From mark.blaxter at ed.ac.uk Fri Jan 8 14:26:07 2010 From: mark.blaxter at ed.ac.uk (Mark Blaxter) Date: Fri, 8 Jan 2010 14:26:07 +0000 Subject: [Sbforum-general] =?iso-8859-1?q?Fwd=3A_2_post-doc_and_one_PhD_po?= =?iso-8859-1?q?sitions_at_the__Bioinformatics_and_Genomics_Department_of_?= =?iso-8859-1?q?the_Centro_de_Investigaciones_Pr=EDncipe_Felipe=2C_Valenci?= =?iso-8859-1?q?a=2C_Spain=2E?= References: <201001081322.25136.aconesa@cipf.es> Message-ID: <56B78974-E52C-4070-8CAD-188F18FF40AE@ed.ac.uk> Begin forwarded message: > From: Ana Conesa > Date: 8 January 2010 12:22:17 GMT > To: Bioconductor , Ana Conesa > > Cc: Blast2GO at googlegroups.com, obo-discuss-request at lists.sourceforge.net > , Bioc-sig-sequencing at r-project.org, basedb-users at lists.sourceforge.net > Subject: 2 post-doc and one PhD positions at the Bioinformatics and > Genomics Department of the Centro de Investigaciones Pr?ncipe > Felipe, Valencia, Spain. > Reply-To: aconesa at cipf.es > > Dear colleague(s), > > Please find below the announcement of bioinformatics positions at our > Department. Please, send it to potentially interested colleagues > > Thank you in advance > > Ana Conesa > ------------------------------------------------------------------------------------------------------------------ > > We are seeking for qualified and motivated researchers to be > enrolled in > different bioinformatics projects in the field of Functional > Genomics and > analysis of Next Generation Sequencing Data. > > - One post-doc (2 years) to participate in the ERA-Net Pathogenomics > Project ?Pathomics, Host-pathogen protein-protein interactomes and > their > influence on the host metabolome? > - One post-doc (3 years) and one PhD student (4 years) to > participate in the > Spanish MCINN project ?Exploring novel genome-transcriptome > relationships by > next generation sequencing approaches? > > PostDoc applicants should have a doctor degree in Bioinformatics, > Biochemistry, Computer Sciences or related disciplines with a > bioinformatics > orientation. Programming skills and fluent English are required. > Pre-doctoral applicants must hold a degree in Biology, > Biotechnology, Computer > or Statistical Sciences. Additional training in bioinformatics is > highly > recommended. > > Researchers will address different biological questions related to > pathogenicity mechanisms and genome regulation through transcriptome > analysis > using high-throughout sequencing approaches. We offer incorporation > into a > multidisciplinary, cooperative and dynamic team of above 20 > scientist within > an internationally oriented research institute. For further > questions and > applications (before January 21st), contact Ana Conesa (aconesa at cipf.es > ) > > > Ana Conesa > Bioinformatics and Genomics Department > Centro de Investigaciones Pr?ncipe Felipe > Avda. Autopista Saler, 16 > 46012 Valencia > Phone: +34 96 328 96 80 > aconesa at cipf.es > http://www.cipf.es > http://bioinfo.cipf.es > http://bioinfo.cipf.es/aconesa > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From anne.smith at st-andrews.ac.uk Mon Jan 11 14:27:47 2010 From: anne.smith at st-andrews.ac.uk (V. Anne Smith) Date: Mon, 11 Jan 2010 14:27:47 +0000 Subject: [Sbforum-general] PhD Studentship in Computational Ecology Message-ID: Dear SBF Members, Please share the below PhD Studentship advertisement with any interested parties. Thank you, Anne Smith PhD Studentship in Computational Ecology Ecological interaction networks: Application to ongoing field work in Tanzania Ecosystems consist of a complex web of interactions: among species, and between species and their environment. Understanding these interactions is important for predicting how factors - such as biological or chemical control agents, grazing pressure, or climate change - may affect ecosystem function. However, unravelling such complex networks of interactions stretches the boundaries of current research; new methods are needed to handle the complexity of real ecosystems. This studentship explores the use of a methodology new to ecological analysis, Bayesian networks, for revealing ecological interaction networks. You will develop Bayesian network algorithms for handling ecological data and incorporating spatial information. Methods developed will be applied to real ecological data, including data collected in an ongoing field project in Tanzania. There is opportunity for a field season in Tanzania, where you would perform targeted manipulation experiments based on your models (e.g., targeted removal and addition of species within caged areas). This project will be based in Dr Anne Smith's lab at St Andrews and be in collaboration with Dr Colin Beale (York University, currently based in Tanzania) and Dr Dirk Husmeier (Biomathematics & Statistics Scotland). In this studentship, you will gain both computational and field skills. For more details, please contact anne.smith at st-andrews.ac.uk and/or visit: http://biology.st-andrews.ac.uk/vannesmithlab/ Funding by NERC: UK residents (stipend and fees) or EU citizens (fees only) A PDF of the above advertisement is downloadable from: http://biology.st-andrews.ac.uk/vannesmithlab/NERC2010.pdf -- Dr V Anne Smith School of Biology Sir Harold Mitchell Building University of St Andrews St Andrews, Fife KY16 9TH United Kingdom +44 (0)1334-463368 anne.smith at st-andrews.ac.uk biology.st-andrews.ac.uk/vannesmithlab/ The University of St Andrews is a charity registered in Scotland : No SC013532? -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjanssen at sbforum.org Wed Jan 20 09:45:04 2010 From: cjanssen at sbforum.org (Chris Janssen) Date: Wed, 20 Jan 2010 09:45:04 +0000 Subject: [Sbforum-general] ICMS seminar on discovering patterns in data using statistical mixture models Message-ID: <25120cb71001200145h374aa6ccsc9f7ec8806032b1a@mail.gmail.com> The ICMS is hosting a seminar on 3rd March on Discovering patterns in data using statistical mixture models. Details below: On Wednesday 3rd March the International Centre for Mathematical Sciences (ICMS) is hosting a public lecture on this topic, given by Kerrie Mengersen, Professor of Statistics and Director of the Centre for Data Analysis, Modelling and Computation at Queensland University of Technology, Australia. The talk is at 6pm at 15 South College and will be followed by a wine reception. In her presentation, Kerrie will discuss the way in which Statistical Mixtures have enabled greater insight into the following problems: ? Describing patterns in environmental data ? How does air pollution change over time? How can we use remotely sensed data to describe and monitor water quality in the Barrier Reef and vegetation change over large landscapes? ? Improving medical understanding ? How can we use symptom, image and signal data to identify subgroups of patients who respond well to treatment for Parkinson?s Disease? Who will suffer ?chemo-brain? after treatment for breast cancer? How is migraine described, and what are the genetic indicators? ? Building networks ? By extending the models underlying Statistical Mixtures to Bayesian Networks, we can gain better insight into the conservation of cheetahs in Southern Africa, airport security practices and whole-of-life large asset management. Further details about the ICMS workshop, of which this talk is a part, as well as information about how to get to 15 South College Street can be found on www.icms.org.uk/workshops/mixture To obtain further information and to register for this event please contact Audrey using audrey.brown at icms.org.uk -- 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 cjanssen at sbforum.org Wed Jan 20 11:09:00 2010 From: cjanssen at sbforum.org (Chris Janssen) Date: Wed, 20 Jan 2010 11:09:00 +0000 Subject: [Sbforum-general] RSE Research Fellowships 2010 Message-ID: <25120cb71001200309t1ffa02bel5abbe0175853cdd2@mail.gmail.com> Royal Society of Edinburgh Research Fellowships 2010 Applications are invited for the following awards:- *CRF Biomedical Personal Research Fellowships ? Application deadline 26 February 2010* 3-year postdoctoral Research Fellowships for research in the biological, biochemical, physical or clinical sciences related to medicine. Fellowships begin on 1 October 2010, based in Scotland. *Scottish Government Personal Research Fellowships co-funded by Marie Curie Actions - Application deadline 29 March 2010* 5-year postdoctoral Research Fellowship for research in any discipline, including inter-disciplinary areas, preference will be given to research likely to enhance the transfer of ideas and technology from the research community into increasing sustainable economic growth for all. The research projects proposed must align to one or more of the Scottish Government?s National Outcomes (see www.scotland.gov.uk/About/scotPerforms). Under the European Commission FP7 Marie Curie COFUND, funding is now available to enhance these Fellowships with additional support to allow international collaborations to be established and networks set up. Fellowships begin on 1 October 2010, based in Scotland. *Scottish Government Support Research Fellowships ? Application deadline 29 March 2010* 1-year sabbatical Research Fellowship for academic staff involved in research as defined above for the Personal Fellowships. Fellowships begin on 1 January 2011, based in Scotland. Eligibility criteria, regulations and application forms are available online at www.royalsoced.org.uk or e-mail: resfells at royalsoced.org.uk -- 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 p.herzyk at bio.gla.ac.uk Wed Jan 20 16:33:05 2010 From: p.herzyk at bio.gla.ac.uk (Pawel Herzyk) Date: Wed, 20 Jan 2010 16:33:05 +0000 Subject: [Sbforum-general] Bioinformatics position in Glasgow Message-ID: <252469B1-211B-4CB6-8739-C2BBDF29C2E6@bio.gla.ac.uk> University of Glasgow Faculty of Biomedical and Life Sciences Integrated Biology Bioinformatics Scientific Officer Ref: 00154-1 Salary: ?25,751 - ?28,983 per annum We are seeking to recruit a highly motivated individual able to provide bioinformatics support for the Sir Henry Wellcome Functional Genomics Facility with a primary focus on bespoke support for Next Generation Sequencing projects as well as designing and implementing pipelines for various data analysis workflows. The Sir Henry Wellcome Functional Genomics Facility, which has been operating for eight years, is a unique facility integrating genomics, transcriptomics, proteomics and metabolomics. The post holder will be involved in analysing data generated by in?house, state-of-an-art, Illumina Genome Analyzer II, as well as data generated in the MRC Sequencing Hub in Edinburgh or other Scottish centres via SULSA Transcriptomics Service. This is a contract position for 3 years. *The duration of the appointment will be dependent on the salary placing at appointment* For informal enquires, please, contact Dr Pawel Herzyk (P.Herzyk at bio.gla.ac.uk ) For detailed job description and to apply online please visit www.glasgow.ac.uk/jobs Closing date: 12th February 2010. --------------------------------------------------------------------- Dr Pawel Herzyk Lecturer in Bioinformatics Integrative & Systems Biology Faculty of Biomedical and Life Sciences Head of Bioinformatics, Microarrays and DNA analysis The Sir Henry Wellcome Functional Genomics Facility Joseph Black Building, University of Glasgow, Glasgow, G12 8QQ p.herzyk at bio.gla.ac.uk +44-141-3303180 http://www.gla.ac.uk:443/ibls/staff/staff.php?who=PGQPA~ http://www.brc.dcs.gla.ac.uk/~ph53d/shwfgf/microarrays.htm -------------- next part -------------- An HTML attachment was scrubbed... URL: From ab at macs.hw.ac.uk Wed Jan 20 22:06:16 2010 From: ab at macs.hw.ac.uk (Albert Burger) Date: Wed, 20 Jan 2010 22:06:16 +0000 Subject: [Sbforum-general] SWAT4LS 2009 proceedings available online Message-ID: <969C96A4-6128-4835-9018-DD2BC0F933C8@macs.hw.ac.uk> If you are interested in the Semantic Web for the Life Sciences, please note that the proceedings for the last SWAT4LS workshop, in Amsterdam on November 20th, 2009, are now available on-line: http://ceur-ws.org/Vol-559 Regards, Albert -- Dr. Albert Burger, Bioinformatics Research Scientist: Human Genetics Unit, MRC Senior Lecturer: Dept. of Computer Science, Heriot-Watt University Edinburgh, Scotland, UK MRC: email: Albert.Burger at hgu.mrc.ac.uk MRC: phone: +44 (131) 332-2471 x4040, fax: +44 (131) 467-8456 HWU: email: ab at macs.hw.ac.uk HWU: phone: +44 (131) 451-3428, fax: (131) 451-3327 WWW: http://www.macs.hw.ac.uk/~ab/ From sandra.borthwick at sbforum.org Fri Jan 22 10:53:36 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Fri, 22 Jan 2010 10:53:36 +0000 Subject: [Sbforum-general] Fwd: Programmatic Access To Biological Databases (Perl): REGISTER BY 29 JANUARY In-Reply-To: <4B5881E5.1090906@ebi.ac.uk> References: <4B5881E5.1090906@ebi.ac.uk> Message-ID: <7f11de471001220253u57a4525ev11f329948690d37f@mail.gmail.com> FYI: Dear Colleagues, We would like to remind you that registration will soon close for the EMBL-EBI Hands-on Course: Programmatic Access To Biological Databases (Perl) 22nd-26th Feb 2010 Please see link below to learn more and to register http://www.ebi.ac.uk/training/handson/course_100222_webservicesperl.html Registration deadline: 12:00 noon on Friday 29 January 2010 This course consists of lectures and hands-on computer-based practical sessions and is ideal for bioinformaticians and biological researchers looking to develop data analysis pipelines or access data in an automated manner for integration into their own applications. The course will provide an overview of public domain biological databases at the EMBL-EBI, introduce the principles of Web Services, how they work and how to find them. You will gain hands on experience integrating data from multiple sources and training in programmatic access to a variety of bioinformatic analysis tools. Participants should have competence in Perl as there is no scope to teach the basics of programming. If you are concerned about what level of expertise you will need, please get in touch with the course organisers. You are welcome to circulate this announcement to interested members and groups within your institute. If you have any questions, please do not hesitate to contact us. Kind regards, Alison Barker Please visit www.embl.org/events for a complete list of all EMBL events Please subscribe at www.embl.de/events/newsletter for our newsletter Follow us on www.twitter.com/embl_events?and www.friendfeed.com/embl -- Alison Barker Outreach and Training Team Secretary EBI EMBL Outstation European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: +44-(0)1223 49- 4604 Fax: +44-(0)1223 49- 4621 email: alison at ebi.ac.uk http://www.ebi.ac.uk/training/ Upcoming hands on training courses (http://www.ebi.ac.uk/training/handson/): 22-26 February 2010: Programmatic Access To Biological Databases (Perl) http://www.ebi.ac.uk/training/handson/course_100222_webservicesperl.html 29-31 March 2010: Plant Informatics http://www.ebi.ac.uk/training/handson/course_100329_plantgenomics.html 14th-18th Jun 2010: Joint EBI-Wellcome Trust Bioinformatics Summer School http://www.ebi.ac.uk/training/handson/course_100614_summerschool.html -- 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 From urmi.trivedi at ed.ac.uk Tue Jan 26 12:42:11 2010 From: urmi.trivedi at ed.ac.uk (Urmi Trivedi) Date: Tue, 26 Jan 2010 12:42:11 -0000 Subject: [Sbforum-general] Reminder - NextGenBUG meeting February 9th in Dundee Message-ID: Dear all, Apologies to all those who had problems accessing our server. Its back (please note the change in the website mentioned below) and you can edit the pages as usual. Just a quick reminder - the next NextGenBUG (next generation sequencing Bioinformatics User Group) will be on 2010, February 9, Tuesday from 13:00-16:00 at College of Life sciences, University of Dundee Agenda: 1. InsectaCentral - assembling and annotating insect transcriptomes - Alexie Papanicolau, Exeter 2. Galaxy: a stairway to NGS heaven - Chris Cole, Dundee 3. Some work on and around the potato genome sequencing project - Dan Bolser, Dundee 4. An Introduction to the CLCBio Genomics Workbench - Darrol Baker, CLCBio Meeting logistics (parking, etc) and details of other short talks available at http://sce-bio-c00556.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209 Please add your name to the list at http://sce-bio-c00556.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209 Please volunteer to give the usual 15 - 20 minute presentations. See you there. Best regards, Urmi -- Urmi Trivedi Sequencing Bioinformatician The Gene Pool Ashworth Laboratories Kings Building's campus University of Edinburgh EH9 3JT Phone: +44 131 650 7403 Fax: +44 131 651 3629 Web: http://genepool.bio.ed.ac.uk/ The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.