From urmi.trivedi at ed.ac.uk Wed May 6 13:26:02 2009 From: urmi.trivedi at ed.ac.uk (Urmi Trivedi) Date: Wed, 06 May 2009 13:26:02 +0100 Subject: [Sbforum-general] NextGenBUG June 2, Tuesday noon, SCRI, Invergowrie, Dundee Message-ID: <20090506132602.ztag6o37cw08wc0g@www.staffmail.ed.ac.uk> The next NextGenBUG (next generation sequencing Bioinformatics User Group) will be on 2009, June 2, Tuesday from 12:30-15:30 at Scottish Crop Research Institute (SCRI), Invergowrie, Dundee, DD2 5DA Agenda: 1. Isilon systems - Methods for Managing Large and Rapidly Growing Data Stores in Life Science Research Environments - Rob Anderson, Life science manager, Isilon systems 2. Assembly of a novel fish herpesvirus genome - Derek Gatherer Meeting logistics (parking, etc) and details of other short talks available at http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20090602/home Please add your name to the list at http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20090602/home Note: you have to be registered on the website to edit pages. If you have been working on a next gen sequencing project and would like to talk about it, please add your name to the list at http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20090602/home If you are not registered to the NextGenBUG mailing list, send an email to majordomo AT lists DOT ed DOT ac DOT uk where the first line of the body is (the subject is ignored): subscribe nextgenbug. You should receive a confirmation email within an hour. Best regards, Urmi Urmi Trivedi Bioinformatics Room 3.54 The Gene Pool Ashworth Labs King's Buildings Campus University of Edinburgh EH9 3JT, UK +44 131 650 7403 http://genepool.bio.ed.ac.uk -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From anne.smith at st-andrews.ac.uk Fri May 8 11:26:46 2009 From: anne.smith at st-andrews.ac.uk (V. Anne Smith) Date: Fri, 8 May 2009 11:26:46 +0100 Subject: [Sbforum-general] PhD opportunities at the University of Plymouth Message-ID: >Begin forwarded message: >> >>Institution >>The University of Plymouth ( www.plymouth.ac.uk >>) is currently advertising an additional 40 >>fully funded PhD scholarships due to our >>success in the RAE2008 >>(http://www.plymouth.ac.uk/pages/view.asp?page=20604). >>We, in Computer Science/Computing, were leaders >>in research for the University's RAE 2008 >>submission, which has put Plymouth among the >>top 15 UK universities for computer science and >>informatics research. Therefore, we are well >>placed to secure studentships provided we can >>get high quality students to apply before the >>deadline which is 26th May 2009. Thus, time is >>of the essence. >> >>Applicant profile >>Note that the emphasis on this call will be on >>the quality of the applicant. So we are looking >>for high quality PhD applicants. >>? The Studentships will be full-time >>for three years and includes a stipend of >>?13,290 and tuition fees of ?3,400 paid for >>Home/EU students. Applications from non EU >>nationals will be considered for part fees only >>support not stipends. International students >>will be expected to secure funds to meet the >>difference between Home/EU and overseas tuition >>fees (?10,000 in 2009/10) for the duration of >>the programme. >>? A student who has studies at MSc is >>preferable, but we are still very interested in >>high quality graduates for these positions. >>? The emphasis on the academic >>background is based on computing/computer >>science/programming. >> >>PhD subject areas >>There are two PhD projects on offer in >>conjunction with the Visualization Lab. These >>are >> >>1. PhD in Information Visualization and Visual Analysis of large data sets >>q The main aim of this research is to develop >>a new approach to the analysis of experimental >>data in neurophysiology based on the use of >>modern computer science techniques such as >>graphical engineering, visualization and >>virtual reality. >>q This new approach will provide >>neuroscientists with an interactive environment >>within which to explore their data sets. The >>primary focus of this research is on the >>analysis of multi-dimensional data sets. By >>navigating through these large data sets, >>researchers will be able to focus on particular >>features of the data as well as identifying >>overall characteristics. This will support the >>integration of the experimental and theoretical >>approaches to the analysis of >>neurophysiological evidence. >>q Our research applies the techniques and >>principles of Information Visualization to >>support the analysis of vast datasets. Our >>major application area is Neurophysiology and >>we specialize in the visual analysis of large >>multi-dimensional spike train datasets. This is >>called the VISA project >>(http://www.tech.plymouth.ac.uk/infovis/LAB_VISA.htm) >> >> >>2. PhD in Usability and User-Centred Systems Design. >>q In this project the user experience will be >>related to the CARMEN project as a case study. >>This PhD will be largely focused on the >>practice of usability and how software >>developers can improve both new and ongoing >>projects to ensure user acceptance and >>satisfaction. The work will include a study of >>the latest and most effective methodologies for >>developing truly usable and user-centred >>software solutions. >>q CARMEN http://www.carmen.org.uk/ is an >>e-Science Pilot Project funded by the >>Engineering and Physical Sciences Research >>Council (UK). It will deliver a virtual >>laboratory for neurophysiology, enabling >>sharing and collaborative exploitation of data, >>analysis code and expertise. Neural activity >>recordings (signals and image series) are the >>primary data types. ?5M are committed to 20 >>scientific investigators at 11 UK universities. >>The project brings together neurophysiologists, >>neuroinformaticists and computer scientists, to >>address the complete lifecycle of >>neurophysiology data. >> >>Overall, there will be flexibility with the >>content of the PhD programme and so the project >>will be subsequently refined. This really is a >>great opportunity. Could I please ask you to >>make this information known to any appropriate >>students and to forward it to any other >>appropriate staff in your area. >> >>Supervision >>I (Liz Stuart) will be acting as Director of >>Studies (first supervisor) for the projects >>specified below and successful candidate(s) >>will be working alongside other staff in the >>Visualization Lab here in >>Plymouthhttp://www.tech.plymouth.ac.uk/infovis/. >>The main focus of this Visualization Lab is the >>relatively new, rapidly increasing field of >>Information Visualization (IV and Visual >>Analysis (VA)). In practice this involves the >>selection, transformation and representation of >>data in a various forms that support data >>mining and novel representation techniques. In >>the past the Visualization lab have worked on >>the development of IV techniques for the >>analysis of neurophysiological data in the form >>of multi-dimensional spike train recordings. >>Investigation of this data is directed towards >>the synchronization of spikes between spike >>trains, to derive the coupling of the >>underlying neurons. Additionally, we are >>involved in projects applying IV techniques in >>Civil Engineering and Artificial Life. >> >>If you are interested, please do email me for more information ? >> >>Regards >>Liz >> >>Further information - For further information >>on research studentship opportunities, and >>postgraduate study at the university of >>Plymouth, please see the Graduate School >>webpages >> >>Dr. Liz Stuart >>The Visualization Lab >>e: lstuart at plymouth.ac.uk >>w: www.plymouth.ac.uk/infovis >>t: 01752 232665 >> >>Office on campus: >>Room B310, Portland Square >> >>Full postal address: >>School of Computing, Comms. & Elecs. >>Faculty of Technology, University of Plymouth >>Drake Circus, Plymouth, Devon, PL4 8AA, United Kingdom -- 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? 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From sborthwick at royalsoced.org.uk Tue May 12 11:16:56 2009 From: sborthwick at royalsoced.org.uk (Sandra Borthwick) Date: Tue, 12 May 2009 11:16:56 +0100 Subject: [Sbforum-general] ** REMINDER ** Scottish Systems Biology meeting Aberdeen - Friday 15th May 2009 ** Message-ID: <818406367E54EC499E989D011C0025CF3E97C6@rsoe_server4.society.local> ** REMINDER ** - REGISTRATION AVAILABLE Please note: We have had a recent problem with the server, which may have prevented some people from registering for this event. This fault has now been resolved and registration is now back to normal, please accept our apologies. For information and links see below: ======================================================================== ============================ 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 programme information see http://www.sbforum.org/cmsimages/event_progs_09/051509_4th%20SBMN%20Mtg_ prog_v2.pdf POSTERS ARE WELCOME, we encourage you to bring a poster on systems modelling/biology; please let us know by email contact at sbforum.org All details can be found at 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 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 g.coghill at abdn.ac.uk Sat May 16 09:51:43 2009 From: g.coghill at abdn.ac.uk (Coghill, Dr George M.) Date: Sat, 16 May 2009 09:51:43 +0100 Subject: [Sbforum-general] Seminar by Edda Klipp Message-ID: Folks There will be a seminar given by Prof. Edda Klipp on the 29th of May at Aberdeen University entitled "Mathematical modeling of cellular stress response". This will take place at 11 am in the Level 7 Conference Room of the Institute of Medical Sciences. We look forward to seeing you there. Cheers George The University of Aberdeen is a charity registered in Scotland, No SC013683. -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.coghill at abdn.ac.uk Wed May 27 13:10:26 2009 From: g.coghill at abdn.ac.uk (Coghill, Dr George M.) Date: Wed, 27 May 2009 13:10:26 +0100 Subject: [Sbforum-general] Reminder: Seminar by Edda Klipp Message-ID: Folks This is to remind you that there will be a seminar given by Prof. Edda Klipp on Friday (29th of May) at Aberdeen University entitled "Mathematical modeling of cellular stress response". This will take place at 11 am in the Level 7 Conference Room of the Institute of Medical Sciences. Edda Klipp is internationally renowned for her modelling of cell signalling and responses. She has, for example, modelled stress responses, pheromone responses, key protein kinase cascades and cell cycle regulation (eg Nature Biotech 23, 975), and her work has provided interesting new insights into these processes. We look forward to seeing you there. Cheers George The University of Aberdeen is a charity registered in Scotland, No SC013683. -------------- next part -------------- An HTML attachment was scrubbed... URL: From O.Vasieva at liverpool.ac.uk Mon May 11 15:37:13 2009 From: O.Vasieva at liverpool.ac.uk (Vasieva, Olga) Date: Mon, 11 May 2009 14:37:13 -0000 Subject: [Sbforum-general] PhD project Message-ID: <90A77B3FE6D390478D90C5174BBBB0BC06C1175E7C@STAFFMBX2.livad.liv.ac.uk> Dear all, My colleague is looking for a good bioinformatician for a PhD project: http://www.liv.ac.uk/working/job_vacancies/studentships/PhD_studentship_bioi.htm The deadline is soon but Andy Johns (jonesar at liverpool.ac.uk) can re-open this position for a good candidate. All the best, Olga ________________________________________ From: Jones, Andy Sent: 11 May 2009 15:16 To: Vasieva, Olga Subject: RE: Meeting Hi Olga, Thanks again for your help and advice. Here is the URL for my studentship: http://www.liv.ac.uk/working/job_vacancies/studentships/PhD_studentship_bioi.htm If you could circulate to any contacts, it would be much appreciated. Cheers, Andy > -----Original Message----- > From: Vasieva, Olga > Sent: 11 May 2009 11:12 > To: Jones, Andy > Subject: FW: Meeting > > > > Hi Andy, > > Did we decide to meet at our room (N 231, the 2nd floor). I'll better meet you > downstairs at 14.00, it is not that easy to find us. > Here are the rferences to our papers on Seed and RAST: > http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2265698&tool=pmcentr > ez > http://nar.oxfordjournals.org/cgi/content/abstract/33/17/5691 > All the best, > > Olga > ________________________________________ > From: Vasieva, Olga > Sent: 06 May 2009 11:08 > To: Jones, Andy > Subject: Meeting > > Hi Andy, > We can make it next week. It is even better, as I need to finish few things here as > well. > Monday? > Olga > ________________________________________ > From: Jones, Andy > Sent: 06 May 2009 10:55 > To: Vasieva, Olga > Subject: RE: Bioinformatics seminar > > Hi Olga, > > Sorry, an unavoidable meeting clash has come up, are you free tomorrow, say at > 1pm? I can come over to your office, > Cheers > Andy > > > > -----Original Message----- > > From: Vasieva, Olga > > Sent: 06 May 2009 10:34 > > To: Jones, Andy > > Subject: RE: Bioinformatics seminar > > > > Hi Andy, > > Are we meeting today at 14.00? I am sorry but I do not remember if we decided > > where.. > > Best, > > Olga > > > > ________________________________________ > > From: Jones, Andy > > Sent: 16 February 2009 11:35 > > To: Vasieva, Olga > > Subject: RE: Bioinformatics seminar > > > > Hi Olga, > > > > Just checking arrangements for tomorrow, we'll bring a laptop over (and some > > donuts!), will there be a projector there already? > > Thanks > > Andy > > > > > -----Original Message----- > > > From: Vasieva, Olga > > > Sent: 12 February 2009 10:45 > > > To: Vasieva, Olga; Cossins, Andrew; Hall, Neil; Spencer, Matthew; Caddick, > > Mark; > > > Ebrahimi, Bahram; Edwards, Steven [biolhos]; Noyes, Harry; Gregory, Richard; > > > Ashelford, Kevin; Sangaralingam, Ajanthah; Darby, Alistair; Weedall, Gareth; > > Vieira > > > de Mello, Luciane; Rigden, Dan; Beynon, Rob; Jones, Andy; Lane, Brian; > Wong, > > > Prudence; Daniel Naguib, Gianluca; Lowe, Christopher; Van 'T Hof, Arjen; > > > Goodhead, Ian; drderekdaly at yahoo.co.uk; Kay, Suzanne; Williams, Daryl; > > > Sibthorp, Christopher; Paterson, Steve; Woodhead, Duncan; Galbraith, > Sareen; > > > Prior, Ian; Mohammed, ManalAhmed; Royle, Steve; Urbe, Sylvie; Clague, > > Michael; > > > Miller, Peter; De Magalhaes, JoaoPedro; Horsburgh, Mal; McCarthy, Alan; > > > McLennan, Alexander; White, Mike; Hurst, Greg; Merry, Brian; Tidd, David; > Hall, > > > Anthony; Hartwell, James; Bennett, Daimark; Iwanejko, Lesley; Jones, Nigel > > > Subject: RE: Bioinformatics seminar > > > > > > Dear colleagues, > > > > > > We will be glad to see you at our next Bioinformatics seminar which will take > > place > > > on the 17th Feb, room SR6, BSB. Andy Johns will present on "Measuring the > > > trade-off between sensitivity and specificity in large scale proteomics studies" > > and > > > James Wright will present on "Spectral Profile Libraries For Cross Species > > > Proteomics". It will be our first 'Proteomics' seminar, and I believe that > > > presentations and a discussion will be of interest for not only bioinformaticians > > but > > > also for biologists who consider using proteomics in their research. > > > > > > On the 3d of March our speakers will be :Daniel Rigden&Duncan Woodhead > > > > > > All the best, > > > > > > Olga > > > > > > Please, forward this letter to who may be interested in the seminars and who > > may > > > want to be on this mailing list. And ,please, do not worry if you do not want to > be > > > on the list. Today I expanded it arbitrary. I'll adjust the list with time to avoid > being > > > annoying.. > > > > > > For ones who joined us recently: > > > It takes place every second week, Tuesday, room SR6. > > > ________________________________________ > > > From: Vasieva, Olga > > > Sent: 29 January 2009 16:24 > > > To: Vasieva, Olga; Cossins, Andrew; Hall, Neil; Spencer, Matthew; Caddick, > > Mark; > > > Ebrahimi, Bahram; Edwards, Steven [biolhos]; Noyes, Harry; Gregory, Richard; > > > Ashelford, Kevin; Sangaralingam, Ajanthah; Darby, Alistair; Weedall, Gareth; > > Vieira > > > de Mello, Luciane; Rigden, Dan; Beynon, Rob; Jones, Andy; Lane, Brian; > Wong, > > > Prudence; Daniel Naguib, Gianluca; Lowe, Christopher; Van 'T Hof, Arjen; > > > Goodhead, Ian; drderekdaly at yahoo.co.uk; Kay, Suzanne; Williams, Daryl; > > > Sibthorp, Christopher; Paterson, Steve; Woodhead, Duncan; Galbraith, > Sareen; > > > Prior, Ian; Mohammed, ManalAhmed; Royle, Steve; Urbe, Sylvie; Clague, > > Michael > > > Subject: RE: Bioinformatics seminar > > > > > > Sorry..I forgot to mention a date! > > > > > > Seminar will take place on > > > Tuesday (the 3d of February) > > > > > > For ones who joined us recently: > > > It takes place every second week, Tuesday, room SR6. > > > > > > All the best, > > > > > > Olga > > > > > > Dr Olga Vasieva > > > School of Biological Sciences > > > Biosciences Building > > > Crown Street > > > University of Liverpool > > > Liverpool L69 7ZB > > > Tel: +44-151-7954551 > > > > > > > > > > > > > > > -----Original Message----- > > > From: Vasieva, Olga > > > Sent: Thu 1/29/2009 4:13 PM > > > To: Vasieva, Olga; Cossins, Andrew; Hall, Neil; Spencer, Matthew; Caddick, > > Mark; > > > Ebrahimi, Bahram; Edwards, Steven [biolhos]; Noyes, Harry; Gregory, Richard; > > > Ashelford, Kevin; Sangaralingam, Ajanthah; Darby, Alistair; Weedall, Gareth; > > Vieira > > > de Mello, Luciane; Rigden, Dan; Beynon, Rob; Jones, Andy; Lane, Brian; > Wong, > > > Prudence; Daniel Naguib, Gianluca; Lowe, Christopher; Van 'T Hof, Arjen; > > > Goodhead, Ian; drderekdaly at yahoo.co.uk; Kay, Suzanne; Williams, Daryl; > > > Sibthorp, Christopher; Paterson, Steve; Woodhead, Duncan; Galbraith, > Sareen; > > > Prior, Ian; Mohammed, ManalAhmed; Royle, Steve; Urbe, Sylvie; Clague, > > Michael > > > Subject: RE: Bioinformatics seminar > > > > > > Dear colleagues, > > > > > > I would like to remind you that our next Bioinformatics seminar will take place > at: > > > Room SR6, 2nd Floor, Life Science Building, 11.00 a.m. > > > > > > Kevin Ashelford and Richard Gregory will give an introduction to 454 > sequencing > > > and exiting aspects of the following data analysis ,storage, retrieval. > > > > > > Hope to see you all on Tuesday, > > > > > > All the best, > > > > > > Dr Olga Vasieva > > > School of Biological Sciences > > > Biosciences Building > > > Crown Street > > > University of Liverpool > > > Liverpool L69 7ZB > > > Tel: +44-151-7954551 > > > > > > > > > > > > > > > -----Original Message----- > > > From: Vasieva, Olga > > > Sent: Fri 1/23/2009 10:32 AM > > > To: Vasieva, Olga; Cossins, Andrew; Hall, Neil; Spencer, Matthew; Caddick, > > Mark; > > > Ebrahimi, Bahram; Edwards, Steven [biolhos]; Noyes, Harry; Gregory, Richard; > > > Ashelford, Kevin; Sangaralingam, Ajanthah; Darby, Alistair; Weedall, Gareth; > > Vieira > > > de Mello, Luciane; Rigden, Dan; Beynon, Rob; Jones, Andy; Lane, Brian; > Wong, > > > Prudence; Daniel Naguib, Gianluca; Lowe, Christopher; Van 'T Hof, Arjen; > > > Goodhead, Ian; drderekdaly at yahoo.co.uk; Kay, Suzanne; Williams, Daryl; > > > Sibthorp, Christopher; Paterson, Steve; Woodhead, Duncan; Galbraith, Sareen > > > Subject: RE: Bioinformatics seminar > > > > > > Dear Colleagues, > > > > > > It seems that our first seminar went well. Thank you very much to all who > > managed > > > to come and take part in a discussion and many thanks to our first speakers > (Ian, > > > Kevin, Andy) who made it all so exiting! > > > > > > Here is a list of people who are willing to speak in the nearest future (I am > > > apologizing for screwing up the dates in preliminary communications). You are > > > very welcome to send you requests for new talks and discussion topics. We > > > decided to have a pretty informal style. > > > > > > I would appreciate you letting me know in advance if you want to make > changes > > in > > > the list: > > > > > > Group, names Topic date > > > Kevin, Richard: 454 Sequencing 03/02/2009 > > > Veterinary School (Speaker(s)?) 17/02/2009 > > > Daniel Rigden&Duncan Woodhead 03/03/2009 > > > Ajanthah and Olga (or Lu)?? 17/03/2009 > > > Steve Patherson and Lu (or Ajanthah?) 31/03/2009 > > > > > > We are going to bring an espresso machine to our next seminar! > > > > > > All the best, > > > > > > Olga > > > > > > Dr Olga Vasieva > > > School of Biological Sciences > > > Biosciences Building > > > Crown Street > > > University of Liverpool > > > Liverpool L69 7ZB > > > Tel: +44-151-7954551 > > > > > > > > > > > > > > > -----Original Message----- > > > From: Vasieva, Olga > > > Sent: Mon 1/19/2009 3:24 PM > > > To: Vasieva, Olga; Cossins, Andrew; Hall, Neil; Spencer, Matthew; Caddick, > > Mark; > > > Ebrahimi, Bahram; Edwards, Steven [biolhos]; Noyes, Harry; Gregory, Richard; > > > Ashelford, Kevin; Sangaralingam, Ajanthah; Darby, Alistair; Weedall, Gareth; > > Vieira > > > de Mello, Luciane; Rigden, Dan; Beynon, Rob; Jones, Andy; Lane, Brian; > Wong, > > > Prudence; Daniel Naguib, Gianluca; Lowe, Christopher; Van 'T Hof, Arjen; > > > Goodhead, Ian; drderekdaly at yahoo.co.uk; Kay, Suzanne; Williams, Daryl; > > > Sibthorp, Christopher; Paterson, Steve > > > Subject: RE: Bioinformatics seminar > > > > > > Dear Colleagues, > > > > > > I want to remind you that our First Bioinformatics seminar will take place at: > > > Room SR6, 2nd Floor, Life Science Building at 11.00 a.m., Tomorrow > (Tuesday) > > > Ian Goodhead decided to get an advantage of Neil's and Harry's absence and > to > > > give a short talk entitled:"Genomic Approaches to Parasite Virulence and Host > > > Adaptation" (about 20 min). > > > > > > After that we'll have a discussion regarding a future format of our seminar. > > > > > > See you tomorrow, All the best, > > > > > > Olga > > > > > > > > > Dr Olga Vasieva > > > School of Biological Sciences > > > Biosciences Building > > > Crown Street > > > University of Liverpool > > > Liverpool L69 7ZB > > > Tel: +44-151-7954551 > > > > > > > > > > > > > > > -----Original Message----- > > > From: Vasieva, Olga > > > Sent: Tue 1/13/2009 2:57 PM > > > To: Vasieva, Olga; Cossins, Andrew; Hall, Neil; Stevenp11 at liverpool.ac.uk; > > > Spencer, Matthew; Caddick, Mark; Ebrahimi, Bahram; Edwards, Steven > [biolhos]; > > > Noyes, Harry; Gregory, Richard; Ashelford, Kevin; Sangaralingam, Ajanthah; > > > Darby, Alistair; Weedall, Gareth; Vieira de Mello, Luciane; Rigden, Dan; > Beynon, > > > Rob; Jones, Andy; Lane, Brian; Wong, Prudence; Daniel Naguib, Gianluca; > > Lowe, > > > Christopher; Van 'T Hof, Arjen; Goodhead, Ian; drderekdaly at yahoo.co.uk; > Kay, > > > Suzanne; Williams, Daryl; Sibthorp, Christopher > > > > > > Subject: RE: Bioinformatics seminar > > > > > > Dear Colleagues, > > > > > > After an emotional discussion we would like to suggest to devote the first > > seminar > > > to > > > defining a structure and a goal of our Bioinformatics seminars. > > > > > > You are very welcome to express your vision of how we should proceed. What > > > would you like to hear and what would you like to discuss at 11-12am on > > > Tuesdays? > > > > > > All the best, > > > > > > Olga > > > > > > > > > > > > > > > > > > > > > Dr Olga Vasieva > > > School of Biological Sciences > > > Biosciences Building > > > Crown Street > > > University of Liverpool > > > Liverpool L69 7ZB > > > Tel: +44-151-7954551 > > > > > > > > > > > > > > > -----Original Message----- > > > From: Vasieva, Olga > > > Sent: Thu 1/8/2009 2:23 PM > > > To: Vasieva, Olga; Cossins, Andrew; Hall, Neil; Stevenp11 at liverpool.ac.uk; > > > Spencer, Matthew; Caddick, Mark; Ebrahimi, Bahram; Edwards, Steven > [biolhos]; > > > Noyes, Harry; Gregory, Richard; Ashelford, Kevin; Sangaralingam, Ajanthah; > > > Darby, Alistair; Weedall, Gareth; Vieira de Mello, Luciane; Rigden, Dan; > Beynon, > > > Rob; Jones, Andy; Lane, Brian; Wong, Prudence; Daniel Naguib, Gianluca; > > Lowe, > > > Christopher; Van 'T Hof, Arjen; Goodhead, Ian; drderekdaly at yahoo.co.uk; > Kay, > > > Suzanne; Williams, Daryl; Sibthorp, Christopher > > > > > > Subject: RE: Bioinformatics seminar > > > > > > Dear colleagues, > > > > > > We are finally starting our Bioinformatics seminar! > > > > > > The room: SR6, 2nd Floor, Life Science Building at 11.00 a.m. > > > for one hour for every other Tuesday starting with Tuesday, 20th January. > > > > > > We need to decide what the 1st seminar should be about..I would suggest Neil > > > Hall (or Alastair (?)) to tell us about new capabilities of sequencing and > > > sequencing-related bioinformatics analysis, availability of those for who is > > > interested in collaboration, interesting aspects of ongoing sequencing projects. > > > Any other suggestions? > > > > > > If you aware of any one who may be interested in this seminar, please, let me > > > know. > > > > > > All the best, > > > > > > Olga > > > > > > > > > > > > Dr Olga Vasieva > > > School of Biological Sciences > > > Biosciences Building > > > Crown Street > > > University of Liverpool > > > Liverpool L69 7ZB > > > Tel: +44-151-7954551 > > > > > > > > > > > > > > > -----Original Message----- > > > From: Vasieva, Olga > > > Sent: Wed 1/7/2009 10:56 AM > > > To: Vasieva, Olga; Cossins, Andrew; Hall, Neil; Stevenp11 at liverpool.ac.uk; > > > Spencer, Matthew; Caddick, Mark; Ebrahimi, Bahram; Edwards, Steven > [biolhos]; > > > Noyes, Harry; Gregory, Richard; Ashelford, Kevin; Sangaralingam, Ajanthah; > > > Darby, Alistair; Weedall, Gareth; Vieira de Mello, Luciane; Rigden, Dan; > Beynon, > > > Rob; Jones, Andy > > > Subject: RE: Bioinformatics seminar > > > > > > > > > Wednesday should be also excluded. > > > So, we have Tuesday 11.00 and Monday 14.00.. > > > > > > Dr Olga Vasieva > > > School of Biological Sciences > > > Biosciences Building > > > Crown Street > > > University of Liverpool > > > Liverpool L69 7ZB > > > Tel: +44-151-7954551 > > > > > > > > > > > > > > > -----Original Message----- > > > From: Vasieva, Olga > > > Sent: Wed 1/7/2009 10:46 AM > > > To: Cossins, Andrew; Hall, Neil; Stevenp11 at liverpool.ac.uk; Spencer, > Matthew; > > > Caddick, Mark; Ebrahimi, Bahram; Edwards, Steven [biolhos]; Noyes, Harry; > > > Gregory, Richard; Ashelford, Kevin; Sangaralingam, Ajanthah; Darby, Alistair; > > > Weedall, Gareth; Vieira de Mello, Luciane; Rigden, Dan; Beynon, Rob; Jones, > > > Andy > > > Subject: Bioinformatics seminar > > > > > > Dear Colleagues. > > > > > > We are starting a regular weekly (or once in two-weeks) Bioinformatics > seminar. > > > We will discuss new projects, interesting papers and approaches and will > > welcome > > > anybody who is interested in bioinformatics assistance/collaboration to make a > > > presentation. Right now we are trying to find the optimal time/day for > > everybody's > > > convenience. > > > After preliminary questioning Thursday,Friday and Wednesday seem to be off > > the > > > consideration. The Best option seems to be: Tuesday at 11am. Does it sound > > > good? > > > (Monday or Wednesday after 14pm would be also not bad (Lu would you be > able > > > to attend (??))) > > > > > > All the best, > > > > > > Olga > > > > > > > > > Dr Olga Vasieva > > > School of Biological Sciences > > > Biosciences Building > > > Crown Street > > > University of Liverpool > > > Liverpool L69 7ZB > > > Tel: +44-151-7954551 > > > > > > > > > > > > > > > > > > > > > > > > > > > From C.Collins at MARLAB.AC.UK Sat May 23 19:45:13 2009 From: C.Collins at MARLAB.AC.UK (Catherine Collins) Date: Sat, 23 May 2009 18:45:13 -0000 Subject: [Sbforum-general] bootstrapping ML trees Message-ID: Hello. I would like to ask a question regarding bootstrapping maximum likelihood trees. Currently we are generating trees with neighbour joining and maximum likelihood. I would like to know if we can use bootstrap values generated by neighbour joining, using maximum likelihood settings, for the ML trees. If not, is there an alternative way of bootstrapping the ML trees which does not require a large computing resource? Thanks. Catherine Collins. -------------- next part -------------- An HTML attachment was scrubbed... URL: