From C.Cole at dundee.ac.uk Thu Feb 2 14:23:56 2012 From: C.Cole at dundee.ac.uk (Christian Cole) Date: Thu, 2 Feb 2012 14:23:56 +0000 Subject: [Sbforum-general] Reminder: NextGenBUG meeting next week Message-ID: Hi all, Apologies if you receive this twice, but yesterday's attempt didn't appear to work. Here's a reminder of next week's NextGenBUG meeting here in Dundee: http://genepool.bio.ed.ac.uk/nextgenbug/meeting/20120209 *Important* Please remember to register by tomorrow so that we can cater for the correct number of people. Looks like we're going to have some interesting talks including three 'external' speakers. Below is the current agenda. 12:30-13:30 Lunch 13:30-13:50 Thymic Epithelial Cells: Steve Sansom, CGAT Fellow, University of Oxford 13:50-14:10 mRNA stability in Dicty: Marek Gierli?ski, University of Dundee 14:10-14:30 What can Direct RNA Sequencing tell about plant transcriptome?: Alexander Sherstnev, University of Dundee 14:30-14:50 An alternative approach to assembly validation: Micha Bayer, James Hutton Institute, Dundee 14:50-15:10 The CRAM sequence data compression framework: Vadim Zalunin, European Bioinformatics Institute,15:10-15:30 Tea/Coffee 15:30 - 15:50 Sequence data compression: needs and goals: Guy Cochrane, European Bioinformatics Institute, There's still room for any late additions. Looking forward to seeing you all there. Cheers, Chris -- Dr Chris Cole Senior Research Associate (Bioinformatics) College of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland, UK e-mail: c.cole at dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish Charity, No: SC015096 From dan.bolser at gmail.com Mon Feb 13 10:00:13 2012 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 13 Feb 2012 10:00:13 +0000 Subject: [Sbforum-general] Interested in Variation? Message-ID: Job up in Cambridge: "... the primary responsibility of the post-holder will be the development of pipelines and storage solutions for variation data deriving from whole genome re-sequencing." http://goo.gl/eQrRu or http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=LktVsYDaNlCOtQqCli&jobid=47627,4187528723&key=45520467&c=126152212583&pagestamp=dbnjwyufpgvrmyvkmt From mark.blaxter at ed.ac.uk Tue Feb 14 21:33:02 2012 From: mark.blaxter at ed.ac.uk (Mark Blaxter) Date: Tue, 14 Feb 2012 21:33:02 +0000 Subject: [Sbforum-general] talk by Davide Pisani at University of Edinburgh, February 22nd 2012: "Molecular Palaeobiology of Metazoa: Recent progresses and open questions"? Message-ID: <109072FD-DF5C-4396-B33F-2EC2B088B407@ed.ac.uk> Dear colleagues A short note to say that Davide Pisani of Maynooth, Ireland will be speaking at the Ashworth Labs, King's Buildings on 22nd February at 4 pm on "Molecular Palaeobiology of Metazoa: Recent progresses and open questions"? see http://bioinf.nuim.ie/davide-pisani/ for Davide's research profile: the talk should be of interest to phylogeneticists and bioinnformaticians as well as a generally fascinating look at the evolution of animals. If you would like to meet Davide before the talk, do contact me. Mark Mark Blaxter mark.blaxter at ed.ac.uk Institute of Evolutionary Biology The University of Edinburgh +++++++++++ Room 408, Ashworth Laboratories, King's Buildings, Edinburgh EH9 3JT UK +++++++++++ The GenePool Genomics Facility genepool.bio.ed.ac.uk genepool at ed.ac.uk -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From mick.watson at roslin.ed.ac.uk Wed Feb 15 10:02:11 2012 From: mick.watson at roslin.ed.ac.uk (WATSON Mick) Date: Wed, 15 Feb 2012 10:02:11 +0000 Subject: [Sbforum-general] Bioinformatics opportunity within ARK-Genomics Message-ID: <597C436137A55D4AB6FE2152CAD5988801F7728807@EXSEEDMD.is.ed.ac.uk> Dear All Please find below details of an opportunity within the bioinformatics group at ARK-Genomics: http://www.roslin.ed.ac.uk/vacancies/3015374/bioinformatician/ This is a great opportunity to work directly with the latest next-generation Illumina sequencing technology, and you will be joining a vibrant research and support team. Any questions, please ask Mick -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From kemp at chalmers.se Mon Feb 27 08:33:34 2012 From: kemp at chalmers.se (Graham Kemp) Date: Mon, 27 Feb 2012 08:33:34 +0000 Subject: [Sbforum-general] PhD position, Structural Bioinformatics, Chalmers University of Technology Message-ID: <3E5A3376570BD24C97F20A8FBC21C506023BCC@thane.ita.chalmers.se> PhD student position in Computing Science: Structural Bioinformatics ==================================================================== The Department has 76 faculty members and enrolls about 70 PhD students from more than 30 countries. The research spans the whole spectrum, from theoretical underpinnings to applied systems development. There is extensive national and international collaboration with academia and industry all around the world. The Division of Computing Science has research and education activities in a wide range of areas, including algorithms and bioinformatics. Job description --------------- You will undertake research in the field of structural bioinformatics, within an interdisciplinary project on "Computational protein modelling supported by NMR data" between the Department of Computer Science and Engineering at Chalmers, and the Department of Chemistry and Molecular Biology at the University of Gothenburg. The aim of this project is to improve the speed and accuracy with which three-dimensional models of protein structures can be generated from easily and rapidly obtainable data from nuclear magnetic resonance (NMR) experiments. The project will benefit from close connections to the Swedish NMR Centre (www.nmr.gu.se) which will be able to provide new experimental data that can be used to test and refine the system that will be developed, and also the Chalmers e-Science Centre (www.chalmers.se/rss/e-science-en) which gives access to a local network of expertise in large-scale scientific computation. The majority of your working time is devoted to your own research studies. As a PhD student you are expected to develop your own ideas and communicate scientific results orally as well as in written form. In addition, the position will normally include 20% departmental work, mostly teaching duties. The employment is limited to a maximum of five years. Qualifications -------------- Applicants must have a strong background in Computing Science, Bioinformatics, or related fields. You must have obtained a Master's degree or a 4-year Bachelor's degree, or expect to complete that degree within a few months. You should have an interest in bioinformatics, algorithms and programming. * This project requires protein modelling software to be developed and tested, so you should have strong programming skills (e.g. C, Linux). * Knowledge about NMR and/or proteins is an advantage. * Good written and oral communication skills are necessary. English is our working language. Application procedure --------------------- The application should be marked with Ref 20120061 and written in English. The application should consist of three pdf-files, as below: 1. Application: - CV, - attested copies of education certificates, including grade reports and other documents, English language test, e.g. TOEFL score, - letters of recommendation from academic institutions and/or previous employers (optional), 2. A letter of application detailing your specific qualifications for the position - maximum one A4 page 3. Publications: - relevant work such as bachelor's or master's thesis (or outline of a thesis under preparation). Apply using the online application form at: http://www.chalmers.se/en/about-chalmers/vacancies/Pages/default.aspx Application deadline: 2012-03-20 For questions, please contact: ------------------------------ Graham Kemp, Computer Science and Engineering, Chalmers University of Technology e-mail: kemp at chalmers.se Martin Billeter, Chemistry and Molecular Biology, University of Gothenburg e-mail: martin.billeter at chem.gu.se