From bioscience.ws from gmail.com Mon Aug 4 06:33:04 2008 From: bioscience.ws from gmail.com (bioscience.ws@gmail.com) Date: Wed Aug 6 13:14:34 2008 Subject: [Bionews] BioScience Web Site ( http://www.bioscience.ws/ ) Message-ID: We have launched a new BioScience Web Site ( http://www.bioscience.ws/ ) BioScience Web Site's mission is to organize the world's biological science information and make it universally accessible and useful by utilizing the skyrocketing success of the World Wide Web. The objective of this site is to promote biological knowledge in everyday life to serve science and society. The site aims to be a one stop location for everyone: the concerned public, educators, students, and biological science professionals. We intend to educate, facilitate, inform, and direct attention to as many sources of biology- related information as possible. BioScience Web Site offers specialized search engines, a comprehensive encyclopedia, a dictionary with thousands of terms, an events scheduler, a job board application, method and protocol articles, free blog and web hosting services, interactive location maps, links to external resources, tools and tutorials, and many other biology- related products. Please help us grow our content! Let us know about anything that we may have missed to list here. We welcome any comments and suggestions for improvement of the site. -Admin BioScience.ws http://www.bioscience.ws/ From watson from ebi.ac.uk Wed Aug 13 09:12:33 2008 From: watson from ebi.ac.uk (James Watson) Date: Wed Aug 13 12:52:41 2008 Subject: [Bionews] Hands-on courses at the European Bioinformatics Institute Message-ID: <48A2EBD1.2090807@ebi.ac.uk> Dear colleagues, As part of the European Molecular Biology Laboratory, the European Bioinformatics Institute (www.ebi.ac.uk) is a non-profit research institute that plays a central role in Europe's efforts to store, organise and make biological data freely available. As part of our mission, we provide hands-on training courses to assist wet-lab researchers in accessing this information and using the tools we provide to analyse their own data. For details of all of our training opportunities please visit our website (www.ebi.ac.uk/training/) We would like to draw your attention to one of our upcoming hands-on courses called "A two-day dip into the EBI’s data resources: Understanding your data". This will be held on 6-8 October 2008 at the European Bioinformatics Institute in Hinxton, Cambridgeshire, UK. This course provides a broad introduction to EBI core resources and practical, trainer-guided demonstration of when, why and how to use them. Several resources will be covered spanning genomics to systems biology. In addition to presenting practical information on the range of EBI resources and how to use these tools, this course aims to illustrate their application to research by using a range of case studies. In this way, use of the resources is presented with reference to biological questions. Topics include * EB-eye search engine * EBI Literature resources * Ensembl (genomes) * ArrayExpress (microarray data) * UniProt (protein sequences) * MSD (macromolecular structures) * IntAct (protein–protein interactions) * PRIDE (proteomics) * Reactome (pathways) The course costs £50 and interested candidates are encouraged to apply online at the URL below (the training is free, however we need to charge participants an administration fee of £25 per day to cover food and materials, and participants need to pay their own travel and accommodation): http://www.ebi.ac.uk/training/handson/course_081006_ebidata.html This course will have a maximum number of 40 participants on a first come first serve basis, so please register early to avoid disappointment. *The deadline for registering for this event is Monday 8 September 2008* Best regards, James Watson -- James D Watson Scientific Training Officer EMBL-EBI Wellcome Trust Genome Campus Hinxton Tel: +44(0)1223 492541 http://www.ebi.ac.uk/training/ Upcoming hands on training courses (http://www.ebi.ac.uk/training/handson/): 26-27 August 2008: Interactions and Pathways 1-3 September 2008: Joint EBI–ENFIN workshop - Protein function prediction tools 8-11 September 2008: Programmatic access in Perl: webservices & work flows 6-8 October 2008: 2-day dip into the EBI’s data resources: Understanding your data 24-27 November 2008: Programmatic access in Java: webservices & work flows From sticher from bioc.unizh.ch Mon Aug 18 10:36:56 2008 From: sticher from bioc.unizh.ch (Patrick Sticher) Date: Mon Aug 18 16:05:00 2008 Subject: [Bionews] 6th NCCR Symposium on New Trends in Structural Biology: New Program / Registration deadline August 29 Message-ID: <48A99718.9090001@bioc.unizh.ch> Dear colleagues, 6th International NCCR Symposium on New Trends in Structural Biology 8 + 9 September 2008, University of Z?rich, Z?rich, Switzerland NEW PROGRAM. The opening lecture will now be given by Gebhard Schertler about "Structure of the stress hormone receptor: beta1 adrenergic receptor". Confirmed plenary lecturers are Markus Gr?tter, Stephen C. Kowalczykowski, Kaspar Locher, Keiichi Namba, Poul Nissen, Andrej Sali, Gebhard F.X. Schertler, Jeffrey Skolnick, and A. Joshua Wand. The meeting will be held together with the Annual Meeting of the Swiss Society for Crystallography. Speakers of the society are Clemens Schulze-Briese and Colin Nave. Please see the symposium website for the complete program. REGISTRATION SLOT EXPIRES AUGUST 29. Please note that online registrations can be accepted for only a few more days until August 29. INFORMATION AND REGISTRATION. www.structuralbiology.uzh.ch/symposium2008.asp Please do not hesitate to contact me anytime if you need further information (sticher@bioc.uzh.ch). With best regards, Patrick Sticher The NCCR Structural Biology is a research initiative of the Swiss Science Foundation. Its research encompasses the fields of recombinant protein technologies, macromolecular structure determination and computational biomolecular sciences with a special focus on membrane proteins and supramolecular assemblies/interactions. 19 research groups from Swiss Universities and Research Institutions participate in this network. www.structuralbiology.uzh.ch/ _________________________________ Dr. Patrick Sticher Moser NCCR Scientific Officer Institute of Biochemistry University of Z?rich Winterthurerstrasse 190 CH - 8057 Z?rich Phone +41 / (0)44 / 635 54 84 Fax +41 / (0)44 / 635 59 08 From jacoponegroni from hotmail.it Thu Aug 21 07:43:45 2008 From: jacoponegroni from hotmail.it (Jacopo Negroni) Date: Thu Aug 21 11:58:34 2008 Subject: [Bionews] Invitation to the 10th EMBL PhD Symposium Oct 23 - 25 Message-ID: Dear Subscribers, The 2008 EMBL PhD Symposium held at EMBL Heidelberg from October 23rd to 25th calls for applications from PhD students and young scientists. The symposium is the 10th in a series of very successful international conferences for young scientists, organized by PhD students of the European Molecular Biology Laboratroy - EMBL. The topic of this year's symposium is „Decision Making in Biology – Nature at the Crossroads". Four sessions will adress decisions at different levels of complexity, moving from cells to populations and from molecules to the animal mind. Confirmed Speakers include Nobel Prize Laureate Tim Hunt (Cambridge University), Baroness Susan Greenfield (Oxford University), Nenad Ban (ETH Zuerich) and Hans Schoeler (MPI Muenster). Beside excellent lectures, the symposium offers an interactive environment which is acclaimed by both the junior and the senior scientists. Online registration closes 7th September, we strongly encourage submission of poster abstracts and applications for participant talks. The speakers will choose a poster prize winner. Registration fee is 100 Euros and includes accomodation and meals. Selected participants, e.g. the winner of the poster prize, are refunded their registration fee. For further information about Heidelberg, the EMBL and the symposium itself, please visit the symposium website at http://phdsymposium.embl.org or write to phdsymposium2008@embl.de We appreciate your assistance in forwarding the notice to colleagues who may be interested in the symposium. Thank you for your help. Yours sincerely, The PhD Student Symposium Organising Committee This conference is supported by the European Commission's Marie Curie SCF (Series of Conferences & Training Courses) Action, under the Sixth Framework Programme (FP6). _________________________________________________________________ Connect to the next generation of MSN Messenger  http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline From koster.jan from gmail.com Mon Aug 25 06:23:02 2008 From: koster.jan from gmail.com (koster) Date: Mon Aug 25 09:58:08 2008 Subject: [Bionews] Pubreminer Update Message-ID: <12d7c086-6b9b-47c2-904e-8e194d9c5a62@s50g2000hsb.googlegroups.com> PubMed PubReminer: Detailed analysis of PubMed search results In the vast amounts if medical literature, finding information tailored to your needs and interest is becoming more and more complex. Using the right keywords is essential for effective searches, but which ones should you use? Pubreminer is a free web-based tool that allows simple text-based query building and information gathering (mining) of the NCBI literature search engine PubMed. Pubreminer presents its results, gathered from abstracts, in frequency tables of journals, authors, words, year of publication, mesh terms, substances and countries which can subsequently be included/excluded in an iterative fashion. This process provides you a guide through large bodies of literature automatically homes in on papers of your interest. Once done with refinements, you simply take the query build in pubreminer and view it in PubMed with a click of the mouse. Next to building efficient queries, Pubreminer can also be helpful in other areas: *Selecting a journal for your current work (by scanning the most often used journals of similar research) *Finding experts in a research area (by viewing the authors associated with your query) *Determine the research interest of an author (by viewing the keywords associated with an author) Recently, field subtypes (like first and last author) and toggles for output have been added. Furthermore some routines have been rewritten to allow the processing of up to 10.000 abstracts for initial queries. The Website can be accessed at : http://bioinfo.amc.uva.nl/human-genetics/pubreminer From Rob.Reedijk from douglasconnect.com Wed Aug 27 08:52:11 2008 From: Rob.Reedijk from douglasconnect.com (Robby) Date: Wed Aug 27 12:30:28 2008 Subject: [Bionews] Bursary Award - eCheminfo Community of Practice Workshop, India, December 2008 Message-ID: I am posting details for the eCheminfo Community of Practice Drug Discovery Design Methods & Applications Workshop Meeting in December 2008 in Hyderabad, India. Please note that the deadline to apply for the bursary is September 12, 2008. Drug Discovery Design Methods & Applications Workshop December 15-18, 2008 IIIT Hyderabad, Hyderabad, India Please visit http://echeminfo.colayer.net/comty_hyderabadworkshop08 Virtual screening, structure-based drug design, lead optimisation and predictive ADME/toxicology supporting decision making in drug discovery a Hands-on eCheminfo Workshop This workshop precedes the “Latest Advances in Drug Discovery Modelling & Informatics” eCheminfo Community of Practice InterAction Meeting December 19-20, 2008 Co-organised in Partnership by IIIT Hyderabad , JNU NewDelhi , Seascape Learning, and Douglas Connect Facilitated by Barry Hardy Work through in detail and discuss practical examples, methods and emerging techniques with leading modelling experts! Virtual Screening & Docking Structure-based Drug Design Ligand Optimisation & Library Design Structure Search, Similarity and Property Estimation Data Mining, Analysis & Visualisation Pharmacophore Modelling for Lead Identification Fragment-based Drug Design Predictive ADME QSAR-based Predictive Toxicology These workshops are aimed to provide a set of stimulating workshops using latest advanced modelling techniques of relevance to chemists, life scientists and modellers working in drug discovery. Participants should return to their labs with new ideas, best practices and software experiences to maximise productivity in their own drug discovery research activities. Workshop groups will study problems with hands-on examples using leading-edge software and discuss complex issues highlighted by examples and case studies presented by instructors. Software packages and an IT classroom will be used by instructors and participants to work through drug discovery and optimisation problems. Participants may propose problems and issues to the faculty ahead of the workshop. Participants will also have ample opportunity to discuss their perspectives and criticisms of the methods studied and should take-away key nuggets of understanding from these intensive sessions. Workshop Leaders Johann Gasteiger (Molecular Networks, Germany), Jeff Wiseman (Locus Pharmaceuticals, USA), Indira Ghosh (JNU, New Delhi, India), Paul Hawkins (OpenEye, USA), Barry Hardy (Douglas Connect, Switzerland), Peter Oledzki (BioSolveIT, Germany), Dhananjay Bhattacharyya (Saha Institute of Nuclear Physics, India), Ismael Zamora (Pompeu Fabra University and Lead Molecular Design, Spain), Wojciech Plonka (Fujitsu Group, Japan), Madhavi Sastry (Schrodinger) A Bursary Award will be used to support the attendance of one academic participant at the workshop. Please visit http://echeminfo.colayer.net/comty_hyderabadworkshop08 For further information and questions on the Workshop program, please contact Dr. Barry Hardy at: barry.hardy -[at]- douglasconnect.com, Tel: +41 61 851 0170 . For international registrations, please contact Nicki Douglas, nicki.douglas –[at]- douglasconnect.com, Tel: +41 61 851 0461 If you are located in India, please contact Sunil Chawla at: sunil - [at] -seascapelearning.com, Tel: +91 981 0305 923 or Om Prakash at Tel: +91 985 0709 150 to complete your registration and payment in Rs. For more information, please visit http://seascapelearning.com/echeminfo_reg.html Rob Reedijk eCheminfo Community of Practice From gws from ncifcrf.gov Wed Aug 27 14:18:36 2008 From: gws from ncifcrf.gov (Gary Smythers) Date: Thu Aug 28 11:04:03 2008 Subject: [Bionews] Announcement: GenPept 167.0 available Message-ID: <20080827191836.2720A13C4C4@bio1.ncifcrf.gov> This is to announce the availability of release 167.0 of the GenPept(R) (GenBank Gene Products) Database. GenPept is provided in a format similar to that formerly distributed by GenBank(R) under the administration of Intelligenetics Inc. This GenPept release IS _NOT_ AN OFFICIAL RELEASE FROM THE NCBI-GENBANK, but an attempt to provide a data file format compatible with existing software products. This data format is suitable as an input data file for the GCG program genbanktogcg -genpept. Compatibility with other software has not been tested. Site: ftp.ncifcrf.gov Directory: pub/genpept Files: gprel.txt.gz, gpdat.seq.gz, gpdat.fasta.gz Directory: pub/genpept/divisions Files: 1 file for each GenBank file Directory: pub/genpept/updates (daily, cumulative) Files: gpseq_updates.dat.gz Rel. Date: 27-Aug-2008 If you have questions or comments concerning this data, or you experience any difficulty in downloading the data via ftp, please contact: Gary Smythers gws@ncifcrf.gov 301-846-5778 or Bob Stephens bobs@ncifcrf.gov ================================================================ GenPept (R) and GenBank (R) are registered trademarks of the U.S. Department of Health and Human Services for the GenBank Gene Products and the GenBank Genetic Sequence Data Banks.