From sandra.borthwick at sbforum.org Fri Apr 9 13:59:42 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Fri, 9 Apr 2010 13:59:42 +0100 Subject: [Sbforum-general] 22nd June 2010 - EBI/SBF Advanced Transcriptomics Workshop Message-ID: This is a great opportunity to receive training on the resources availablefrom the European Bioinformatics Institute, spaces are limited, and restricted to first come basis. ======================================================== The EBI Outreach & Training Team will be here in Edinburgh again for another 1 day course Date: 22nd June 2010 - Advanced Transcriptomics Workshop Location: The Royal Society of Edinburgh Tutor: Ibrahim Emam ======================================================== Programme now available http://www.sbforum.org/cmsimages/event_progs_10/062210_EBI_Transcriptomics_wkshop_progx.pdf This Bioinformatics Hands On Training Courses is now open for registration, for further information please see http://www.sbforum.org/events.php?e_id=82 * * * * * * * * * * * * * * * Early registration is encouraged as numbers are limited. Greatly reduced registration fees of ?20 regular and ?10 student. Please register on-line at: www.sbforum.org/events.php * * * * * * * * * * * * * * * Thank you for your time, we look forward to seeing you on 22nd June. -- Sandra Borthwick, Executive Assistant Scottish Bioinformatics Forum The Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ Tel: +44 (0)131 240 2783 Fax: +44 (0)131 240 2786 email: sandra.borthwick at sbforum.org www.sbforum.org 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 http://www.icsb-2010.net/ The SBF is a project of the RSE Scotland Foundation, 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From asidhu at biomap.org Mon Apr 26 07:11:16 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Mon, 26 Apr 2010 14:11:16 +0800 Subject: [Sbforum-general] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Message-ID: <8DA968FA-4F9A-405B-B9C5-C661A649EE3F@biomap.org> IEEE CBMS 2010 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Perth, Australia, 12-15 October 2010 http://www.cbms2010.curtin.edu.au/ The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2010 will consist of invited keynote talks given by leading scientists in the field, and regular and special track sessions that cover a broad array of issues which relate computing to medicine. RELEVANT TOPICS Network and Telemedicine Systems Medical Databases & Information Systems Computer-Aided Diagnosis Medical Devices with Embedded Computers Bioinformatics in Medicine Software Systems in Medicine Pervasive Health Systems and Services Web-based Delivery of Medical Information Medical Image Segmentation & Compression Content Analysis of Biomedical Image Data Knowledge-Based & Decision Support Systems Hand-held Computing Applications in Medicine Knowledge Discovery & Data Mining Signal and Image Processing in Medicine Multimedia Biomedical Databases CBMS 2010 invites original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Many of the above listed topics are represented by corresponding Special Tracks, while others are solely covered by the general CBMS track. Prospective authors are expected to submit their contributions to one of the corresponding Special Tracks or to the general track if none of the special tracks is relevant. SPECIAL TRACKS ST1: Computational Proteomics and Genomics ST2: Knowledge Discovery and Decision Systems in Biomedicine ST3: Ontologies for Biomedical Systems ST4: HealthGrid & Cloud Computing ST5: Technology Enhanced Learning in Medical Education ST6: Intelligent Patient Management ST7: Data Streams in Healthcare ST8: Supporting Collaboration among Healthcare Workers ST9: Telemedicine ST10: Computer-Based Systems for Mental Health ST11: Image Informatics in Biomedical Research and Clinical Medicine ST12: e-Health SUBMISSION GUIDELINES Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission web site: http://www.easychair.org/conferences/?conf=cbms2010 All submissions will be peer-reviewed by at least three reviewers. The proceedings will be published by the IEEE Computer Society Press. At least one of the authors of accepted papers is required to register and present the work at the conference; otherwise their papers will be removed from the digital library after the conference. IMPORTANT DATES Submission deadline for regular papers: 24 June 2010 Deadline for tutorial submission: 24 June 2010 Notification of acceptation for papers and tutorials: 2 Aug 2010 Final camera ready due: 2 Sep 2010 Author registration: 2 Sep 2010 INTENDED AUDIENCE Engineers, scientists, clinicians and managers involved in medical computing projects are encouraged to submit papers to the symposium and/or attend the symposium. The symposium provides its attendees with an opportunity to experience state-of-the-art research and development in a variety of topics directly and indirectly related to their own work. In addition to research papers, keynote speakers and tutorial sessions it provides participants with an opportunity to come up-to-date on important technological issues. The symposium encourages the participation of students engaged in research/development in computer-based medical systems. Organizing Committee GENERAL CHAIRS Tharam Dillon, Curtin University of Technology, Australia Daniel Rubin, National Center for Biomedical Ontologies, USA William Gallagher, University College Dublin, Ireland PROGRAM CHAIRS Amandeep Sidhu, Curtin University of Technology, Australia Alexey Tsymbal, Siemens, Germany PUBLICATION CHAIRS Mykola Pechenizkiy, Eindhoven University of Technology, Netherlands Tony Hu, Drexel University, USA SPECIAL TRACK CHAIRS Maja Hadzic, Curtin University of Technology, Australia Jake Chen, Indiana University, USA TUTORIAL CHAIRS Phoebe Chen, La Trobe University, Australia Xiaofang Zhou, University of Queensland, Australia PUBLICITY CHAIRS Carolyn McGregor, University of Ontario Institute of Technology, Canada Meifania Chen, Curtin University of Technology, Australia From magic_roses at hotmail.com Wed Apr 28 13:59:45 2010 From: magic_roses at hotmail.com (Nafisa Mohamed) Date: Wed, 28 Apr 2010 15:59:45 +0300 Subject: [Sbforum-general] Functional annotation Message-ID: Dear All, I hope this email finds you well. We need tools for functional annotation that we enter the sequence of gene, and obtain the already annotated functions and sequence features of the site found, So can anyone help me please? I appreciate your help. Kind regards, _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -------------- next part -------------- An HTML attachment was scrubbed... URL: From prash at bioclues.org Thu Apr 29 12:06:23 2010 From: prash at bioclues.org (Prash) Date: Thu, 29 Apr 2010 16:36:23 +0530 Subject: [Sbforum-general] Sbforum-general Digest, Vol 32, Issue 3 In-Reply-To: References: Message-ID: Dear Nafisa, I'm not sure if I udnerstand your question. Are you talking about a kind of workflows which automate the things? If it is the case Taverna is the best. Else, you may use the following tools for functional annotation: BLAST2Go TargetP SignalP TMHMM RBSFinder ESTScan InterPro etc Regards prash Prashanth Suravajhala http://wiki.bioinformatics.org/prash "Science is built up of facts, as a house is with stones. But a collection of facts is no more a science than a heap of stones is a house." ~Henri Poincare, 1913 On Thu, Apr 29, 2010 at 4:30 PM, wrote: > Send Sbforum-general mailing list submissions to > sbforum-general at sbforum.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://sbforum.org/mailman/listinfo/sbforum-general_sbforum.org > or, via email, send a message with subject or body 'help' to > sbforum-general-request at sbforum.org > > You can reach the person managing the list at > sbforum-general-owner at sbforum.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Sbforum-general digest..." > > > Today's Topics: > > 1. Functional annotation (Nafisa Mohamed) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Apr 2010 15:59:45 +0300 > From: Nafisa Mohamed > To: > Subject: [Sbforum-general] Functional annotation > Message-ID: > Content-Type: text/plain; charset="windows-1256" > > > > Dear All, > I hope this email finds you well. We need tools for functional annotation > that we enter the sequence of gene, and obtain the already annotated > functions and sequence features of the site found, So can anyone help me > please? > I appreciate your help. > Kind regards, > _________________________________________________________________ > Hotmail: Trusted email with powerful SPAM protection. > https://signup.live.com/signup.aspx?id=60969 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://sbforum.org/pipermail/sbforum-general_sbforum.org/attachments/20100428/5996e4ab/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > Sbforum-general mailing list > Sbforum-general at sbforum.org > http://sbforum.org/mailman/listinfo/sbforum-general_sbforum.org > > > End of Sbforum-general Digest, Vol 32, Issue 3 > ********************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vaughan at ebi.ac.uk Thu Apr 29 12:22:08 2010 From: vaughan at ebi.ac.uk (RJ Vaughan) Date: Thu, 29 Apr 2010 12:22:08 +0100 Subject: [Sbforum-general] Sbforum-general Digest, Vol 32, Issue 3 In-Reply-To: References: Message-ID: <4BD96BE0.3000002@ebi.ac.uk> Hi Nafisa, If your annotation will be more manual, then you could take a look at Artemis; if you're generating the sequence as well, and planning to submit to the INSDC then Artemis is good for large scale sequences (complete genomes etc.), while the European Nucleotide Archive supplies a range of systems for submitting annotation of smaller scale sequences. http://www.sanger.ac.uk/resources/software/artemis/ Regards, Bob Vaughan. ENA Curation co-ordinator. On 29/04/2010 12:06, Prash wrote: > Dear Nafisa, > I'm not sure if I udnerstand your question. Are you talking about a > kind of workflows which automate the things? > > If it is the case Taverna is the best. > > Else, you may use the following tools for functional annotation: > BLAST2Go > TargetP > SignalP > TMHMM > RBSFinder > ESTScan > InterPro etc > > Regards > prash > > Prashanth Suravajhala > http://wiki.bioinformatics.org/prash > > "Science is built up of facts, as a house is with stones. But a > collection of facts is no more a science than a heap of stones is a > house." > ~Henri Poincare, 1913 > > > On Thu, Apr 29, 2010 at 4:30 PM, > wrote: > > Send Sbforum-general mailing list submissions to > sbforum-general at sbforum.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://sbforum.org/mailman/listinfo/sbforum-general_sbforum.org > or, via email, send a message with subject or body 'help' to > sbforum-general-request at sbforum.org > > > You can reach the person managing the list at > sbforum-general-owner at sbforum.org > > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Sbforum-general digest..." > > > Today's Topics: > > 1. Functional annotation (Nafisa Mohamed) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Apr 2010 15:59:45 +0300 > From: Nafisa Mohamed > > To: > > Subject: [Sbforum-general] Functional annotation > Message-ID: > Content-Type: text/plain; charset="windows-1256" > > > > Dear All, > I hope this email finds you well. We need tools for functional > annotation that we enter the sequence of gene, and obtain the > already annotated functions and sequence features of the site > found, So can anyone help me please? > I appreciate your help. > Kind regards, > _________________________________________________________________ > Hotmail: Trusted email with powerful SPAM protection. > https://signup.live.com/signup.aspx?id=60969 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > Sbforum-general mailing list > Sbforum-general at sbforum.org > http://sbforum.org/mailman/listinfo/sbforum-general_sbforum.org > > > End of Sbforum-general Digest, Vol 32, Issue 3 > ********************************************** > > > > _______________________________________________ > Sbforum-general mailing list > Sbforum-general at sbforum.org > http://sbforum.org/mailman/listinfo/sbforum-general_sbforum.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjanssen at sbforum.org Thu Apr 29 16:17:25 2010 From: cjanssen at sbforum.org (Chris Janssen) Date: Thu, 29 Apr 2010 16:17:25 +0100 Subject: [Sbforum-general] 7th Annual Aberdeen Systems Biology Symposium Message-ID: 7th Annual Aberdeen Systems Biology Symposium Friday May 14th, 10.00-15.30 Institute of Medical Sciences: Level 7 seminar room, Univeristy of Aberdeen All welcome; lunch provided; A range of speakers from Aberdeen plus keynote external speakers will be covering a diversity of topics, including: Martin Howard (John Innes Centre) ; Modelling morphogen gradients in development Ken Haynes (Imperial College); Fungal pH adaptation in Candida pathogenicity Hermman-Georg Holzhutter (Charite, Berlin); Modelling liver metabolism Emma Hart (Napier); Artificial immune systems Local speakers will cover a diverse range of topics including neuronal networks / modelling ribosome traffic / seasonal responses in sheep /Polyamine regulation in yeast /bacterial stress responses and survivability. Full program available here: http://www.sbforum.org/cmsimages/event_progs_10/Systems%20biology%20Symposium%202010.pdf From urmi.trivedi at ed.ac.uk Fri Apr 30 12:54:50 2010 From: urmi.trivedi at ed.ac.uk (Urmi Trivedi) Date: Fri, 30 Apr 2010 12:54:50 +0100 Subject: [Sbforum-general] NextgenBUG meeting - June 1 at IMS, University of Aberdeen Message-ID: Dear all, The next NextGenBUG (next generation sequencing Bioinformatics User Group) will be on 2010, June 1, Tuesday from 13:30-16:30 at Aberdeen University, Institute of Medical Sciences (IMS), Foresterhill, Aberdeen A buffet lunch will be provided between 12:30 and 1:30 in Level 7 Conference Room IMS Agenda: 1. Microbial diversity analysis - Christopher Quince, Department of Civil Engineering, University of Glasgow 2. RNAseq analysis - Pawel Herzyk, The Sir Henry Wellcome Functional Genomics Facility, University of Glasgow Meeting logistics (parking, etc) and details of other short talks available at http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100601 Please add your name to the list at http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100601 Please volunteer to give the usual 15 - 20 minute presentations. See you there. Best regards, Urmi -- Urmi Trivedi Highthroughput sequencing bioinformatician The GenePool Room 3.54, Ashworth Laboratories Kings building's campus University of Edinburgh EH9 3JT, Edinburgh, UK. Phone: +44 131 650 7403 Email: urmi.trivedi at ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.