From sandra.borthwick at sbforum.org Wed Apr 15 15:01:32 2009 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Wed, 15 Apr 2009 15:01:32 +0100 Subject: [Sbforum-general] POSTDOCTORAL FELLOWSHIP - University of Dundee Message-ID: <3B9D78AA69524A9986388FDC599CCC2B@society.local> ** Re-advertisement ** This post would be an ideal first postdoc for a bioinformatician with an interest in proteomics. ============================================================================ ============ MRC PROTEIN PHOSPHORYLATION UNIT COLLEGE OF LIFE SCIENCES UNIVERSITY OF DUNDEE, SCOTLAND POSTDOCTORAL FELLOWSHIP An MRC Postdoctoral Fellowship (Career Development Fellow) is available to work with Professor Carol MacKintosh and Dr Nick Morrice in the area of proteomic data handling. The position will involve data mining of LC-MS data (generated on our two LTQ-orbitrap mass spectrometry systems) of complex proteomes and phosphoproteomes isolated by both protein-protein affinity chromatography and phosphopeptide enrichment chromatography. The successful candidate will demonstrate strong analytical and data management skills with proven technical ability in data integration and mining. Programming and relational database expertise would be a distinct advantage. CDF posts are for 3 years and offer a planned period of training and development for post-doctoral scientists who have just completed their doctoral studies or post-doctoral researchers wishing to move into a new research discipline. This post offers the opportunity for an ambitious scientist to make a considerable contribution to the field. The appointment will be made on the Medical Research Council?s Band 4 Scientist scale (?25,368 - ?31,048 plus superannuation) with initial placement depending on achievements and experience. The positions can start at any time up to April 2009. Other benefits include 30 days annual leave and final salary pension scheme. The MRC Protein Phosphorylation Unit is a major international centre for research on cell signalling. Research funding to the Unit is one of the highest in the UK and its innovative collaboration with the pharmaceutical industry (The Division of Signal Transduction Therapy) received a Queen?s Anniversary Award in 2006. For further information consult the Unit?s website: (http://www.ppu.mrc.ac.uk/ ). Applications for this role must be made online at http://jobs.mrc.ac.uk. Please include a CV and a list of publications. If you do not have internet access or experience technical difficulties, please call 01793 301159, quoting reference number PPU08/587. Informal enquiries are encouraged and may be made to either Carol MacKintosh or Nick Morrice via email: c.mackintoish at dundee.ac.uk or n.a.morrice at dundee.ac.uk Original closing date: 5th December 2008 -- From sandra.borthwick at sbforum.org Thu Apr 16 16:07:15 2009 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Thu, 16 Apr 2009 16:07:15 +0100 Subject: [Sbforum-general] Summer School - Bioinformatics and Comparative Genomics followed by One-day International Conference Message-ID: <0B2FF7DD324546E4ADAF9A853201694D@society.local> **************************************************************************** * The Scottish Bioinformatics Forum and University of St Andrews will be hosting: Summer School - Bioinformatics and Comparative Genomics Date: 15th August 2009, 9:00 am End Date: 17th August 2009 Location: University of St Andrews **************************************************************************** * The Scottish Bioinformatics Forum and the University of St. Andrews are pleased to announce the first Summer School on Bioinformatics and Comparative Genomics. The summer school will be held in St. Andrews on 15th-17th August 2009, and will be followed by a one day International Conference on Comparative Genomics on the 18th August. The summer school on bioinformatics and comparative genomics will address practical bioinformatics for sequence analysis and comparative genomics for use in biological and biomedical research. Internationally renowned invited speakers will discuss current challenges, applications, and future outlook in the field. Confirmed speakers: Dr. Zemin Ning, Wellcome Trust Sanger Institute, UK Prof. Neil Hall, University of Liverpool, UK Dr. David Martin, University of Dundee, UK Prof. Geoff Barton, University of Dundee, UK Prof. Ziheng Yang FRS, University College London, UK Dr. Daniel Barker, University of St Andrews, UK Dr. Chris Janssen, SBF and University of Glasgow, UK Prof. Ian Korf, UC Davis Genome Center, USA, Prof. Dannie Durand, Carnegie Mellon University, USA Dr David Ferrier, University of St Andrews, UK For more information and registration details, please see http://www.genome-bioinformatics.org/index.html ***************************************************** Comparative Genomics one-day International Conference Date: 18th August 2009, Time: 9:00 am Location: Bute Building, University of St Andrews ***************************************************** Comparative genomics is a new field of increasing power. Thousands of genome sequences are now available, and the amount of data on genomes continues to increase. This presents enormous opportunities to make discoveries of biological and medical interest, but also requires newapproaches. The bottleneck has shifted from the effort required to obtain genomic data, to the effort required to analyse them. However, exciting and novel results are already emerging, in a vast range of areas within biology and medicine. Internationally renowned invited speakers and a poster session will present new developments in this cutting-edge field. For more information on the one-day Comparative Genomics International Conference, please see http://www.sbforum.org/events.php?e_id=70 Looking forward to seeing you in St Andrews! Kind Regards 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 The SBF is a project of 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 sandra.borthwick at sbforum.org Fri Apr 17 15:04:37 2009 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Fri, 17 Apr 2009 15:04:37 +0100 Subject: [Sbforum-general] ** SBF/EBI Training Events in Scotland - 22nd April 2009 ** Message-ID: ======================================================== This is a great opportunity to receive training on the resources available from the European Bioinformatics Institute, spaces are limited, and restricted to first come basis. ======================================================== The EBI Outreach & Training Team will be here in The Royal Society of Edinburgh for a 1 day course 22nd April 2009 - Proteomics and Protein Structures This Bioinformatics Hands On Training Courses is now open for registration, please see http://www.sbforum.org/events.php?e_id=58 for further information. Thank you for your time, it is very much appreciated. Kind Regards Sandra 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 The SBF is a project of 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 sandra.borthwick at sbforum.org Fri Apr 17 16:40:38 2009 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Fri, 17 Apr 2009 16:40:38 +0100 Subject: [Sbforum-general] ** Scottish Systems Biology meeting Aberdeen - 15th May 2009 ** Message-ID: <85648331A16A453BB4DF7364B92D81BC@society.local> The Scottish Bioinformatics Forum are pleased to announce the 4th meeting of the Scottish Biosystem Modelling Network jointly with the 6th annual Aberdeen Systems Biology Symposium. Date: 15th May 2009, 10:30 am Location: Aberdeen University, IMS, Foresterhill ============================================================================ ======================== Speakers for the day will include: Prof Mike White, (University of Liverpool) Prof Vincent Danos, (University of Edinburgh) Prof Mark Girolami, (University of Glasgow) Dr Anne Smith, (St Andrews University) Dr Eric Bullinger, (University of Liege) Dr Fordyce Davidson, (University of Dundee) Dr John Mackenzie, (Strathclyde University) Dr Alessandro Moura, (University of Aberdeen) Dr Kate Adcock, (Wellcome Trust) For more information and registration details please see http://www.sbforum.org/events.php?e_id=64 Thank you for your time. Best wishes Sandra 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 The SBF is a project of 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 jeedward at yahoo.com Sat Apr 18 17:53:15 2009 From: jeedward at yahoo.com (John Edward) Date: Sat, 18 Apr 2009 09:53:15 -0700 (PDT) Subject: [Sbforum-general] Extended draft paper submission: BCBGC-09 call for papers Message-ID: <886569.22078.qm@web45910.mail.sp1.yahoo.com> Extended draft paper submission: BCBGC-09 call for papers ? This Extended Call for Papers is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 ? ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. 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 sborthwick at royalsoced.org.uk Mon Apr 20 13:24:45 2009 From: sborthwick at royalsoced.org.uk (Sandra Borthwick) Date: Mon, 20 Apr 2009 13:24:45 +0100 Subject: [Sbforum-general] Bio++ workshop: rapid development of robust applications - 16th June Message-ID: <818406367E54EC499E989D011C0025CF39918D@rsoe_server4.society.local> ************************************************ Bio++ workshop: rapid development of robust applications Date: 16th June 2009, Time: 9:00 am End Date: 18th June 2009 Location: Glasgow University The Bio++ workshop is a three-day, hands-on course, to be taught at the University of Glasgow from the 16th - 18th of June 2009 (9am - 5.30pm). Bio++ (http://kimura.univ-montp2.fr/BioPP/) is a highly efficient set of C++ libraries for applications in bio-sequence analysis, molecular evolution and population genetics. For more information please see http://www.sbforum.org/events.php?e_id=63 ************************************************ 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 The SBF is a project of 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 The Royal Society of Edinburgh, Scotland's National Academy, is Scottish Charity No. SC000470 The RSE Scotland Foundation, a charitable body connected to the Society, 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 RSE/RSE Scotland Foundation, unless specifically stated Tel: 0131 240 5000. Fax: 0131 240 5024 http://www.royalsoced.org.uk ____________________________________________________________________________ All RSE staff now have direct dial telephone lines. See http://www.royalsoced.org.uk/organisation/staff.htm SAVE PAPER. DO YOU NEED TO PRINT THIS EMAIL? From contact at sbforum.org Wed Apr 22 16:00:25 2009 From: contact at sbforum.org (Scottish Bioinformatics Forum) Date: Wed, 22 Apr 2009 16:00:25 +0100 Subject: [Sbforum-general] Seminar: 'Omic Empiricism Message-ID: <49EF3109.1090307@sbforum.org> David B. Searls Omic Empiricism Tuesday 28th April Room 4.31/4.33 Informatics Forum 10 Crichton Street The rise of omics signals a shift from hypothesis-driven to data-driven, "bottom-up" research, while systems biology stresses modeling and claims to move beyond reductionism. These trends are at opposite poles of a long-standing duality between empiricism and rationalism. Twenty-first century biology might benefit from a consideration of how philosophers have approached and attempted to reconcile this duality. BIO: David B. Searls is an independent consultant, until recently the senior vice president of bioinformatics at GlaxoSmithKline Pharmaceuticals. He holds an adjunct appointment at the University of Pennsylvania, where he was formerly research associate professor of genetics. He holds degrees from MIT, Johns Hopkins, and Penn. -- Scottish Bioinformatics Forum Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ Tel: ++ (0)131 240 2783 Fax: ++ (0)131 240 2786 email: contact 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 contact at sbforum.org Wed Apr 22 16:26:19 2009 From: contact at sbforum.org (Scottish Bioinformatics Forum) Date: Wed, 22 Apr 2009 16:26:19 +0100 Subject: [Sbforum-general] Seminar: 'Omic Empiricism time 11:00 In-Reply-To: <93526FBB-68A0-43DB-AA1F-282D8A5D4908@roslin.ed.ac.uk> References: <49EF3109.1090307@sbforum.org> <93526FBB-68A0-43DB-AA1F-282D8A5D4908@roslin.ed.ac.uk> Message-ID: <49EF371B.2050709@sbforum.org> oops, the time for the David B. Searls "Omic Empiricism" seminar on 28th April is 11:00. Sorry, SBF Andy Law (RI) wrote: > And the time of the talk is....? > > :o} > > Later, > > Andy > -------- > Yada, yada, yada... > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336 > Disclaimer: This e-mail and any attachments are confidential and > intended solely for the use of the recipient(s) to whom they are > addressed. If you have received it in error, please destroy all copies > and inform the sender. > > > > On 22 Apr 2009, at 16:00, Scottish Bioinformatics Forum wrote: > >> David B. Searls >> >> Omic Empiricism >> >> Tuesday 28th April >> Room 4.31/4.33 >> Informatics Forum >> 10 Crichton Street >> >> The rise of omics signals a shift from hypothesis-driven to data-driven, >> "bottom-up" research, while systems biology stresses >> modeling and claims to move beyond reductionism. These trends are at >> opposite poles of a long-standing duality between empiricism and >> rationalism. Twenty-first century biology might benefit from a >> consideration of how philosophers have approached and attempted to >> reconcile this duality. >> >> BIO: David B. Searls is an independent consultant, until recently the >> senior vice president of bioinformatics at GlaxoSmithKline >> Pharmaceuticals. He holds an adjunct appointment at the University of >> Pennsylvania, where he was formerly research associate professor of >> genetics. He holds degrees from MIT, Johns Hopkins, and Penn. >> >> -- >> Scottish Bioinformatics Forum >> Royal Society of Edinburgh >> 22-26 George Street >> Edinburgh >> EH2 2PQ >> >> Tel: ++ (0)131 240 2783 >> Fax: ++ (0)131 240 2786 >> >> email: contact 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 >> >> >> >> >> >> _______________________________________________ >> Sbforum-general mailing list >> Sbforum-general at sbforum.org >> http://sbforum.org/mailman/listinfo/sbforum-general_sbforum.org > > -- Scottish Bioinformatics Forum Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ Tel: ++ (0)131 240 2783 Fax: ++ (0)131 240 2786 email: contact 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 contact at sbforum.org Wed Apr 22 16:41:47 2009 From: contact at sbforum.org (Scottish Bioinformatics Forum) Date: Wed, 22 Apr 2009 16:41:47 +0100 Subject: [Sbforum-general] StoMP conference 2009 "Noisy Bugs" Message-ID: <49EF3ABB.1030000@sbforum.org> I would like to draw your attention to a conference that we are organising this July, at NeSC in Edinburgh, entitled "Noisy Bugs: Modelling and Microbiology". The conference website is at www.ph.ed.ac.uk/StoMP. The conference will feature an excellent lineup of speakers from both modelling and microbiology, and it would be great if you could come. Brief summary: Microbes are everywhere: in our bodies, in our food, in the soil and in the oceans. They are the most numerous and versatile living beings on our planet and they impact on our lives for both good and ill. It is essential that we seek to better understand how microbes work. Despite their apparent simplicity, microbes are complex beings. In particular, it is well known that genetically and environmentally identical microbial cells may behave very differently. This stochasticity can have profound consequences for how microbes respond to stimuli, survive stresses, establish communities and adapt to new environments. This is an area where both experiments and mathematical models have an important role to play. This meeting, organised by the BBSRC-funded StoMP network and hosted by the e-Science Institute in central Edinburgh, aims to bring together microbiologists and modellers with a series of cutting-edge talks, discussions, and hands-on computer practical sessions. To register, please visit the website at www.ph.ed.ac.uk/StoMP. Best wishes Rosalind Allen -- Dr. Rosalind Allen Room 2507 School of Physics The University of Edinburgh James Clerk Maxwell Building The King's Buildings Mayfield Road Edinburgh EH9 3JZ, UK -- Scottish Bioinformatics Forum Royal Society of Edinburgh 22-26 George Street Edinburgh EH2 2PQ Tel: ++ (0)131 240 2783 Fax: ++ (0)131 240 2786 email: contact 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 dan.bolser at gmail.com Mon Apr 27 13:31:05 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 27 Apr 2009 13:31:05 +0100 Subject: [Sbforum-general] Assessing a 454 run? In-Reply-To: <2c8757af0904240305q188a4bf0mfc018ab5cb23daa9@mail.gmail.com> References: <2c8757af0904240305q188a4bf0mfc018ab5cb23daa9@mail.gmail.com> Message-ID: <2c8757af0904270531x5852498cl23cd780684f7debd@mail.gmail.com> Hi all, We recently got data from a 1/8th of a 454 run. The read length shows the typical distribution that I have seen at various Next Generation Bug meetings. However, how should I go about assessing the 'overall quality' of the run (if such a clear cut concept exists)... So far I have plotted the distribution of quality per base and the distribution of mean quality per read. Of course the qualities will never be 'perfect', but without any experience or any other reference, I don't know what kind of distributions I should be looking for. i.e. we see about 20% of all bases with a quality score below 20... is that a) as good as we are likely to get, b) not bad, c) woah! ask for 20% of your money back ;-) It would be great to get any feedback from the experience on the list. Note that we do not have a reference genome to align the reads to, but we do have a reasonable coverage of the chloroplast DNA, and a reference for that (estimated 2-4 % chloroplast contamination by read, giving approximately 10x coverage). What is a good tool to identify SNPs between our read data and that reference? (If I can first identify the SNPs, I can then estimate the per base error rate using the reference). Thanks very much for any information, Dan.