students to obtain  
hands-on experience writing and extending open-source software for  
evolutionary informatics under the mentorship of experienced  
developers from around the world. The program is the participation of  
the US National Evolutionary Synthesis Center (NESCent) as a mentoring  
organization in the Google Summer of Code(tm) (http://code.google.com/soc/ 
).

Students in the program will receive a stipend from Google (and  
possibly more importantly, a T-shirt solely available to successful  
participants), and may work from their home, or home institution, for  
the duration of the 3 month program. Each student will have at least  
one dedicated mentor to show them the ropes and help them complete  
their project.

NESCent is particularly targeting students interested in both  
evolutionary biology and software development. Initial project ideas  
are listed on the website. These range from visualizing viral  
epidemics to 3D protein structure evolution, rich annotation for  
TreeBASE content, exposing phenotype observations to the Encyclopedia  
of Life, to enhancing R packages for phylogenetic analysis. All  
project ideas are flexible and many can be adjusted in scope to match  
the skills of the student.  We also welcome novel project ideas that  
dovetail with student interests.

TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/ 
), where you will also find GSoC  program rules and eligibility  
requirements.  Each organization has a slightly different application  
format, and ours is at http://bit.ly/PhyloSoC2011-apptemplate. The 12- 
day application period for students opens on Monday, March 28th, and  
runs through Friday, April 8th, 2011.

INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all  
interested students to get in touch with us with their ideas as early  
on as possible. Working closely with potential mentors to develop your  
project proposal greatly increases your chance for acceptance. Do not  
underestimate the amount of time it takes to develop a competitive  
proposal.

2011 NESCent Phyloinformatics Summer of Code:
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011

Google Summer of Code FAQ:
http://socghop.appspot.com/document/show/gsoc_program/google/gsoc2011/faqs

---------

Karen Cranston and Hilmar Lapp
National Evolutionary Synthesis Center
http://nescent.org



From mahef111 at link.net  Sun Mar 27 19:16:21 2011
From: mahef111 at link.net (Mahmoud ElHefnawi)
Date: Mon, 28 Mar 2011 01:16:21 +0200
Subject: [BiO BB] multiple pathways quering tool
In-Reply-To: <60DE2847-19AC-4E68-9324-A5B82AD7D139@gmx.net>
Message-ID: <mailman.2.1457372270.4754.bbb@bioinformatics.org>

Hi all.

Do u know of a tool that can query  most pathway databases?

Thanks,

Mahmoud

-----Original Message-----
From: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org]
On Behalf Of Hilmar Lapp
Sent: Thursday, February 17, 2011 1:02 AM
To: General Forum at Bioinformatics.Org
Subject: [BiO BB] Call for Abstracts open for Conference on Informatics
forPhylogenetics, Evolution, and Biodiversity (iEvoBio)

The Call for Abstracts for full talks is now open for the 2011  
conference on Informatics for Phylogenetics, Evolution, and  
Biodiversity (iEvoBio), at
http://ievobio.org/ocs/index.php/ievobio/2011. See below for  
instructions.

Accepted talks will be about 15-20 minutes in length and will be  
presented during the full talk sessions in the morning of each of the  
two conference days, following the day's keynote presentation.

Submitted talks should be in the area of informatics aimed at  
advancing research in phylogenetics, evolution, and biodiversity,  
including new tools, cyberinfrastructure development, large-scale data  
analysis, and visualization.

Submissions consist of a title and an abstract at most 1 page long.  
The abstract should provide an overview of the talk's subject.  As the  
number of program slots for full talks is limited, the abstract should  
give enough detail so reviewers can decide whether the submission  
merits a full talk or whether it should be moved to one of the  
Lightning Talk sessions.  If the subject of the talk is a specific  
software component for use by the research community, the abstract  
must state the license and give the URL where the source code is  
available so reviewers can verify that the open-source requirement(*)  
is met.

The deadline for submission is March 18, 2011. We intend to notify  
authors of accepted talks before early registration for iEvoBio (and  
Evolution) ends. Further instructions for submission are at the  
following URL:

http://ievobio.org/ocs/index.php/ievobio/2011/schedConf/cfp

Full talks are 1 of 5 kinds of contributed content that iEvoBio will  
feature. The other 4 are: 1) Lightning talks (5 mins long), 2)  
Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- 
a-Feather gatherings. The Call for Challenge entries is already open  
(see http://ievobio.org/challenge.html). The calls for contribution to  
the other 3 sessions will open later, and will remain open until  
shortly before the conference or until the respective track fills up.

More details about the program and guidelines for contributing content  
are available at http://ievobio.org.  You can also find continuous  
updates on the conference's Twitter feed at http://twitter.com/ 
iEvoBio , or subscribe to the low-traffic iEvoBio announcements  
mailing list at http://groups.google.com/group/ievobio-announce

iEvoBio is sponsored by the US National Evolutionary Synthesis Center  
(NESCent) in partnership with the Society for the Study of Ecolution  
(SSE) and the Society of Systematic Biologists (SSB). Additional  
support has been provided by the Encyclopedia of Life (EOL).


The iEvoBio 2011 Organizing Committee:
Rob Guralnick (University of Colorado at Boulder) (Co-chair)
Cynthia Parr (Encyclopedia of Life) (Co-chair)
Dawn Field (UK National Environmental Research Center)
Mark Holder (University of Kansas)
Hilmar Lapp (NESCent)
Rod Page (University of Glasgow)

(*) iEvoBio and its sponsors are dedicated to promoting the practice  
and philosophy of Open Source software development (see
http://www.opensource.org/docs/definition.php) 
  and reuse within the research community. For this reason, if a  
submitted talk concerns a specific software system for use by the  
research community, that software must be licensed with a recognized  
Open Source License (see http://www.opensource.org/licenses/), and be  
available for download, including source code, by a tar/zip file  
accessed through ftp/http or through a widely used version control  
system like cvs, Subversion, git, Bazaar, or Mercurial.  Authors of  
full talks who cannot meet this requirement at the time of submission  
should state their intentions, and are advised that the requirement  
must be met by June 19, 2011, at the latest.

_______________________________________________
BBB mailing list
BBB at bioinformatics.org
http://www.bioinformatics.org/mailman/listinfo/bbb





From Robin.Haw at oicr.on.ca  Sun Mar 27 23:58:41 2011
From: Robin.Haw at oicr.on.ca (Robin Haw)
Date: Sun, 27 Mar 2011 23:58:41 -0400
Subject: [BiO BB] Genome Informatics - Student Recruitment for Google Summer
 of Code 2011
Message-ID: <C9B57FB1.E2CF%robin.haw@oicr.on.ca>

The Genome Informatics group, encompassing Reactome, Wormbase and GMOD will be participating in Google Summer of Code 2011. This is a great opportunity for students to contribute to the work of one of three bioinformatics projects. More information on project ideas and the program is published at the GMOD website (http://www.gmod.org/wiki/GSoC). If you have any questions or queries, please feel free to send a post to the Genome Informatics Google Groups (http://groups.google.com/group/genome-informatics). Candidate students need to start discussing application ideas with Genome Informatics as soon as possible. The application period for students is March 28 to April 8. All student proposals will be matched with a mentor by April 22, and the final list of accepted students and their projects will be announced on April 25 (3pm EST).

?Google Summer of Code (GSoC, http://socghop.appspot.com<http://socghop.appspot.com/>) is a global program that offers student developers stipends to write code for various open source software projects. We have worked with several open source, free software, and technology-related groups to identify and fund several projects over a three month period. Since its inception in 2005, the program has brought together over 4,500 students and more than more than 4,000 mentors & co-mentors from over 85 countries worldwide, all for the love of code. Through Google Summer of Code, accepted student applicants are paired with a mentor or mentors from the participating projects, thus gaining exposure to real-world software development scenarios and the opportunity for employment in areas related to their academic pursuits. In turn, the participating projects are able to more easily identify and bring in new developers. Best of all, more source code is created and released for the use and benefit of all."

Wormbase (http://www.wormbase.org<http://www.wormbase.org/>)
An online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. The database is constantly updated and new versions are released on a monthly basis. WormBase is a collaboration among the Wellcome Trust Sanger Institute, Ontario Institute for Cancer Research, Washington University in St. Louis, and the California Institute of Technology.

Reactome (http://www.reactome.org<http://www.reactome.org/>)
A manually curated database of core pathways and reactions in human biology that functions as a data mining resource and electronic textbook. The Reactome data model describes diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, signal transduction, and high-level processes, such as the cell cycle. Reactome software uses only freely available (and often open source) components and has been created with cross-platform compatibility and wide usability in mind. Data is stored in a MySQL database, the web site is implemented in Perl and data entry tool in Java programming language. The Reactome team is composed of individuals who are both biologists and programmers at the Ontario Institute for Cancer Research, New York University Langone Medical Center, Cold Spring Harbor Laboratory, and The European Bioinformatics Institute.

Generic Model Organism Database (GMOD, http://www.gmod.org<http://www.gmod.org/>)
An open source project to develop a complete set of software for creating and administering a model organism database. Components of this project include genome visualization and editing tools, literature curation tools, a robust database schema, biological ontology tools, and a set of standard operating procedures. This project is collaboration of several database projects, including WormBase, FlyBase, Mouse Genome Informatics, Gramene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database.

Contact Information
Email: robin.haw at oicr.on.ca<mailto:robin.haw at oicr.on.ca> - contact me to find out more about a project or your potential mentor(s).
Website: http://www.gmod.org/wiki/GSoC
Discussion mailing lists: Genome Informatics Google Groups (http://groups.google.com/group/genome-informatics) - ask about our projects; join the community!



From rwagner at faw.at  Mon Mar 28 02:58:44 2011
From: rwagner at faw.at (Prof. Roland Wagner)
Date: Mon, 28 Mar 2011 08:58:44 +0200
Subject: [BiO BB] ITBAM 2011: EXTENDED DEADLINE: April 4, 2011
Message-ID: <4D9031A4.7010702@faw.at>

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

Please accept our apologies if you receive multiple copies of this Call 
for Papers (CFP).


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


Call for Papers and Posters
===============================================================

International Conference on

Information Technology in Bio- and Medical Informatics

ITBAM 2011
================================================================

In conjunction with DEXA 2011
www.dexa.org

29 August ? 2 September 2011
Paul Sabatier University, Toulouse, France

Data intensive disciplines like life sciences and medicine are promoting 
vivid research activities in the area of databases. Modern technologies 
such as high-throughput mass-spectrometry and sequencing, micro-arrays, 
high-resolution imaging, etc. produce enormous and continuously 
increasing amounts of data. Huge public databases provide access to 
aggregated and consolidated information on genome and protein sequences, 
biological pathways, diseases, anatomy atlases, and scientific 
literature. There has never been more potentially available information 
to study biomedical systems ranging from single cells to complete 
organisms. However, it is a non-trivial task to transform the vast 
amount of biomedical data into actionable information triggering 
scientific progress and supporting patient management. Major biomedical 
application scenarios for research in the database community include but 
are not limited to:

* Systems biology
* Genomics, proteomics, and metabolomics
* Genome-wide association studies
* Drug target discovery and personalized medicine
* Neuroscience
* Electronic patient records
* Patient monitoring
* Surgery planning and support
* etc.
Various emerging database technologies for coping with the challenges of 
these application scenarios have been developed and are an active area 
of research in information technology:
* Administration of vast amounts of data
* Integration of heterogeneous data sources
* Federated and distributed databases
* Data warehouses
* Data mining techniques like classification, clustering, association 
rule mining, etc.
* Decision support systems
* Information and image retrieval
* Signal processing and streaming databases
* Privacy protection and data security
* Data quality assurance
* Process management and collaborative work
* User interfaces and visualization
* etc.

Designing database technology to support applications in life sciences 
and medicine is an inspiring field of interdisciplinary research. Often 
there is a long way from an idea to practical application which involves 
intensive discussion between experts in information technology, life 
sciences and medicine. ITBAM accompanies and supports this way by 
providing an excellent venue for the exchange of ideas, fruitful 
discussion, and effective interaction among interdisciplinary researchers.
In addition to the regular conference program featuring presentations of 
full and short research papers published in the proceedings, ITBAM 
encourages the submission of posters reporting work in progress. All 
accepted posters will be displayed during the whole event and abstracts 
will also be included in the proceedings.

IMPORTANT DATES

ITBAM conference papers and poster submissions:
* Submission of full papers (firm): March 7, 2011 --- deadline extended 
to April 3, 2011 !!!!
* Notification of acceptance: May 11, 2011
* Submission of posters (firm): May 16, 2011
* Camera-ready copies due: June 9, 2011

Paper Submission Details:

Authors are invited to submit electronically original contributions or 
experience reports in English. The submitted manuscript should closely 
reflect the final paper as it will appear in the proceedings.
* Paper submissions should not exceed 15 pages in LNCS format. Poster 
submissions are expected to consist of 1 page Abstract 
(http://www.springer.de/comp/lncs/authors.html).
* Any submission that exceeds length limits or deviates from formatting 
requirements may be rejected without review.
* For registration and electronic submission see: 
http://confdriver.ifs.tuwien.ac.at/
* The submission system will be open starting from January 2011.
* Submitted papers will be carefully evaluated based on originality, 
significance, technical soundness, and clarity of exposition.
* Duplicate submissions are not allowed. Authors are expected to agree 
to the following terms: "I understand that the paper being submitted 
must not overlap substantially with any other paper that I am a 
co-author of and that is currently submitted elsewhere. Furthermore, 
previously published papers with any overlap are cited prominently in 
this submission."

Accepted Papers:

All accepted conference papers will be published in "Lecture Notes in 
Computer Science" (LNCS) by Springer Verlag. Accepted full papers will 
be of 15 pages length, short papers 8 pages. Authors of accepted papers 
must sign a Springer copyright release form. For further inquiries, 
please contact the Conference Organisation Office (gabriela at dexa.org).

General Chairperson:

Christian B?hm, University of Munich, Germany

Program Committee Co-chairpersons:

Sami Khuri, San Jos? State University, USA
Lenka Lhotska, Czech Technical University Prague, Czech Republic
Nadia Pisanti, University of Pisa, Italy

Program Committee:

Werner Aigner, FAW, Austria
Fuat Akal, Functional Genomics Center Zurich, Switzerland
Tatsuya Akutsu, Kyoto University, Japan, Japan
Andreas Albrecht, Queen's University Belfast, United Kingdom
Julien Allali, LABRI, University of Bordeaux 1, France
Lijo Anto, University of Kerala, India
Rub?n Arma?anzas Arnedillo, Technical University of Madrid, Spain
Peter Baumann, Jacobs University Bremen, Germany
Balaram Bhattacharyya, Visva-Bharati University, India
Christian Blaschke, Bioalma Madrid, Spain
Veselka Boeva, Technical University of Plovdiv, Bulgaria
Gianluca Bontempi, Universit? Libre de Bruxelles, Belgium
Roberta Bosotti, Nerviano Medical Science s.r.l., Italy
Rita Casadio, University of Bologna, Italy
S?nia Casillas, Universitat Aut?noma de Barcelona, Spain
Kun-Mao Chao, National Taiwan University, China
Vaclav Chudacek, Czech Technical University in Prague, Czech Republic
Coral del Val Mu?oz, University of Granada, Spain
Hans-Dieter Ehrich, Technical University of Braunschweig, Germany
Mourad Elloumi, University of Tunis, Tunesia
Maria Federico, University of Modena and Reggio Emilia, Italy
Christoph M. Friedrich, Univ. of Applied Sciences and Arts, Dortmund, 
Germany
Xiangchao Gan, University of Oxford, United Kingdom
Alejandro Giorgetti, University of Verona, Italy
Alireza Hadj Khodabakhshi, Simon Fraser University, Canada
Volker Heun, Ludwig-Maximilians-Universit?t M?nchen, Germany
Chun-Hsi Huang, University of Connecticut, USA
Lars Kaderali, University of Heidelberg, Germany
Alastair Kerr, University of Edinburgh, United Kingdom
Sami Khuri, San Jose State University, USA
Michal Kr?tk?, Technical University of Ostrava, Czech Republic
Josef K?ng, University of Linz, Austria
Gorka Lasso-Cabrera, CIC bioGUNE, Spain
Marc Lensink, ULB, Belgium
Lenka Lhotska, Czech Technical University, Czech Republic
Roger Marshall, Plymouth Ystate University, USA
Elio Masciari, ICAR-CNR, Universit? della Calabria, Italy
Henning Mersch, RWTH Aachen University, Germany
Aleksandar Milosavljevic, Baylor College of Medicine, USA
Jean-Christophe Nebel, Kingston University, United Kingdom
Vit Novacek, National University of Ireland, Galway, Ireland
Nadia Pisanti, University of Pisa, Italy
Cinzia Pizzi, Universit? degli Studi di Padova, Italy
Clara Pizzuti, Institute for High Performance Computing and Networking 
(ICAR)-National Research Council(CNR), Italy
Meikel Poess, Oracle Corporation,
Hershel Safer, Weizmann Institute of Science, Israel
Nick Sahinidis, Carnegie Mellon University, USA
Roberto Santana, Technical University of Madrid, Spain
Kristan Schneider, University of Vienna, Austria
Jens Stoye, University of Bielefeld, Germany
A Min Tjoa, Vienna University of Technology, Austria
Paul van der Vet, University of Twente, Netherlands
Roland R. Wagner, University of Linz, Austria
Oren Weimann, Weizmann Institute, Israel
Viacheslav Wolfengagen, Institute JurInfoR-MSU, Russia
Borys Wrobel, Polish Academy of Sciences, Poland
Filip Zavoral, Charles University in Prague, Czech Republic
Songmao Zhang, Chinese Academy of Sciences, China
Qiang Zhu, The University of Michigan, USA
Frank Gerrit Zoellner, University of Heidelberg, Germany




From announce at CS.ColoState.EDU  Tue Mar 29 15:01:07 2011
From: announce at CS.ColoState.EDU (IEEE HiPC 2011 Announce)
Date: Tue, 29 Mar 2011 13:01:07 -0600
Subject: [BiO BB] IEEE HiPC 2011 Call for Papers
Message-ID: <ec998640bf4f3a4a64e30fd582be6fbe.squirrel@webmail.cs.colostate.edu>

           C A L L   F O R   P A P E R S

18th IEEE International Conference on High Performance Computing
                   (HiPC 2011)

              December 18-21, 2011



            Bengaluru (Bangalore),
            INDIA


            http://www.hipc.org



    Paper Submission Deadline: May 16, 2011



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



IMPORTANT DATES


April 04, 2011        Conference Paper Submission Begins

May 16, 2011          Conference Paper Submission Ends

May 16, 2011          Workshop Proposals Due

July 18, 2011         Notification of Acceptance/Rejection

Aug 18, 2011          Camera-Ready Paper Submission

Sep 16, 2011          Student Symposium Submissions Due

Oct 15, 2011          Student Symposium Accept/Reject Decisions

Nov 19, 2011          Early Registration Deadline



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

The 18th annual IEEE International Conference on High Performance
Computing (HiPC 2011) will be held in Bengaluru (Bangalore), India,
during December 18-21, 2011. It will serve as a forum for researchers
from around the world to present their current research efforts and
findings, and will act as a venue for stimulating discussions and for
highlighting high performance computing (HPC) activities in Asia. The
conference has a history of attracting participation from reputed
researchers from all over the world. HiPC 2011 will focus on the design
and analysis of high performance computing and networking systems and
their scientific, engineering, and commercial applications. In addition
to technical sessions consisting of contributed papers, the conference
will include invited presentations, a student research symposium,
tutorials, and vendor presentations.The 17th meeting, held in Goa in
December 2010, had 40 contributed papers chosen from 208 submissions
from 22 countries; and more than 280 attendees. The 16th meeting, held
in Kochi, India in December 2009, had 49 contributed papers that were
selected from 261 submissions from 20 countries, and about 225
participants attended the meeting. The 15th meeting, held in Bangalore,
India in December 2008, had 46 contributed papers that were selected
from over 317 submissions and approximately 250 participants attended
the meeting. The HiPC attendance is approximately 300 with a good mix of
participants from India and the rest of the world.



Further information about HiPC 2011 and the HiPC series of meetings is
available on the conference website at http://www.hipc.org.

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



CO-SPONSORED BY:

* HPCwire - Platinum Media Sponsor

* IEEE Computer Society Technical Committee on Parallel Processing
(TCPP) - Pending

* HiPC Education Trust



IN COOPERATION WITH:



* ACM SIGARCH - Pending



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



VENUE AND MEETING INFORMATION



HiPC will be held at Bengaluru (Bangalore), India. The advance program
will be available in July 2011. Please check the conference website at
http://www.hipc.org for updated information.



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



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

                      HiPC 2011



                  CALL FOR PAPERS

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



Authors are invited to submit original unpublished manuscripts that
demonstrate current research in all areas of high performance computing
including design and analysis of parallel and distributed systems,
embedded systems, and their applications in scientific, engineering, and
commercial areas.



Topics of interest include but are not limited to:

* High-Performance Computing

* Parallel and Distributed Algorithms

* Parallel Languages and Programming Environments

* Load Balancing, Scheduling and Resource Management

* Resilient/Fault-Tolerant Algorithms and Systems

* Scientific/Engineering/Commercial Applications and Workloads

* Emerging Applications such as Biotechnology and Nanotechnology

* Cluster, Cloud, and Grid Cloud Computing

* Peer-to-peer Algorithms and Networks

* Heterogeneous Computing

* Interconnection Networks and Architectures

* Scalable Servers and Systems

* High Performance/Scalable Storage Systems

* Power-Efficient and Reconfigurable Architectures

* Compiler Technologies for High-Performance Computing

* Software Support and Advanced Micro-architecture Techniques

* Operating Systems for Scalable High-Performance Computing





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



MANUSCRIPT GUIDELINES



Submitted manuscripts should be structured as technical papers and may
not exceed 10 letter size (8.5 x 11) pages including figures, tables and
references using the IEEE format for conference proceedings (print area
of 6-1/2 inches (16.51 cm) wide by 8-7/8 inches (22.51 cm) high,
two-column format with columns 3-1/16 inches (7.85 cm) wide with a 3/8
inch (0.81 cm) space between them, single-spaced 10-point Times fully
justified text).



Submissions not conforming to these guidelines may be returned without
review. Authors should submit the manuscript in PDF format and make sure
that the file will print on a printer that uses letter size (8.5 x 11)
paper. The official language of the meeting is English.



Manuscript submission will start on April 4, 2011. Manuscript submission
procedures will then be available over the Web at http://www.hipc.org.
Electronic submissions must be in the form of a readable PDF file.
Manuscripts must be received by May 16, 2011. Manuscripts should
demonstrate current research in any area of high performance computing.
All manuscripts will be reviewed and will be judged on correctness,
originality, technical strength, significance, quality of presentation,
and interest and relevance to the conference attendees.



Submitted papers must represent original unpublished research that is
not currently under review for any other conference or journal. Papers
not following these guidelines will be rejected without review and
further action may be taken, including (but not limited to)
notifications sent to the heads of the institutions of the authors and
sponsors of the conference. Submissions received after the due date,
exceeding length limit, or not appropriately structured may also not be
considered. Authors may contact the Program Chair at the address below
for further information or clarification. Notification of review
decisions will be mailed by July 18, 2011. Camera-ready papers are due
by August 18, 2011. A published proceedings will be available at the
conference.



Program Chair:   Satoshi Matsuoka

	         Tokyo Institute of Technology, Japan

             Email: matsu at is.titech.ac.jp



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



WORKSHOPS



Proposals are solicited for workshops to be held in conjunction with the
main conference. Interested individuals should submit a proposal by May
16, 2011 to the Workshops Chair. Additional details and submission
guidelines will be available at the conference website.



Workshops Co-Chairs:


Manimaran Govindarasu, Iowa State University, USA

Email: gmani at iastate dot edu


Pavan Balaji, ANL, USA

Email: balaji at mcs.anl.gov



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



STUDENT RESEARCH SYMPOSIUM



HiPC 2011 will feature the third student research symposium on High
Performance Computing (HPC) aimed at stimulating and fostering student
research, and providing an international forum to highlight student
research accomplishments. The symposium will also expose students to the
best practices in HPC in academia and industry. The one-day symposium
will feature brief presentations by student authors on their research,
followed by a poster exhibit. Short invited talks by leading HPC
researchers/ practitioners will be included in the program. The
Conference Reception and Student Symposium Poster Exhibits will provide
an opportunity for students to interact with HPC researchers and
practitioners (and recruiters) from academia and industry. To be
considered, students should submit a 5 page extended abstract of their
research. Submission procedures will be available at the Student
Symposium web site, accessible from http://www.hipc.org, after August
17, 2011. For additional details, please see the conference web site or
contact the Symposium Co-Chairs.



Symposium Co-Chairs:
Ashok Srinivasan

Florida State University

Email: student_symposium at hipc dot org

Yogesh Simmhan

University of Southern California

Email: student_symposium at hipc dot org



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



INDUSTRY/USER SYMPOSIUM



The HiPC Industry/User Symposium aims at bringing together the users /
practitioners of HPC including both commercial and non-commercial users,
and giving them a platform to share their challenges and successes, as
well as to discuss relevant technology issues.


Symposium Co-Chair:
Jigar Halani
Wipro, India

         Email:    jigar.halani at wipro dot com


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



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

               HiPC 2011 ORGANIZATION

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



GENERAL CO-CHAIRS

Manish Parashar, Rutgers University, USA

Rajeev Muralidhar, Intel, India



VICE GENERAL CO-CHAIRS

Rajendra V. Boppana, University of Texas at San Antonio, USA

Rama Govindaraju, Google, USA



PROGRAM CHAIR
Satoshi Matsuoka
Tokyo Institute of Technology, Japan



PROGRAM VICE CHAIRS



Algorithms:

Sanjay Ranka, University of Florida, USA

Application:

Gabrielle Allen, Lousiana State University, USA
Architecture:

Hiroshi Nakashima, Kyoto University, Japan

Communication Networks:

Dhabaleswar Panda, Ohio State University, USA

Systems software:

Andrew Lumsdaine, Indiana University



STEERING CHAIR

Viktor K. Prasanna, University of Southern California, USA



WORKSHOPS CO-CHAIRS

Manimaran Govindarasu, Iowa State University, USA

Pavan Balaji, ANL, USA



STUDENT RESEARCH SYMPOSIUM CO-CHAIRS

Ashok Srinivasan, Florida State University, USA

Yogesh Simmhan, University of Southern California, USA



INDUSTRY/USER SYMPOSIUM CHAIR
Jigar Halani, Wipro, India

INDUSTRY LIAISON CO-CHAIRS

Badri Ramamurthy, HP, India

Milind Bhandarkar, LinkedIn, USA


LOCAL COORDINATION CHAIR

Santhosh Daivajna, 8KMiles, India


INDUSTRY EXHIBITS COORDINATOR
Kalyana Krishna, USA


PUBLICATIONS CO-CHAIRS

Sushil K. Prasad, Georgia State University, USA

Raghavendra Hebbalalu, Intel, India


PRODUCTION CHAIR

Animesh Pathak, INRIA, France



CYBER CHAIR

Saima Aman, University of Southern California, USA



FINANCE CO-CHAIRS

Ajay Gupta, Western Michigan University, USA

Thondiyil Venugopalan, India



PUBLICITY CO-CHAIRS
Shrideep Pallickara, Colorado State University, USA

Chakravarthy Nagarajan, Wipro, India

Dinesh Kaushik, KAUST, Saudi Arabia



REGISTRATION CO-CHAIRS

Sally Jelinek, Electronic Design Associates, USA

Jyothsna Kasturirengan, Fiberlink, India



STEERING COMMITTEE
Srinivas Aluru, Iowa State University, USA, IIT Bombay, India

P. Anandan, Microsoft Research, India

David A. Bader, Georgia Institute of Technology, USA

Ramamurthy Badrinath, HP, India

Frank Baetke, HP, USA

Luc Boug?, ENS Cachan, Brittany extension, France

R. Govindarajan, Indian Institute of Science, India

Rama Govindaraju, Google Inc., USA

Manish Gupta, India Systems and Technology Lab, IBM, India

Stefan Heinzel, Garching Computing Centre (RZG), Max Planck
Society, Germany

Victor Malyshkin, Russian Academy of Sciences, Russia

Ashwini K. Nanda, HPC Research Inc.

Siddhartha Nandi, NetApp, India

Manish Parashar, NSF and Rutgers University, USA

Ishwar Parulkar, Cisco, India

Viktor K. Prasanna, University of Southern California, USA (Chair)

Ramesh Rajagopalan, Dell India R&D, Bangalore, India

Venkat Ramana, Cray-Hinditron, India

Sartaj Sahni, University of Florida, USA

Lokendra Shastri, Infosys, India

Sunil Sherlekar, Intel, India

Santosh Sreenivasan, Talentain Technologies, India

V. Sridhar, SRM Research Institute, India

Harrick M. Vin, Tata Research, Development and Design Center
(TRDDC), Pune, India



Steering Committee 2011 membership also includes the general co-chairs,
program chairs and vice general co-chairs from 2010, 2011 and 2012.





From dan.bolser at gmail.com  Wed Mar 30 09:04:42 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Wed, 30 Mar 2011 14:04:42 +0100
Subject: [BiO BB] Announcing OBF Summer of Code
Message-ID: <AANLkTim1tDBeGkM7+d92kF2WxMinikY3OUGfjJZNaZT2@mail.gmail.com>

OPEN BIOINFORMATICS FOUNDATION SUMMER OF CODE 2011

Applications due 19:00 UTC, April 8, 2010.
http://www.open-bio.org/wiki/Google_Summer_of_Code

The Open Bioinformatics Foundation Summer of Code program provides a
unique opportunity for undergraduate, masters, and PhD students to
obtain hands-on experience writing and extending open-source software
for bioinformatics under the mentorship of experienced developers from
around the world. The program is the participation of the Open
Bioinformatics Foundation (OBF) as a mentoring organization in the
Google Summer of Code(tm) (http://code.google.com/soc/).

Students successfully completing the 3 month program receive a $5,000
USD stipend, and may work entirely from their home or home
institution. ?Participation is open to students from any country in
the world except countries subject to US trade restrictions. ?Each
student will have at least one dedicated mentor to show them the ropes
and help them complete their project.

The Open Bioinformatics Foundation is particularly seeking students
interested in both bioinformatics (computational biology) and software
development. Some initial project ideas are listed on the website.
These range from Galaxy phylogenetics pipeline development in
Biopython to lightweight sequence objects and lazy parsing in BioPerl,
a DAS Server for large files on local filesystems, and mapping Java
libraries to Perl/Ruby/Python using Biolib+SWIG+JNI. ?All project
ideas are flexible and many can be adjusted in scope to match the
skills of the student. We also welcome and encourage students
proposing their own project ideas; historically some of the most
successful Summer of Code projects are ones proposed by the students
themselves.

TO APPLY: Apply online at the Google Summer of Code website
(http://socghop.appspot.com/), where you will also find GSoC program
rules and eligibility requirements. The 12-day application period for
students runs from Monday, March 28 through Friday, April 8th, 2011.

INQUIRIES:

We strongly encourage all interested students to get in touch with us
with their ideas as early on as possible. ?See the OBF GSoC page for
contact details.

2011 OBF Summer of Code:
http://www.open-bio.org/wiki/Google_Summer_of_Code

Google Summer of Code FAQ:
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs



_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hayit at eng.tau.ac.il  Wed Mar 30 01:03:34 2011
From: hayit at eng.tau.ac.il (Hayit Greenspan)
Date: Tue, 29 Mar 2011 22:03:34 -0700
Subject: [BiO BB] IEEE_HISB call for Tutorials and Demos
In-Reply-To: <AANLkTiky2EW3SBy0BMeNfFnUbPV0EetT-Dv24nsATAi-@mail.gmail.com>
References: <AANLkTiky2EW3SBy0BMeNfFnUbPV0EetT-Dv24nsATAi-@mail.gmail.com>
Message-ID: <AANLkTik4L9e6UvLq3VJcc6K2qHPx7QxUzrcZaPooVM4p@mail.gmail.com>

*First IEEE International Conference on*

*Healthcare Informatics, Imaging, and Systems Biology (HISB)*

July 27-29, San Jose, California

http://www.ieee-hisb.org/



                      *** *Call for Tutorials and Demos*  ***


The First IEEE International Conference on Healthcare Informatics, Imaging
and Systems Biology now invites proposals for tutorials and demonstrations
at the conference to be held in San Jose, July 26-29, 2011.



The purpose of tutorials is to provide a comprehensive overview by subject
matter experts on topics relevant to HISB, keeping in mind the
inter-disciplinary audience. The purpose of demos is to give researchers the
opportunity to showcase the state of the art in areas relevant to HISB.
Industrial exhibitors may also demonstrate their products through demos as
long as they are relevant to the topic areas of the main conference.



We encourage submissions of tutorial and demonstration proposals on all
topics relevant to the conference in the general areas of healthcare
informatics, biomedical imaging, bioinformatics, and systems biology. A full
list of topics is available in the call for papers for HISB at
(http://www.ieee-hisb.org). Specialized subtopics that address computational
or clinical aspects of the main topics will also be considered.

Please refer to the main conference site (http://www.ieee-hisb.org) for
further details.

Key Dates:



Submission deadline (for both tutorials and demos): April 20, 2011

Notification of Acceptance: May 20, 2011

Conference Dates: July 27-29, 2011


From jprudhomme at healthtech.com  Wed Mar 30 12:31:27 2011
From: jprudhomme at healthtech.com (James Prudhomme)
Date: Wed, 30 Mar 2011 12:31:27 -0400
Subject: [BiO BB] Scientific Advisor to President Obama to Keynote at
	Upcoming SBDD Conference
Message-ID: <00bd01cbeef7$eae85aa0$c0b90fe0$@com>

** Please distribute this announcement to those who may be interested.**

 

 

Scientific Advisor to President Obama to Keynote Upcoming CHI Conference

 

Cambridge Healthtech Institute and Bio-IT World Present the Eleventh Annual 

STRUCTURE-BASED DRUG DESIGN

 

June 6-8, 2011

Royal Sonesta Boston Hotel - Cambridge, MA http://www.healthtech.com/sbd


Keynote Speaker:

 

Millisecond-Long Molecular Dynamics Simulations of Proteins on a
Special-Purpose Machine

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

David E. Shaw serves as chief scientist of D. E. Shaw Research and as a
senior research fellow at the Center 
for Computational Biology and Bioinformatics at Columbia University. He
received his Ph.D. from Stanford 
University in 1980, served on the faculty of the Computer Science Department
at Columbia until 1986, and 
founded the D. E. Shaw group in 1988. Since 2001, Dr. Shaw has been involved
in full-time, hands-on research 
in the field of computational biochemistry. His lab is currently involved in
the development of new algorithms 
and machine architectures for high-speed molecular dynamics simulations of
biological macromolecules, 
and in the application of such simulations to basic scientific research and
computer-assisted drug design.

Dr. Shaw was appointed to the President's Council of Advisors on Science and
Technology by President 
Clinton in 1994, and again by President Obama in 2009. He is a fellow of the
American Academy of Arts 
and Sciences and of the American Association for the Advancement of Science.

Conference Highlights:

 

* Protein Flexibility

* Fully Synthetic Protein-Protein Interaction Inhibitor

* Fragment-to-Lead Optimization

* High Performance Computing and Collaborative Drug Design

* State-of-the-Art Molecular Dynamics Simulations

 

Dinner Short Course (June 8)*

Identification of Druggable Sites for Protein-Protein Interaction Targets

 

Register by April 29 at the Advanced Registration Disount:

Web: https://chidb.com/register/2011/sbd/reg.asp

Call: +1 781-972-5400

 

For details on sponsorship and exhibit opportunities, contact:

Katelin Fitzgerald, +1 781-972-5458, kfitzgerald at healthtech.com

 

For details on group discounts, contact:

David Cunningham, +1 781-972-5472, cunningham at healthtech.com

 

 

*Separate registration is required to attend the dinner short course.

 

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

 



From cannataro at unicz.it  Thu Mar 31 09:50:16 2011
From: cannataro at unicz.it (Mario Cannataro)
Date: Thu, 31 Mar 2011 15:50:16 +0200 (CEST)
Subject: [BiO BB] HiBB 2011 Euro-Par Workshop on High Performance
 Bioinformatics and Biomedicine
Message-ID: <89fcd4920aba54875b92466cc15a37e3.squirrel@email.unicz.it>

       I apologize for any cross-posting of this announcement.
=====================================================================
                    2nd International Workshop on
         High Performance Bioinformatics and Biomedicine (HiBB)
                  August 30th 2011, Bordeaux, France
                             HiBB 2011
            http://staff.icar.cnr.it/cannataro/hibb2011/

                        held in conjunction with
                              Euro-Par 2011
                            Bordeaux, France
                    August 29th - September 2nd, 2011
                  http://europar2011.bordeaux.inria.fr/
=====================================================================
                        * * * CALL FOR PAPERS * * *
=====================================================================
High-throughput technologies (e.g. microarray and mass spectrometry) and
clinical diagnostic tools (e.g. medical imaging) are producing an
increasing amount of experimental and clinical data. In such a scenario,
large scale databases and bioinformatics tools are key tools for
organizing and exploring biological and biomedical data with the aim to
discover new knowledge in biology and medicine.
High-performance computing may play an important role in many phases of
life sciences research, from raw data management and processing, to data
analysis and integration, till data exploration and visualization. In
particular, at the raw data layer, Grid infrastructures may offer the huge
data storage needed to store experimental and biomedical data, while
parallel computing can be used for basic pre-processing (e.g. parallel
BLAST) and for more advanced analysis (e.g. parallel data mining). In such
a scenario, novel parallel architectures (e.g. e.g. CELL processors, GPUs,
FPGA, hybrid CPU/FPGA) coupled with emerging programming models may
overcome the limits posed by conventional computers to the mining and
exploration of large amounts of data.
At an higher layer, emerging biomedical applications need to use in a
coordinated way both bioinformatics tools, biological data banks and
patient?s clinical data, that require seamless integration, privacy
preservation and controlled sharing. Service Oriented Architectures and
semantic technologies, such as ontologies, may allow the building and
deployment of the so called ?collaboratories?, where experimental research
may be conducted by remote scientists in a collaborative way.
The goal of HiBB is to bring together scientists in the fields of high
performance computing, computational biology and medicine to discuss,
among the others, the organization of large scale biological and
biomedical databases and the parallel implementation of bioinformatics
algorithms and biomedical applications. Furthermore, the use of novel
parallel architectures and dedicated hardware to implement bioinformatics
and biomedical algorithms will be discussed.

TOPICS OF INTEREST
The workshop is seeking original research papers presenting applications
of parallel and high performance computing to biology and medicine. Topics
of interest include, but are not limited to:

- Large scale biological and biomedical databases
- Data integration and ontologies in biology and medicine
- Parallel bioinformatics algorithms
- Parallel visualization and exploration of biomedical data
- Parallel visualization  and analysis of biomedical images
- Computing environments for large scale collaboration
- Scientific workflows in bioinformatics and biomedicine
- (Web) Services for bioinformatics and biomedicine
- Grid Computing for bioinformatics and biomedicine
- Peer-To-Peer Computing for bioinformatics and biomedicine
- Emerging architectures and programming models (e.g. Cell, GPUs) for
bioinformatics and biomedicine
- Parallel processing of bio-signals
- Modeling and simulation of complex biological processes

PROGRAM
The workshop will take place on August, 30th. It is scheduled as full-day.
The program is not available yet.


PAPER SUBMISSION, REGISTRATION AND PUBLICATION
We invite original previously unpublished contributions. Submission
implies that at least one author will register for the workshops at
Euro-Par 2011 and present the paper in the workshop session, if accepted.
Full papers should not exceed 10 pages in the Springer LNCS style
(http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0).
Paper submission has to be performed by using the HiBB EasyChair
submission server (https://www.easychair.org/conferences/?conf=hibb2011).
In case of problems, authors may send their manuscript in PDF to the
workshop chair: cannataro AT unicz.it.
Papers accepted for publication must also be supplied in source form
(Latex or Word).
All accepted and presented papers will be included in the Workshops
proceedings, that will be published in a separate Springer LNCS Euro-Par
2010 Workshop volume after the conference. Deadline for submitting camera
Authors of accepted papers will be required to sign up a Springer
copyright form.

JOURNAL SPECIAL ISSUE
At the end of the workshop, we plan to invite the best 4-6 papers of the
workshop for a special section on an international journal.

IMPORTANT DATES
Full papers submission: 	June 6, 2011
Decision Notification: 	July 15, 2011
Final papers due: 	August 5, 2011
Workshop session: 	August 30, 2011

Final review comments:	 October 1, 2011
Camera ready papers for EuroPar Workshop Proceedings: October 15, 2011

WORKSHOP ORGANIZER
Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy

PROGRAM COMMITTEE (TO BE CONFIRMED)
1. Pratul K. Agarwal, Oak Ridge National Laboratory, USA
2. David A. Bader, College of Computing, Georgia University of Technology,
USA
3. Ignacio Blanquer; Universidad Polit?cnica de Valencia, Valencia, Spain
4. Daniela Calvetti, Case Western Reserve University, USA
5. Werner Dubitzky, University of Ulster, UK
6. Ananth Y. Grama, Purdue University, USA
7. Concettina Guerra, University of Padova, Italy
8. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain
9. Salvatore Orlando, University of Venezia, Italy
10. Omer F. Rana, Cardiff University, UK
11. Richard Sinnott; National e-Science Centre, University of Glasgow,
Glasgow, United Kingdom
12. Fabrizio Silvestri, ISTI-CNR, Italy
13. Erkki Somersalo, Case Western Reserve University, USA
14. Paolo Trunfio, University of Calabria, Italy
15. Albert Zomaya, University of Sydney, Australia




****************************************
New book release
Handbook of Research on Computational Grid Technologies for Life Sciences,
Biomedicine, and Healthcare
ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical
Information Science Reference an imprint of IGI Global
http://www.igi-global.com/reference/details.asp?id=34292
Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy
****************************************
Prof. Mario Cannataro,
Informatics and Biomedical Engineering,
University "Magna Gr?cia" of Catanzaro,
Viale Europa (Localit? Germaneto), 88100 CATANZARO, ITALY,
Tel: 0961-369 4100, Fax: 0961-369 4073/4090, Email: cannataro at unicz.it,
Web: http://bioingegneria.unicz.it/~cannataro/
****************************************