From mark.blaxter at ed.ac.uk Wed Dec 2 13:24:16 2009 From: mark.blaxter at ed.ac.uk (Mark Blaxter) Date: Wed, 2 Dec 2009 13:24:16 +0000 Subject: [Sbforum-general] Fwd: R User Meeting: Call for Speakers References: Message-ID: Begin forwarded message: > From: "Muriel Mewissen" > Date: 2 December 2009 13:01:48 GMT > To: > Subject: R User Meeting: Call for Speakers > > > Dear R User, > > Following on the success of the first R User Meeting at Nesc in > 2008, we are > planning a second meeting for January 2010. > > Date: Wednesday 20th January 2010 > Time: 2 to 5 pm > Venue: Nesc, Edinburgh > Registration: http://www.nesc.ac.uk/esi/events/1044/ > > The format for the afternoon is intended to be informal with > presentations > as well as time for discussion and networking. This is a great > opportunity > to share your experience with R and parallel computing with the > growing R > user community in Edinburgh. > > We are looking for speakers to present their latest projects using R > in any > scientific area. Research using the ECDF or other High Performance > Computing > facilities would be of particular interest. The SPRINT project > (http://www.r-sprint.org/) will present its latest developments. > > Please contact me if you are interested in speaking at this meeting. > > Further information on talks and agenda will be sent closer to the > date. > > Kind regards, > Muriel > > > --- > Muriel Mewissen (+44 131 242 6283) > > Division of Pathway Medicine > University of Edinburgh Medical School > The Chancellor's building > 49 Little France Crescent > Edinburgh, EH16 4SB > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > Mark Blaxter mark.blaxter at ed.ac.uk ~ may all beings be happy ~ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From d.m.a.martin at dundee.ac.uk Mon Dec 7 22:48:46 2009 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Mon, 07 Dec 2009 22:48:46 +0000 Subject: [Sbforum-general] Tools for preparing short read archive submission Message-ID: <4B1D864E.9020109@dundee.ac.uk> We are preparing a dataset for submission to the European short read archive. The submission appears to require the creation of handcrafted XML with poorly specified fields. Does anyone have any tools for ENA submission packaging? They woudl be really useful. I really don't relish the task of having to handcraft XML. ..d From bioinformatics.lists at gmail.com Wed Dec 9 09:43:14 2009 From: bioinformatics.lists at gmail.com (Dan Swan) Date: Wed, 9 Dec 2009 09:43:14 +0000 Subject: [Sbforum-general] Tools for preparing short read archive submission In-Reply-To: <4B1D864E.9020109@dundee.ac.uk> References: <4B1D864E.9020109@dundee.ac.uk> Message-ID: David, Pretty sure that the ISA Infrastructure tools : http://isatab.sourceforge.net/index.html support submission to the ENA. I'd get in touch with Phillipe Rocca-Serra (rocca at ebi.ac.uk) - they were very accommodating when I went down to the EBI to learn about the tools. regards, Dan 2009/12/7 David Martin : > We are preparing a dataset for submission to the European short read > archive. The submission appears to require the creation of handcrafted XML > with poorly specified fields. Does anyone have any tools for ENA submission > packaging? They woudl be really useful. I really don't relish the task of > having to handcraft XML. > > ..d > > _______________________________________________ > Sbforum-general mailing list > Sbforum-general at sbforum.org > http://sbforum.org/mailman/listinfo/sbforum-general_sbforum.org > -- Bioinformatics Support Unit || http://bsu.ncl.ac.uk/ Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle, NE2 4HH Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A - Mon/Wed) Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26 - Thu/Fri) From g.kalna at beatson.gla.ac.uk Thu Dec 10 09:50:50 2009 From: g.kalna at beatson.gla.ac.uk (Gabriela Kalna) Date: Thu, 10 Dec 2009 09:50:50 -0000 Subject: [Sbforum-general] Bioinformatics job at the Beatson Message-ID: Dear All, Could you please circulate this job advert, please? Regards Gabriela ? SCIENTIFIC OFFICER IN BIOINFORMATICS Salary range ?22,100 - ?37,100 The Beatson Institute in Glasgow is one of Europe's leading cancer research centres. It is core funded by Cancer Research UK and supports cutting edge research into the molecular mechanisms of cancer development. The Institute has recently moved to a new facility that provides an outstanding research environment, underpinned by state-of-the art core services and advanced technologies. We are seeking a bioinformatician skilled in analysing large biological data sets, who enjoys working in a multi-disciplinary environment and can provide support in solving complex biological problems relating to cancer genetics. Essential Skills: *???????? Experience in biomedical research, functional genomics, proteomics or modelling biological systems (1 year minimum), or a good relevant post-graduate degree; *???????? Demonstrable experience of programming in at least one of Perl, Python, Java or C/C++; *???????? Excellent communication skills. Desired Skills: * Knowledge of statistics, including R and Bioconductor, and/or experience in database administration; * Experience in Linux/Unix; * Familiarity with molecular biology and genomics. Applications with a covering letter and CV including the names of three referees, should be sent to Dr Gabriela Kalna, The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, Scotland (FAX: 0141-942 6521) or by email to g.kalna@ beatson.gla.ac.uk Informal enquiries may also be made to Dr Kalna. Closing date for applications: 15 January 2010. ? ----- Dr?Gabriela Kalna The Beatson Institute for Cancer Research Garscube Estate Switchback Road Glasgow G61 1BD United Kingdom Tel: +44(0) 141 3308704 g.kalna at beatson.gla.ac.uk www.beatson.gla.ac.uk From geoff at compbio.dundee.ac.uk Tue Dec 15 17:31:28 2009 From: geoff at compbio.dundee.ac.uk (Geoff Barton) Date: Tue, 15 Dec 2009 17:31:28 +0000 Subject: [Sbforum-general] Bioinformatics post-doc position at Dundee Message-ID: <4B27C7F0.50006@compbio.dundee.ac.uk> I have a good opportunity for a computational post-doc who would like to work on Next Gen sequence data and see their analyses tested in the lab. Please see the links to the job advert and further particulars on http://www.compbio.dundee.ac.uk The closing date for applications is 15th Jan 2010. With thanks, Geoff. -- Geoff Barton, Professor of Bioinformatics, College of Life Sciences University of Dundee, Scotland, UK. g.j.barton at dundee.ac.uk Tel:+44 1382 385860/388731 (Fax:385764) www.compbio.dundee.ac.uk The University of Dundee is registered Scottish charity: No.SC015096 From Muriel.Mewissen at ed.ac.uk Thu Dec 17 14:02:20 2009 From: Muriel.Mewissen at ed.ac.uk (Muriel Mewissen) Date: Thu, 17 Dec 2009 14:02:20 -0000 Subject: [Sbforum-general] R User Meeting @ Nesc on Wed 20 January 2010 Message-ID: <05A40E6E3275471F99321AAF7AA330C7@MMNTRACLAPTOP> Dear R User, Please find below the agenda for the upcoming R User Meeting at Nesc. The format for the afternoon is intended to be informal with presentations from various projects as well as time for discussion and networking. The main theme is using R on High Performance Computing facilities such as the ECDF. The meeting is free but please register at http://www.nesc.ac.uk/esi/events/1044/ for catering purpose. Date: Wednesday 20th January 2010 Time: 2 to 5 pm Venue: Nesc, Edinburgh Registration: http://www.nesc.ac.uk/esi/events/1044/ Agenda: 14:00 Welcome & R User Survey Results, Muriel Mewissen, Division of Pathway Medicine 14:30 MAGIC, a consensus clustering package for R, Dr Ian Simpson, Centre for Integrative Physiology 14:55 R and Eddie for Breast Cancer Bioinformatics, Dr Duncan Sproul, Breakthrough Breast Cancer Group 15:15 Using large datasets in R with ff, Michal Piotrowski, EPCC 15:35 Coffee/Tea 16:05 SPRINT & MPI IO, Savvas Petrou, EPCC 16:25 RMPI, Ms Xu Guo, EPCC 16:50 Wrap up, Muriel Mewissen, Division of Pathway Medicine Kind regards, Muriel --- Muriel Mewissen (+44 131 242 6283) Division of Pathway Medicine University of Edinburgh Medical School The Chancellor's building 49 Little France Crescent Edinburgh, EH16 4SB -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From sandra.borthwick at sbforum.org Thu Dec 17 14:44:46 2009 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Thu, 17 Dec 2009 14:44:46 -0000 Subject: [Sbforum-general] Upcoming "R" workshops Message-ID: <4A566DDEBB73437987FDA23EB3AEE925@society.local> Dear All Thanks to all who gave input regarding the "R" training workshop. At present we are in the process of organising these workshops with a view to hold these in the new year. Meanwhile there is an "R" user group meeting being held in the NeSc Edinburgh http://www.nesc.ac.uk/esi/events/1044/ If you are already working on "R" please check these links, or if you are interested in attending one of our upcoming workshops, it may be useful to try to go to this meeting until we finalise the dates for the workshops. Please don't hesitate if you have any suggestions or require further information. 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 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 s.watterson at ed.ac.uk Thu Dec 10 12:34:38 2009 From: s.watterson at ed.ac.uk (Steven Watterson) Date: Thu, 10 Dec 2009 12:34:38 +0000 Subject: [Sbforum-general] ICSB 2010, Edinburgh, UK. 10th-15th October 2010 - Call for Tutorials Message-ID: <4B20EADE.4000908@ed.ac.uk> Subject: ICSB 2010, Edinburgh, UK. 10th-15th October 2010 - Call for Tutorials Call For Tutorials 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 The ICSB tutorials series is meant to prepare attendees for a better understanding of certain aspects of the main conference, by giving them an introduction to the tools and methods of general interest for systems biology and by providing hands-on experience where appropriate. We would now like to invite prospective tutorial organisers to submit proposals for ICSB2010 tutorials to the organising commitee. Proposals should include the purpose and background of the subject area, the name of organizer and speakers, a description of their organisation, an estimate of the numbers of participants and mention whether demonstration facilities other than a standard AV system will be used. If tutorial material already exists even in draft stage, it would be helpful for the programme committee to make a more informed decision, if it were included with the proposal. Tutorials will last up to 4hrs. Enquiries can be made directly to Prof. Vincent Danos (vdanos at inf.ed.ac.uk) and Dr. Hong Yue (hong.yue at eee.strath.ac.uk). Examples of tutorials given at recent ICSB meetings can be found at http://www.icsb-2007.org/tutorials/index.html http://www.icsb-2008.org/main.php?display=tutorials http://icsb-2009.org/schedule.php#tutorial1 Deadline for tutorial proposals: Jan 15 2010 Tutorial venue and date: Edinburgh International Conference Centre, Oct 10 2010 Submission can be made directly to Prof Danos and Dr Yue or via the conference website. Registration and Fees: There is no charge to present an academic/non-profit tutorial. Registration for tutorials will be handled by ICSB and participants will be charged to cover the local expenses. Tutorial presenters and attendees are expected to register for the main conference. Appropriate badging for all tutorial attendees will be provided. Commercial tutorials may be presented at a cost of GBP500. Commercial tutorials are tutorials that primarily focus on using specific commercial products or systems, or at which commercial products are advertised, promoted, or sold, or which are primarily taught by the distributors or producers of those products. The program committee will make the final determination of whether or not a tutorial is commercial. For more information about ICSB2010, please see http://www.icsb-2010.net/ Sent on behalf of: Chair of the Scientific Program Committee and Congress Chairman, Prof. Igor Goryanin Vice Chair of the Scientific Program Committee, Dr. Andrew B. Goryachev 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 http://www.icsb-2010.net/ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From s.watterson at ed.ac.uk Thu Dec 10 14:00:29 2009 From: s.watterson at ed.ac.uk (Steven Watterson) Date: Thu, 10 Dec 2009 14:00:29 +0000 Subject: [Sbforum-general] ICSB 2010 Edinburgh, UK. 15-19th Oct 2010. Call for workshops. *New deadline*. Message-ID: <4B20FEFD.9080106@ed.ac.uk> Call for Workshops at ICSB2010. We are now accepting proposals for workshops to be held in conjunction with the 11th International Conference on Systems Biology, which will be held October 10-15, 2010 in the Edinburgh International Edinburgh International Conference Centre (EICC), Edinburgh, UK. Deadline for Proposals for Workshops: 15 January, 2009. It is expected that workshops will be held on the 15th October, 2010 at the EICC. However, additional workshops may be organised before or after ICSB2010 at a separate venue, subject to approval by the local organising committee. Please contact Prof. Igor Goryanin for further details. Workshops can vary from a half day (approximately 4 hours) to a full day, extended if necessary through participation of a local organiser. The proposal shall describe the purpose, background, estimated number of attendees, possible names of speakers, and general format of the workshop. Strong consideration will be given to workshop proposals that are of interest to an interdisciplinary community, and provide a framework for future research agendas. Early decisions may be made for workshops that require advanced preparations as well as for workshops that are held regularly with ICSB. The EICC is an international-class conference venue with a range of flexible seminar and meeting rooms (http://www.eicc.co.uk). Meeting rooms will be provided on a space-available basis in the Conference Centre. Space is available for up to 12 workshops to be held simultaneously, with capacities of 15 to 100 people (classroom-style seating) or 30-300 people (theatre-style seating). The smaller venues can be arranged to seat up to 36 people boardroom-style for committee meetings. An additional boardroom for up to 14 people is available. Further information about ICSB2010 workshops together with proposal forms can be found at http://www.icsb2010.org.uk/workshops." Sent on behalf of: Chair of the Scientific Program Committee and Congress Chairman, Prof. Igor Goryanin Vice Chair of the Scientific Program Committee, Dr. Andrew B. Goryachev 10th International Conference on Systems Biology Edinburgh, UK. 10th-15th October 2010 http://www.icsb-2010.net/ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.