From jeedward at yahoo.com Sun Mar 8 11:02:19 2009 From: jeedward at yahoo.com (John Edward) Date: Sun, 8 Mar 2009 04:02:19 -0700 (PDT) Subject: [Sbforum-general] Draft paper submission is extended (will not be extended further): BCBGC-09 Message-ID: <392052.91267.qm@web45908.mail.sp1.yahoo.com> Draft paper submission is extended (will not be extended further): BCBGC-09 ? ? *Apologies if you receive multiple copies of this email. Please forward to interested people.* ? The deadline for draft paper submission at the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is extended due to numerous requests from the authors. The conference will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From watson at ebi.ac.uk Fri Mar 13 09:07:52 2009 From: watson at ebi.ac.uk (watson) Date: Fri, 13 Mar 2009 09:07:52 +0000 Subject: [Sbforum-general] Upcoming hands on courses at EMBL-EBI Message-ID: <49BA2268.3040702@ebi.ac.uk> Dear all, We have three courses that may be of interest to you with close registration deadlines. If you are interested in attending please visit our training pages for full information on all three courses. Please feel free to circulate this information as you feel appropriate: _Programmatic Access: to biological databases (Java) - 27-29 April 2009_ This course will give you the skills to leverage webservice technology to access and manipulate bioinformatics data resources and tools. You will start with simple scripts accessing individual services and then build upon this to create work flows to solve more complex problems in a reusable manner. Participants will be exposed to open standards such as Simple Object Access Protocol (SOAP); the Distributed Annotation System (DAS); REST services and the BioMart web service. Several examples of specific web services will be included, covering programmatic access to both databases and tools at the EBI. http://www.ebi.ac.uk/training/handson/course_090427_databases.html _Short Read Bioinformatics - 30th April -1st May 2009_ With the advent of next-generation DNA sequencing technologies, researchers encounter new challenges to analyse their data. As a primary nucleotide sequence resource, the EBI tackled these new challenges developing new tools for the /European Reads Archive/ (ERA) in close collaboration with our colleagues at the /Short Read Archive/ (NCBI). These massively parallel platforms require finishing pipelines either relying on a reference genome /(MAQ) /or attempting /de novo/ assemblies /(Velvet)/; furthermore, enhancing the signal produced by the sequencers /(AYB)/ will be covered in this eminently practical workshop. http://www.ebi.ac.uk/training/handson/course_090430_XF.html _A Walkthrough EBI Bioinformatics Resources - 11-15 May 2009 _ The EMBL-EBI maintains the world?s most comprehensive range of molecular databases. 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. The course will consist of intensive five-day course that combines lectures and hands-on tutorials to help the participants actively learn and resolve biologically relevant problems. http://www.ebi.ac.uk/training/handson/course_090511_walkthrough.html Many thanks, James Watson From clements at nescent.org Tue Mar 17 05:24:03 2009 From: clements at nescent.org (Dave Clements) Date: Mon, 16 Mar 2009 22:24:03 -0700 Subject: [Sbforum-general] 2009 GMOD Summer School - Europe Message-ID: GMOD (http://gmod.org/) is a collection of interoperable open source software components for managing, visualizing, annotating and integrating biological, mainly genomic, data. GMOD is also a community of developers and users dealing with similar challenges. GMOD tools are used in diverse contexts, with both emerging and established model organisms. GMOD summer schools introduce new GMOD users to the GMOD project and include several days of hands-on training on how to install, configure and administer GMOD tools. We are now accepting applications for the 2009 GMOD Summer School - Europe: - 3-6 August, 2009 - University of Oxford, Oxford, United Kingdom - Part of GMOD Europe 2009 (http://gmod.org/wiki/GMOD_Europe_2009) - Student tuition is ?95 - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe The course includes training on these 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 ***If you are interested please submit an application by the end of 6 April 2009. *** Applications are submitted online. Enrollment is limited to 25 students. ?If applications exceed capacity (and we expect they will) then participants will be picked based on the strength of their application. ?Applicants will be notified of their admission status in mid-April. Please let me know if you have any questions. Cheers, Dave Clements GMOD Help Desk help at gmod.org http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe http://gmod.org/wiki/GMOD_Europe_2009 From Tom.Freeman at roslin.ed.ac.uk Tue Mar 17 10:59:29 2009 From: Tom.Freeman at roslin.ed.ac.uk (Tom Freeman (RI)) Date: Tue, 17 Mar 2009 10:59:29 -0000 Subject: [Sbforum-general] Network Analysis Practical Course, 28th April, eScience Centre, Edinburgh Message-ID: <1F16910BB8546C4DA5526FABB0C98D09024CB591@ebre2ksrv1.ebrc.bbsrc.ac.uk> Network-based approaches are becoming increasing popular for the visualisation and analysis of 'omics and other high dimensional data. Networks can be produced from a wide variety of biological relationships, such as interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades etc. This short practical course aims to examine some of the theory and uses of network graphs, and demonstrate how they may be used in biology to describe and analyse complex systems. The course will introduce network editing tools for the construction of networks, covering issues such as data exchange formats, layout options for small to medium size graphs and pathway depiction. We will also focus specifically on the use of networks to visualise and analyse 'omics data, in particular microarray expression data, using the tool BioLayout Express3D. This tool has been designed by us for the layout, clustering and analysis of very large network graphs in two- and three-dimensional space and offers a powerful new approach for analysing expression data. The overall aim of the course is to provide an introduction to network graphs, the informatics tools that support their editing, display and analysis, and in so doing hopefully enable participants to apply some of what they have learnt to their own research. Spaces on this workshop are limited so please register early to avoid disappointment. For more details see: http://www.nesc.ac.uk/esi/events/984/ Best wishes Dr Tom Freeman, Roslin Institute, University of Edinburgh, Mithlothian EH25 9PS Scotland, UK From urmi.trivedi at ed.ac.uk Wed Mar 18 11:27:28 2009 From: urmi.trivedi at ed.ac.uk (Urmi Trivedi) Date: Wed, 18 Mar 2009 11:27:28 +0000 Subject: [Sbforum-general] NextGenBUG April 7, Tuesday noon, Ashworth Labs, University of Edinburgh. Message-ID: <20090318112728.kp4nilvaqoggocks@www.staffmail.ed.ac.uk> The next NextGenBUG (next generation sequencing Bioinformatics User Group) will be on 2008, April 7, Tuesday from 12:30-15:30 at Ashworth Labs, Kings buildings, University of Edinburgh Agenda: TBC Meeting logistics (parking, etc) and details of other short talks available at http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20090407 Please add your name to the list at http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20090407 Note: you have to be registered on the website to edit pages. If you have been working on a next gen sequencing project and would like to talk about it, please add your name to the list at http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20090407 If you are not registered to the NextGenBUG mailing list, send an email to majordomo AT lists DOT ed DOT ac DOT uk where the first line of the body is (the subject is ignored): subscribe nextgenbug. You should receive a confirmation email within an hour. Best regards, Urmi Urmi Trivedi Bioinformatics Room 3.54 The Gene Pool Ashworth Labs King's Buildings Campus University of Edinburgh EH9 3JT, UK +44 131 650 7403 http://genepool.bio.ed.ac.uk -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From jimp at compbio.dundee.ac.uk Fri Mar 20 09:20:44 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Fri, 20 Mar 2009 09:20:44 +0000 Subject: [Sbforum-general] [PhyloSoC] Summer of Code 2009 Message-ID: <49C35FEC.7080403@compbio.dundee.ac.uk> Hello All. Please read or forward the message below to students that may be interested in applying for a Google Summer of Code scholarship to work on a Phyloinformatics related project coordinated by the US's National Evolutionary Sciences Centre. Regards. Jim Procter. ---- PHYLOINFORMATICS SUMMER OF CODE 2009 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 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 hardware accerelation for phylogenetic inference, to tree visualization within a wiki, to alignment of next-gen sequencing data, to development of a reusable ontology term markup module for biocuration. 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. The 12-day application period for students opens on Monday March 23rd and runs through Friday, April 3rd, 2009. 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. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/ Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/ about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org _______________________________________________ PhyloSoC mailing list PhyloSoC at nescent.org https://lists.nescent.org/mailman/listinfo/phylosoc From d.m.a.martin at dundee.ac.uk Tue Mar 24 14:41:39 2009 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Tue, 24 Mar 2009 14:41:39 +0000 Subject: [Sbforum-general] Parsing pepXML files Message-ID: <49C8F130.6F09.00E0.0@dundee.ac.uk> Has anyone done this or now of code to do this? Putting together a stream based parser (the files I have are fairly chunky) is not on my list of favourite things to do so I was wondering if there were existing resources. ..d -- David Martin PhD College of Life Sciences University of Dundee The University of Dundee is a Scottish Registered Charity, No. SC015096. The University of Dundee is a registered Scottish charity, No: SC015096 From nir at rosettadesigngroup.com Wed Mar 25 16:27:13 2009 From: nir at rosettadesigngroup.com (Nir London) Date: Wed, 25 Mar 2009 18:27:13 +0200 Subject: [Sbforum-general] Rosetta Academic Training Webinar Message-ID: <57895805-7696-4C4F-8170-4A01DFAB89A8@rosettadesigngroup.com> The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring webinars to kick-off our Rosetta Academic Workshop Series. What: Protein-Protein Docking When: May 4th 2009, 0800-1000 AM EST Where: Your office! Click here for more details and registration (For non html emails: http://rosettadesigngroup.com/RDGLS/index.php?sid=54479&lang=en ) Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta version. Hope to see you there, Nir London. Rosetta Design Group | http://rosettadesigngroup.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjanssen at sbforum.org Wed Mar 25 18:14:16 2009 From: cjanssen at sbforum.org (Chris Janssen) Date: Wed, 25 Mar 2009 18:14:16 +0000 Subject: [Sbforum-general] SBF - Computational Methods in Synthetic Biology Summer School - 22-26th June 2006 Message-ID: <49CA7478.4050402@sbforum.org> ***************************************************************************** Heriot Watt University, the University of Edinburgh, and The Scottish Bioinformatics Forum will be hosting: Summer School - Computational Methods in Synthetic Biology Date: 22nd June 2009, 09:30 am End Date: 26th June 2009 Location: Heriot Watt University, Edinburgh http://www.compsynbio.org ***************************************************************************** The summer school is a meeting bringing together theoreticians and experimentalists interested in the theoretical and experimental techniques as well as long term prospects and vision for Synthetic Biology. We aim to have a working meeting with a good balance of talks, discussions, and collaborative problem solving. Participants will be strongly encouraged to present their own contribution to Synthetic Biology. The targeted audience are PhD students, Postdocs and scientists with a general interest in this fascinating field of research. Confirmed Invited Speakers Dr. Jane Calvert: (The University of Edinburgh, UK) Dr. Chris French: (The University of Edinburgh, UK) Dr. Emma Frow: (The University of Edinburgh, UK) Prof. Alfonso Jaramillo: (Ecole Polytechnique, CNRS, France) Prof. Kunihiko Kaneko: (The University of Tokyo, Japan) Prof. Bruce E. Logan: (Penn State University, USA) Prof. Andrew Millar: (The University of Edinburgh, UK) Dr. Jean Peccoud: (Virginia Bioinformatics Inst., USA) Prof. Vitor A. P. Martins dos Santos: (Helmholtz Center for Infection Research, Germany) Prof. Vincent Schachter: (Genoscope - Centre National de Sequencage, France) Full details and registration please see http://www.compsynbio.org/ We look forward to seeing you in June. -- Dr. Chris S. Janssen Director, Scottish Bioinformatics Forum Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ United Kingdom http://www.sbforum.org Tel.: +44 131 240 2783 Fax: TBC e-mail: cjanssen at sbforum.org The RSE Scotland Foundation is Scottish Charity No. SC024636 The information contained in this e-mail is confidential, intended for the above named individual/s and may be legally privileged. This message may contain personal views which are not the views of the Foundation/Forum, unless specifically stated www.rsescotlandfoundation.org.uk www.sbforum.org From clements at nescent.org Mon Mar 30 05:44:59 2009 From: clements at nescent.org (Dave Clements) Date: Sun, 29 Mar 2009 21:44:59 -0700 Subject: [Sbforum-general] 2009 GMOD Summer School - Europe In-Reply-To: References: Message-ID: Hello all, This is a reminder that the application deadline for the 2009 GMOD Summer School - Europe is 6 April, one week from now. The 2009 GMOD Summer School - Europe (http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe) will be held 3-6 August, 2009 at the University of Oxford, as a part of GMOD Europe 2009 (http://gmod.org/wiki/GMOD_Europe_2009). Tuition is ?95. GMOD (http://gmod.org/) is a collection of interoperable open source software components for managing, visualizing, annotating and integrating biological data. It is also a community of developers and users dealing with similar challenges. The course offers hands-on training on how to deploy and administer: * Genome / Comparative Genomics Viewers - GBrowse, JBrowse, GBrowse_syn, Apollo * Genome Annotation - Apollo, Artemis-Chado Integration * Databases - Chado, BioMart Please contact the GMOD Help Desk (help at gmod.org) if you have questions. Thanks, Dave Clements GMOD Help Desk On Mon, Mar 16, 2009 at 10:24 PM, Dave Clements wrote: > GMOD (http://gmod.org/) is a collection of interoperable open source > software components for managing, visualizing, annotating and > integrating biological, mainly genomic, data. ?GMOD is also a > community of developers and users dealing with similar challenges. > GMOD tools are used in diverse contexts, with both emerging and > established model organisms. > > GMOD summer schools introduce new GMOD users to the GMOD project and > include several days of hands-on training on how to install, configure > and administer GMOD tools. > > We are now accepting applications for the 2009 GMOD Summer School - Europe: > ?- 3-6 August, 2009 > ?- University of Oxford, Oxford, United Kingdom > ?- Part of GMOD Europe 2009 (http://gmod.org/wiki/GMOD_Europe_2009) > ?- Student tuition is ?95 > ?- http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe > > The course includes training on these 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 > > ***If you are interested please submit an application by the end of 6 > April 2009. *** > > Applications are submitted online. ?Enrollment is limited to 25 > students. ?If applications exceed capacity (and we expect they will) > then participants will be picked based on the strength of their > application. ?Applicants will be notified of their admission status in > mid-April. > > Please let me know if you have any questions. > > Cheers, > > Dave Clements > GMOD Help Desk > help at gmod.org > > http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe > http://gmod.org/wiki/GMOD_Europe_2009 >