From dan.bolser at gmail.com Wed Jun 2 11:23:50 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 2 Jun 2010 16:23:50 +0100 Subject: [BiO BB] SOL2010: early registration extended until June 14th Message-ID: SOL2010 ANNUAL CONFERENCE, DUNDEE SCOTLAND, September 5 ? 9 Dear Colleague The SOL2010 conference is approaching fast. Many thanks to those who have already registered it looks as if it will be an exciting meeting. We have decided to extend the Early Bird registration rate for two weeks only, until Monday June 14th 2010, so that those who have not yet done so can take advantage of the discounted rate. There will be no further extensions so if you want to save ?100 on the registration fee, please go the website and register now! https://reg.istrations.com/delegate/events/DNDSOL2010=20 Abstract submission can be found on this link: http://www.sol2010.org/Abstracts Accommodation Special rates have been arranged for conference guests at the conference hotel, the Apex City Quay and Spa, Dundee. Online Accommodation booking is available via this link (You will also be given the option to book your accommodation at the time of registration): https://www.conferencebookings.co.uk/delegate/DNDSOL2010 We look forward to welcoming you to Dundee in September. Glenn Bryan Gerard Bishop Graham Seymour ...and the rest of the SOL2010 team Please contact Anne Rendall if you have any enquiries email: SOL2010 at scri.ac.uk This is a reminder that the Call for Challenge entries for the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) closes in two weeks on June 21, 2010. The theme of the 2010 iEvoBio conference challenge is "New visualization methods for evolutionary data". Visualizing evolution is a key part of our discipline and presents opportunities as much as it does obstacles. The iEvoBio Challenge is deliberately wide ranging: entries could range from geophylogenies to visualizing extremely large phylogenetic trees, to mashups showing relationships between lineages and other types of data (e.g. conservation status). Further information on the nature of challenge entries and how to submit them can be found on the iEvoBio website at http://ievobio.org/challenge.html . Selected candidates will make short oral presentations to demonstrate their visualization in a "Challenge session" at the conference, and will automatically be entered into the Software Bazaar if suitable. The winners of the Challenge will be judged collectively by the iEvoBio participants. There will be cash prizes for the first place ($1,000) and runner up entries. Challenge entries are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks, 3) Software Bazaar entries, and 4) Birds-of-a-Feather gatherings. The Calls for Lightning Talks and Software Bazaar entries remain open (see http://ievobio.org/ocs/index.php/ievobio/2010/), and information on the Birds-of-a-Feather session is forthcoming. More details about the program and guidelines for contributing content are available at http://ievobio.org. Continuous updates can also be found on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) From idoerg at gmail.com Tue Jun 8 10:29:51 2010 From: idoerg at gmail.com (Iddo Friedberg) Date: Tue, 8 Jun 2010 10:29:51 -0400 Subject: [BiO BB] COMBREX Workshop for Computational and Experimental Determination of Protein Function Message-ID: Announcing the first COMBREX Workshop for Computational and Experimental Determination of Protein Function COMBREX (Computational Bridge to Experiments) is a new NIH funded effort that aims to increase the pace of experimental determination of the function of large and high priority gene families in bacterial genomes. Led by Richard Roberts (New England Biolabs) Simon Kasif (Boston University) and Martin Steffen (Boston University), this effort will form a consortium of experimental and computational biologists that would collaborate directly to test the predicted functions or specificity of high-priority genes. Central to this effort would be the creation of a community web-based database that would allow computational and experimental scientists to communicate easily and assist experimentalists in identifying high-priority genes with high-quality computational predictions. Experimentalists will be able to submit bids (proposals) to validate individual predictions, and if successful, will receive modest funding from COMBREX to perform the validation. The website can be found at . A workshop to discuss issues related to the formation and operation of COMBREX will take place on Wednesday, September 15, 2010, as part of the 18th Annual International Meeting on Microbial Genomics at Lake Arrowhead, CA, outside of Los Angeles. A preliminary program can be found at http://www.mimg.ucla.edu/arrowhead2010/program.html (COMBREX is formerly SciBay). Confirmed speakers include Richard Roberts, Simon Kasif, Manuel Ferrer (CSIC, Madrid), Patricia Babbit (UCSF), John Gerlt (Illinois), Peter Karp (SRI), Alexander Yakunin (Toronto) Steven Brednner (UC Berkeley) and Bruno Sobral (Virginia Tech). The morning session will provide an overview of COMBREX, including both the experimental and computational challenges, related talks, and a description of topics to be discussed by breakout groups. These groups will convene in the afternoon to discuss the topics and prepare a short summary, for presentation to the entire workshop after dinner. Topics to be discussed by the breakout groups will roughly divide into the following areas: (1) whole genome annotation, (2) assessment of computational predictions, (3) use of structure to predict function, and (4) infrastructure for function annotation. General topics to be discussed include: 1. How to prioritize predictions? 2. How to evaluate experimental bids? 3. How to handle non-enzymatic proteins? 4. How best to handle predictions/phenotypes from high-throughput experimentation. A key desired outcome of the workshop is identifying opportunities and catalyzing collaborations between computational and experimental biologists. We hope you will be able to join us for this event. You can register at http://www.mimg.ucla.edu/arrowhead2010/registration.html For further information please contact the organizers: Co-chairs: Martin Steffen, Boston University, steffen at bu.edu Iddo Friedberg, Miami University, i.friedberg at muohio.edu Steering Committee: Simon Kasif and Richard J. Roberts -- Iddo Friedberg http://iddo-friedberg.net/contact.html From christoph.gille at charite.de Wed Jun 9 06:46:20 2010 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 9 Jun 2010 12:46:20 +0200 Subject: [BiO BB] kegg format changed Message-ID: Dear Colleagues, The format of the reaction-List in KEGG www.genome.jp/kegg/ has changed recently. Therefore features of the STRAP / Metannogen-software http://www.bioinformatics.org/strap/ were not working for a while. Please be aware that also other Bioinformatics software using KEGG might be affected. This shows how important it is to contact the author of a Bioinformatics program if something stopped working. it was: PATHWAY PATH: rn00130 Ubiquinone and other terpenoid-quinone biosynthesis PATH: rn01053 Biosynthesis of siderophore group nonribosomal peptides PATH: rn01100 Metabolic pathways ENZYME 5.4.4.2 Now it is: PATHWAY rn00130 Ubiquinone and other terpenoid-quinone biosynthesis rn01053 Biosynthesis of siderophore group nonribosomal peptides rn01100 Metabolic pathways rn01110 Biosynthesis of secondary metabolites ENZYME 5.4.4.2 Cheers Christoph From marty.gollery at gmail.com Wed Jun 9 13:46:24 2010 From: marty.gollery at gmail.com (Martin Gollery) Date: Wed, 9 Jun 2010 10:46:24 -0700 Subject: [BiO BB] kegg format changed In-Reply-To: References: Message-ID: Thanks for the info, Christoph. I have a rarely-used program that uses KEGG and it is nice to have the info before it breaks! Marty Gollery On Wed, Jun 9, 2010 at 3:46 AM, Dr. Christoph Gille < christoph.gille at charite.de> wrote: > Dear Colleagues, > > The format of the reaction-List in KEGG www.genome.jp/kegg/ has > changed recently. Therefore features of the STRAP / > Metannogen-software http://www.bioinformatics.org/strap/ were > not working for a while. > > Please be aware that also other Bioinformatics software using KEGG > might be affected. > > This shows how important it is to contact the author of a > Bioinformatics program if something stopped working. > > it was: > PATHWAY PATH: rn00130 Ubiquinone and other terpenoid-quinone > biosynthesis > PATH: rn01053 Biosynthesis of siderophore group nonribosomal > peptides > PATH: rn01100 Metabolic pathways > ENZYME 5.4.4.2 > > > > Now it is: > PATHWAY rn00130 Ubiquinone and other terpenoid-quinone biosynthesis > rn01053 Biosynthesis of siderophore group nonribosomal peptides > rn01100 Metabolic pathways > rn01110 Biosynthesis of secondary metabolites > ENZYME 5.4.4.2 > > Cheers > > Christoph > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com From barry.hardy at vtxmail.ch Thu Jun 10 11:03:24 2010 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Thu, 10 Jun 2010 17:03:24 +0200 Subject: [BiO BB] Advancing Predictive Toxicology Strategies and Infrastructure Message-ID: <4C10FEBC.1050102@vtxmail.ch> We have had a lot of activity in recent months on the OpenTox project with regards to developing a linked data and resource infrastructure for the support of interdisciplinary predictive toxicology research and safety assessment. I enclose several links below including our recent overview workshop presentation in Potsdam, reports, demonstrations, technical links and interest groups. A paper will be published as an Open Access publication in coming weeks (reference below). best regards Barry Hardy OpenTox Project Coordinator (www.opentox.org) Connecting Your Resources to OpenTox and Other Connected Resources This is an expanding community effort and we welcome your involvement! If you have a useful resource you would like to see integrated into OpenTox, e.g., a database, bioinformatics tool, computational chemistry program etc., please contact me to discuss.We especially welcome high quality Open Source programs providing a valuable service to users. OpenTox Presentation on Integrating Predictive Toxicology Resources Potsdam, 30 May 2010 OpenTox Presentation: http://www.opentox.org/home/documents/presentations/opentoxpresPotsdam30May2010/view Program: http://www.opentox.org/data/blogentries/public/opentoxworkshoppotsdam2010 Strategies http://barryhardy.blogs.com/theferryman/2010/05/developing-new-predictive-toxicology-strategies.html OpenTox Reports (Open Access) http://www.opentox.org/home/documents/Reports OpenTox Demos (Open to all to Try!) (Please keep in mind these are early prototype applications and may not have features you want. We welcome requests from you for what you additionally need in these applications or others.) http://www.opentox.org/toxicity-prediction OpenTox Signup & Mailing List Complete the form at http://www.opentox.org/join_form Note: If you have a general interest and want to receive a monthly news update e.g., on new applications, data resources, ontology developments, news etc., select the "I'm interested in OpenTox news" option. We also welcome including news from other projects in the newsletter. Do not select the option "I'm interested in OpenTox Technical Development" unless you are doing technical computing work in the field as this list is quite technical and busy! OpenTox Collaboration Pool If you are interested in joining virtual organisation collaborations in predictive toxicology supported by OpenTox, complete the form linked from: http://www.opentox.org/data/blogentries/public/opentoxcollaborationpool Technical Development Details including API (Open Access) http://www.opentox.org/dev http://www.opentox.org/dev/apis Publication Reference (Open Access) Collaborative Development of Predictive Toxicology Applications, B. Hardy, N. Douglas, C. Helma, M. Rautenberg, N. Jeliazkova, V. Jeliazkov, I. Nikolova, R. Benigni, O. Tcheremenskaia, S. Kramer, T. Girschick, F. Buchwald, J. Wicker, A. Karwath, M. G?tlein, A. Maunz, H. Sarimveis, G. Melagraki, A. Afantitis, P. Sopasakis, D. Gallagher, V. Poroikov, D. Filimonov, A. Zakharov, A. Lagunin, T. Gloriozova, S. Novikov, N. Skvortsova, D. Druzhilovsky , S. Chawla, I. Ghosh, S. Ray, H. Patel, S. Escher, accepted 3 June 2010 for Open Access publication in J. Chemical Informatics http://www.jcheminf.com/ (2010). Barry Hardy PhD Director, Community of Practice & Research Activities and OpenTox Project Coordinator (www.opentox.org) Douglas Connect Baermeggenweg 14 4314 Zeiningen Switzerland Tel: +41 61 851 0170 From Phoebe.Chen at latrobe.edu.au Sun Jun 13 06:22:38 2010 From: Phoebe.Chen at latrobe.edu.au (Phoebe Chen) Date: Sun, 13 Jun 2010 20:22:38 +1000 Subject: [BiO BB] Deadline Approaching - APBC2011 (The NINth Asia Pacific Bioinformatics Conference) Message-ID: =============================================================== Deadline Approaching 20 July ! - Call for Papers - APBC2011 The NINth Asia Pacific Bioinformatics Conference Inchon, Korea, 11-14 January 2011 http://sysbio.kribb.re.kr/APBC2011/ =============================================================== The Asia Pacific Bioinformatics Conference (APBC) series, founded in 2003, (Previous APBC meetings APBC2010 (18-21 January 2010, Bangalore, India) APBC2009 (13-16 January 2009, Beijing, China) APBC2008 (14-17 January 2008, Kyoto, Japan) APBC2007 (14-17 January 2007, Hong Kong) APBC2006 (13-16 February 2006, Taipei, Taiwan) APBC2005 (17-21 January 2005, Singapore) APBC2004 (18-22 January 2004, Dunedin, New Zealand) APBC2003 (4-7 February 2003, Adelaide, Australia)) is an annual international forum for exploring research, development and applications of Bioinformatics and Computational Biology. The NINth Asia-Pacific Bioinformatics Conference, APBC2011 will be held in Inchon, Korea. The aim of the conference is to bring together researchers, professionals, and industrial practitioners from all over the world for interaction and exchange of knowledge and ideas in all areas of bioinformatics and computational biology. ---------------------------------------------------------------- Important Dates Paper submission: July 20, 2010 Author Notification: September 17, 2010 Final Version due on: October 9, 2010 Tutorial submission open Aug 1, 2010 Poster submission open September 20, 2010 Registration open Sept 20, 2010 Poster Acceptance Notification: October 20, 2010 Author registration deadline Oct 9, 2010 Early-bird registration Nov 30, 2010 Conference Jan 11-14, 2011 ----------------------------------------------------------------- APBC2011 invites high-quality original papers and posters on any topic related to Bioinformatics and Computational Biology. Accepted papers will be invited to be published in the journal: BMC Bioinformatics. ----------------------------------------------------------------- From hlapp at gmx.net Mon Jun 14 16:49:46 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 14 Jun 2010 16:49:46 -0400 Subject: [BiO BB] Birds-of-a-Feather gatherings for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <6C59B968-25C2-4951-9F8B-D97CFFF5F5DE@gmx.net> In anticipation of the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), we solicit all attendees to propose and discuss Birds-of-a-Feather gatherings. See below for details. Birds-of-a-Feather gatherings (BoFs) are informal, ad-hoc, focused face-to-face discussion groups that form around a shared interest. BoFs have a leader (usually, but not necessarily, the proposer) who initiates or moderates the discussion, but typically not a preset agenda. The topics of BoFs can range widely, including general cultural or computational infrastructure issues, or narrower questions such as how to make the best use of a particular software tool or how to solve a particular computational challenge. Anyone willing to lead such a group can propose a BoF. iEvoBio will provide space that can accommodate up to 8-10 BoFs. Sign-up sheets will be provided on-site on the first day of the conference where attendees can propose a BoF or sign up for one proposed by someone else. BoFs will be about 1 hr in duration and take place in the afternoon of the second day of the conference. In line with their informal nature, there is no official prior call for or submission of BoFs. However, we encourage those intending to propose one to sound out or rally potential attendees ahead of time. We suggest to employ Twitter (http://twitter.com) for this, using the #ievobioBof tag to mark BoF proposals and comments. Birds-of-a-Feather gatherings are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Lightning talks (waiting list only), 3) Challenge entries, and 4) Software Bazaar entries. The Calls for Challenge entries (http://ievobio.org/challenge.html) and Software Bazaar entries (http://ievobio.org/ocs/index.php/ievobio/2010/) remain open. 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. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) From contactus at sooryakiran.com Wed Jun 16 06:30:48 2010 From: contactus at sooryakiran.com (SooryaKiran) Date: Wed, 16 Jun 2010 03:30:48 -0700 Subject: [BiO BB] =?windows-1252?q?M=2E_Phil_Bioinformatics_=9210_=40_Univ?= =?windows-1252?q?ersity_of_Kerala?= Message-ID: *M. Phil Bioinformatics 2010 @ University of Kerala* * * Applications are invited for M. Phil Bioinformatics programme offered by the Centre for Bioinformatics, University of Kerala. MPhil Bioinformatics at Centre for Bioinformatics, University of Kerala is a innovative programme, being the first of its kind in India. The 2-semester M. Phil Bioinformatics programme under Credit and Semester System admits students holding the following degrees and/or Diplomas offered by the University of Kerala or recognized by the University of Kerala as equivalent thereto: ? MSc Computer Science ? MCA ? MSc Information Technology ? MSc. Electronics ? MTech in any branch ? MSc in Life Sciences ? MSc Biotechnology . MSc Mathematics ? M Pharm, MD, etc The following are the subjects of study: Bio-Mathematics & Statistics, Web Programming, Genomics, Proteomics and Computer-Aided Drug Discovery, Introduction to IT (E), Introduction to Life Sciences (E), Algorithms in Computational Biology (E), Micro Array Bioinformatics, and Applied Bioinformatics (E). Admission will be based on marks scored in qualifying examinations and also an entrance examination scheduled to be held at Thiruvananthapuram. *Important Dates -* Notification inviting applications: *20th May 2010* * Last date for receiving applications: *10th August 2010* * Date for Entrance examination:* 18th September 2010* * Classes commences on: *2 December 2010 (tentative)* * * *For more detail, please find the attached flyer.* **** *ABOUT THE CENTRE * The Centre for Bioinformatics was established by the University of Kerala in January, 2005 to take up teaching, research and extension activities in bioinformatics and computational biology. The centre focuses on computational applications in biology, drawing knowledge from mathematics, statistics, computer science, information technology, biology and bio-technology. The centre currently offers a 2-semester post-masters programme (MPhil. in Bioinformatics) and a 4-semester Msc. (Computational Biology) programme, in addition to research programmes leading to PhD. in Bioinformatics/Computational Biology. The Center has attracted funding from various state and national agencies such as Kerala State IT Mission, Dept. of Information Technology, Govt. of India, Dept. of Bio-Technology, Govt. of India, University Grants Commission, Dept. of Science, Technology and Environment, Govt. of Kerala. For more details: Visit www.cbi.keralauniversity.edu or email to admission.cbi at gmail.com with regards Course Coordinator Centre for Bioinformatics University of Kerala Karyavattom Campus 695 581 Thiruvananthapuram, Keralam Phone: 0471 - 2308759 http://cbi.keralauniversity.edu From dan.bolser at gmail.com Thu Jun 17 02:19:21 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 17 Jun 2010 07:19:21 +0100 Subject: [BiO BB] Fwd: Kwwika - World Cup Web Development competition announced In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: Phil Leggetter Date: 17 June 2010 07:16 Subject: Kwwika - World Cup Web Development competition announced To: Geek Down Firstly, apologies for the cross post. I originally posted this here on the TechMeetup forum but Magnus of T-List just informed me of this more Dundee focused group. I'm working on a project called Kwwika which allows anybody to add real-time push functionality to your website. To try and get people developing using Kwwika we've decided to create a competition that will hopefully encourage web developers to sign up for the opportunity of winning an Apple iPad. The purpose of the competition is to see who can build the most engaging real-time push World Cup 2010 web application. More details can be found in the following locations: * Blog post announcment: http://blog.kwwika.com/kwwika-world-cup-2010-real-time-push-web-app * Kwwika Wiki with competition details: http://wiki.kwwika.com/competitions/world-cup-2010-real-time-push-web... * A real-time push World Cup demo created to give people an idea of what can be built: http://kwwika.com/Standalone/Demos/WorldCup2010/ (watch your browser as there is a lot of data here) If you have any questions or ideas please feel free to get in touch with me via phil at kwwika.com Also, if you're not too fussed about the competition but would like to have a play with Kwwika then also get in touch. Thanks, Phil -- You received this message because you are subscribed to the "Geek Down" google group. To post to this group, send email to geek-down at googlegroups.com To unsubscribe from this group, send email to geek-down+unsubscribe at googlegroups.com For more options, visit this group at http://groups.google.co.uk/group/geek-down?hl=en-GB From anthony.goldbloom at kaggle.com Sat Jun 19 10:09:02 2010 From: anthony.goldbloom at kaggle.com (Anthony Goldbloom | Kaggle) Date: Sun, 20 Jun 2010 00:09:02 +1000 Subject: [BiO BB] What has bioinformatics ever done for us? Message-ID: <9A318EFB-D96F-4541-BD20-552A19A73C68@kaggle.com> A British bioinformatician wants to open discussion about the greatest biological discovery made possible by bioinformatics. He has just launched a "brainstorming competition" with nominal prize money to stoke discussion. Kaggle is hosting the "brainstorming competition" at: http://kaggle.com/blog/2010/06/17/%EF%BB%BFwhat-has-bioinformatics-ever-done-for-us/ We would welcome contributions from members of the BBB mailing list. From dan.bolser at gmail.com Sat Jun 19 17:53:18 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 19 Jun 2010 22:53:18 +0100 Subject: [BiO BB] What has bioinformatics ever done for us? In-Reply-To: <9A318EFB-D96F-4541-BD20-552A19A73C68@kaggle.com> References: <9A318EFB-D96F-4541-BD20-552A19A73C68@kaggle.com> Message-ID: I don't call $100 nominal! My entry was 'In 1977 Carl Woese ...' There are no good entries for blast yet. On 19 June 2010 15:09, Anthony Goldbloom | Kaggle wrote: > A British bioinformatician wants to open discussion about the greatest biological discovery made possible by bioinformatics. He has just launched a "brainstorming competition" with nominal prize money to stoke discussion. > > Kaggle is hosting the "brainstorming competition" at: > http://kaggle.com/blog/2010/06/17/%EF%BB%BFwhat-has-bioinformatics-ever-done-for-us/ > > We would welcome contributions from members of the BBB mailing list. > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb >