From drkjroberts from gmail.com Sun Mar 1 13:42:43 2009 From: drkjroberts from gmail.com (Karl Roberts) Date: Sun Mar 1 15:25:23 2009 Subject: [Bionews] International Science and Engineering Fair - Call for Judges Message-ID: Hi, I am the Plant Sciences Grand Awards Co-Chair for the Intel International Science and Engineering Fair to be held May 10-15, 2009 in Reno, Nevada. I am actively seeking individuals to serve as Grand Awards Judges for the upcoming event. The ISEF is the premier world-wide showcase for student researchers from grades 9-12. This year students from 45 different countries compete for over $4 million dollars in cash awards, scholarships and special awards. In order to assure the quality of our winners, we need your help. As professionals in the biological sciences, you provide the knowledge and expertise necessary to choose the absolute best student finalists from among the many excellent research projects at this year's Fair. If you or your collegues are interested in becoming a Grand Awards judge this year, please visit the official ISEF website: http://www.sciserv.org/isef/judges/index.asp or feel to contact me via e-mail at kroberts@pgcc.edu or by phone at (301) 386-7544. Thanks for your consideration, and I hope to hear from you. Karl J. Roberts, Ph.D. Plant Sciences Grand Awards Co-Chair Intel ISEF From Mike.Fursov from gmail.com Wed Mar 11 09:26:08 2009 From: Mike.Fursov from gmail.com (Mikhail Fursov) Date: Wed Mar 11 12:31:53 2009 Subject: [Bionews] Unipro UGENE v1.4 released Message-ID: <85479388-8761-4760-ab99-6c1c0263b5cf@e5g2000vbe.googlegroups.com> After several months of work our team is glad to announce a new version of free and open-source UGENE bioinformatics suite. Version 1.4 adds 4 new plugins and brings numerous improvements and bug fixes. New plugins: restriction enzymes support, complete Smith-Waterman algorithm, repeats analysis and exportable sequence and alignment statistics. The major user interface improvements were made in Workflow Designer, Sequence and Project views. Most of the computational algorithms (like MUSCLE) are now able to work in parallel mode. HMMER2 integration got SSE2 optimized version. PDB and MMDB 3D structures viewer now is able to save 3D models in 2D vector format. ... The complete list of changes can be found here: http://ugene.unipro.ru/changelist.html Project web site: http://ugene.unipro.ru/ From cathy.lawson from rutgers.edu Fri Mar 13 23:11:53 2009 From: cathy.lawson from rutgers.edu (Cathy Lawson) Date: Sat Mar 14 12:21:18 2009 Subject: [Bionews] EM Databank News, March 2009 Message-ID: <71848DFC-BA95-4EA5-9A00-E01AE3F2489F@rutgers.edu> We are pleased to announce improvements to EM Databank deposition and retrieval services hosted by PDBe (Europe) and RCSB PDB (USA). Joint Map + Model Deposition Map deposition has been integrated with fitted coordinate model deposition to the PDB. Upon completion of an EMDEP3 map deposition session, the user is presented with the option to deposit one or more coordinate models to the PDB using AUTODEP (PDBe) or ADIT (RCSB PDB). Experiment-related metadata is automatically transferred to the PDB coordinate deposition session. EMViewer EMViewer, a 3D java map viewer, is now accessible from EMDB atlas visualization pages at both sites. Clicking on the "Launch EMViewer" button will bring up a simple representation of the map displayed at a single isocontour level that can be manipulated by mouse drag and click actions. The EMDB contains more than 600 experimentally determined three- dimensional maps and associated experimental data and files, and is funded by NIH GM079429 to Baylor College of Medicine, Rutgers University, and the European Bioinformatics Institute, and EU Sixth Framework Programme 3D-EM Network of Excellence contract LSHG- CT-2004-502828 to EBI. Sincerely, The Unified Data Resource for CryoEM Project Team Unified Data Resource for CryoEM: http://emdatabank.org EMDB in Europe: http://www.ebi.ac.uk/pdbe/emdb From clements from nescent.org Mon Mar 16 15:51:33 2009 From: clements from nescent.org (Dave Clements) Date: Mon Mar 16 16:15:50 2009 Subject: [Bionews] 2009 GMOD Summer Schools - Americas & Europe In-Reply-To: References: Message-ID: We are now accepting applications for the 2009 GMOD Summer Schools: Americas, 16-19 July ?- National Evolutionary Synthesis Center (NESCent), Durham, NC, USA ?- Student tuition is free, thanks to NIH grant 1R01HG004483-01. ?- http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas Europe, 3-6 August ?- University of Oxford, Oxford, United Kingdom ?- Part of GMOD Europe 2009, which includes the next GMOD Meeting ?- Student tuition is ?95 ?- http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe GMOD (http://gmod.org/) is a collection of interoperable open source software components for managing, visualizing, annotating and integrating biological, mostly genomic, data. ?GMOD is also a community of developers and users dealing with similar challenges. GMOD is used in diverse contexts, with both emerging and established model organisms. GMOD Summer Schools (http://gmod.org/wiki/GMOD_Summer_School) introduce new GMOD users to the GMOD project and feature several days of hands-on training on how to install, configure and administer GMOD tools. The courses includes training on several GMOD components: ?* GBrowse - the widely used Generic Genome Browser ?* Chado - a modular and extensible database schema for biological data ?* Apollo - genome annotation editor ?* BioMart - biological data warehouse system ?* GBrowse_syn - a GBrowse based synteny viewer ?* JBrowse - a brand new Web 2.0 genome browser ?* Artemis-Chado Integration (Europe only) ?* MAKER - Genome annotation pipeline (Americas only) ?* Tripal - Web front end for Chado (Americas only) ***Please submit an application by the end of 6 April 2009, if you are interested in attending. *** Enrollment is limited to 25 students in each course. ?If applications exceed capacity (and we expect they will) then applicants will be picked based on the strength of their application. ?Applicants will be notified of their admission status in mid-April. Thanks, Dave Clements GMOD Help Desk help@gmod.org http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe http://gmod.org/wiki/GMOD_Europe_2009 From tekaia from pasteur.fr Fri Mar 20 13:18:47 2009 From: tekaia from pasteur.fr (Fredj Tekaia) Date: Fri Mar 20 14:23:21 2009 Subject: [Bionews] Last call: Bioinformatics and Comparative Genome Analysis EMBO course in Hong Kong Message-ID: Last Call for application to the : Bioinformatics and Comparative Genome Analysis course August 17 - August 29, 2009 HKU-Pasteur Research Centre - Hong Kong Deadline for application: April 15, 2009. Course program: http://www.pasteur.fr/~tekaia/BCGA2009/ BCGA2009_Prog.html Duration: Full time from August 17 to August 29, 2009. Location: Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China. Accommodation and social: Acceptance to the course includes free accommodation (double room based) breakfast, lunch and dinner. More information about the course, how to apply and application form can be found at the following web page: http://www.pasteur.fr/~tekaia/ BCGA2009.html Organizers/Contact: Roberto Bruzzone, HKU-Pasteur Research Centre - Hong Kong. Si Lok, Genome Research Center The University of Hong Kong - Hong Kong. Tin Wee Tan, National University of Singapore - Singapore. Ueng-Cheng Yang, National Yang-Ming University, Taipei - Taiwan. Fredj Tekaia, Institut Pasteur Paris - France. With financial support from: EMBO - Institut Pasteur Paris. From mourad12345678 from yahoo.com Wed Mar 25 11:31:48 2009 From: mourad12345678 from yahoo.com (Mourad Elloumi) Date: Wed Mar 25 11:45:28 2009 Subject: [Bionews] BIOKDD'09 : Extended Deadline Message-ID: <848939.70341.qm@web31504.mail.mud.yahoo.com> CALL FOR PAPERS Higher School of Sciences and Technologies of Tunis (Tunisia) And Faculty of Applied Sciences, Bucharest (Romania) Organize Biological Knowledge Discovery from Databases (BIOKDD'09) Workshop held in parallel with 20th International Conference on Database and Expert Systems Applications (DEXA'09) www.dexa.org University of Linz, Austria August 31 - September 4, 2009 With the development of Biology during the last decades, we are witnessing an exponential growth of both the volume and the complexity of biological databases. For example, the Human Genome Project provided the sequence of the 3 billion DNA bases that constitute the human genome. And, consequently, we are provided too with the sequences of about 100,000 proteins. Therefore, we are entering the post-genomic era : After having focused so much efforts on the accumulation of biological data in databases, we have now to focus as much efforts, and even more, on the analysis of these data. Analyzing this huge volume of biological data stored in databases is a challenging task because, not only, of its complexity and its multiple numerous correlated factors, but also, because of the continuous evolution of our understanding of the biological structural and evolutionary mechanisms. Knowledge Discovery from Databases (KDD) is a response to these new trends. You are invited to submit a draft paper in PDF format before March 31, 2009 via DEXA'09 ConfDriver. Papers should not exceed 5 pages in IEEE format www.ieee.org/ web/publications /authors/ transjnl/ index.html All accepted papers will be published in the proceedings of DEXA'09 Workshops with IEEE CSP. One of the authors of an accepted paper must register to DEXA'09 conference and present the paper at BIOKDD'09 workshop. Program Committee: Mourad Elloumi, University of Tunis, Tunisia, (PC Chair) Cristian Toma, Politehnica University, Bucharest, Romania (PC Co-Chair) Jin-Kao Hao, University of Angers, France Beatrice Duval, University of Angers, France Abdelouahid Lyhyaoui. Abdelmalek Essaadi University, Tanger, Morocco El-Ghazali Talbi, University of Sciences and Techniques of Lille, France Xiangchao Gan, University of Oxford, UK Kathleen Steinhofel, King's College London, UK Dragan Bosnacki, Eindhoven University of Technology, Netherlands Important Dates: Submission of Full Papers: March 31, 2009 Notification of Acceptance: May 10, 2009 Camera-ready Copies: May 31, 2009 From clements from nescent.org Sun Mar 29 23:32:49 2009 From: clements from nescent.org (Dave Clements) Date: Mon Mar 30 11:52:10 2009 Subject: [Bionews] Re: 2009 GMOD Summer Schools - Americas & Europe In-Reply-To: References: Message-ID: ***The application deadline for both GMOD summer schools is April 6, one week from now.*** GMOD Summer School - Americas will be held 16-19 July at the National Evolutionary Synthesis Center (NESCent), in Durham, NC, USA. Student tuition is free. See http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas GMOD Summer School - Europe will be held 3-6 August at the University of Oxford, in Oxford, UK. This is a part of GMOD Europe 2009, which includes the next GMOD Meeting. Student tuition is ?95. See http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe Please contact the GMOD Help Desk (help@gmod.org) if you have questions. We hope to see you in Durham or Oxford, Dave C. On Mon, Mar 16, 2009 at 1:51 PM, Dave Clements wrote: > We are now accepting applications for the 2009 GMOD Summer Schools: > > Americas, 16-19 July > ?- National Evolutionary Synthesis Center (NESCent), Durham, NC, USA > ?- Student tuition is free, thanks to NIH grant 1R01HG004483-01. > ?- http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas > > Europe, 3-6 August > ?- University of Oxford, Oxford, United Kingdom > ?- Part of GMOD Europe 2009, which includes the next GMOD Meeting > ?- Student tuition is ?95 > ?- http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe > > GMOD (http://gmod.org/) is a collection of interoperable open source > software components for managing, visualizing, annotating and > integrating biological, mostly genomic, data. ?GMOD is also a > community of developers and users dealing with similar challenges. > GMOD is used in diverse contexts, with both emerging and established > model organisms. > > GMOD Summer Schools (http://gmod.org/wiki/GMOD_Summer_School) > introduce new GMOD users to the GMOD project and feature several days > of hands-on training on how to install, configure and administer GMOD > tools. > > The courses includes training on several GMOD components: > ?* GBrowse - the widely used Generic Genome Browser > ?* Chado - a modular and extensible database schema for biological data > ?* Apollo - genome annotation editor > ?* BioMart - biological data warehouse system > ?* GBrowse_syn - a GBrowse based synteny viewer > ?* JBrowse - a brand new Web 2.0 genome browser > ?* Artemis-Chado Integration (Europe only) > ?* MAKER - Genome annotation pipeline (Americas only) > ?* Tripal - Web front end for Chado (Americas only) > > ***Please submit an application by the end of 6 April 2009, if you are > interested in attending. *** > > Enrollment is limited to 25 students in each course. ?If applications > exceed capacity (and we expect they will) then applicants will be > picked based on the strength of their application. ?Applicants will be > notified of their admission status in mid-April. > > Thanks, > > Dave Clements > GMOD Help Desk > help@gmod.org > > http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas > http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe > http://gmod.org/wiki/GMOD_Europe_2009 >