From sandra.borthwick at sbforum.org Fri May 7 16:46:27 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Fri, 7 May 2010 16:46:27 +0100 Subject: [Sbforum-general] BioInformatics - Student Placement Message-ID: Project spec: This placement is part of the Environmental Placement Programme ? further details can be found online at www.thebep.org.uk/epp The project is to be funded by the Genecom Orphans project and is a collaboration between the Bioinformaticians at Moredun Research Institute and FIOS Genomics, a spin out company from Edinburgh University The idea of the project is to use the genomic sequences of bacterial DNA and to use the SNP and other bioinformatics techniques to analyse the difference between individual genomes thus building a phylogenetic ?tree? of the bacterium species. This will enable ready diagnosis of the different strains of the bacteria which is of commercial use to FIOS. The student will be jointly based at MRI and FIOS. The company are ideally looking for a Bioinformatics MSc student (possibly as part of a project dissertation. They would also consider a particularly strong undergraduate. Candidates will have experience of Bioinformatics techniques and programming experience in PERL is essential and experience of JACA desirable. If anyone wants to apply, they can do so by sending their CV and a cover letter to Louise Evison at louise.evison at met.org.uk -- 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 sandra.borthwick at sbforum.org Tue May 11 10:28:21 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Tue, 11 May 2010 10:28:21 +0100 Subject: [Sbforum-general] Fwd: BioInformatics - Student Placement In-Reply-To: References: Message-ID: ** This information was emailed on 7th May: Please note that this is an 8 week STUDENT placement and all applicants have to be current students. Either in Undergraduate or MSc study at a UK based University. ** Project spec: This placement is part of the Environmental Placement Programme ? further details can be found online at www.thebep.org.uk/epp The project is to be funded by the Genecom Orphans project and is a collaboration between the Bioinformaticians at Moredun Research Institute and FIOS Genomics, a spin out company from Edinburgh University The idea of the project is to use the genomic sequences of bacterial DNA and to use the SNP and other bioinformatics techniques to analyse the difference between individual genomes thus building a phylogenetic ?tree? of the bacterium species. This will enable ready diagnosis of the different strains of the bacteria which is of commercial use to FIOS. The student will be jointly based at MRI and FIOS. The company are ideally looking for a Bioinformatics MSc student (possibly as part of a project dissertation. They would also consider a particularly strong undergraduate. Candidates will have experience of Bioinformatics techniques and programming experience in PERL is essential and experience of JACA desirable. If anyone wants to apply, they can do so by sending their CV and a cover letter to Louise Evison at louise.evison at met.org.uk -- 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 -- 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 sandra.borthwick at sbforum.org Tue May 11 11:55:29 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Tue, 11 May 2010 11:55:29 +0100 Subject: [Sbforum-general] SICSA workshop - Biomedical and E-Health Abstractions and Modelling Message-ID: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SICSA workshop - Biomedical and E-Health Abstractions and Modelling Date: 18th June 2010 Location: Royal Society of Edinburgh ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The Scottish Informatics and Computing Science Alliance (SICSA) is sponsoring a workshop on data abstraction and modelling in biomedical and e-health applications. The workshop will cover: ? Exploration of issues arising from different levels of abstraction in the collection of raw biomedical data and the analysis of, and reasoning over, these data sets. ? Fostering collaborations between the research groups involved in the collection, processing and storage of raw biomedical data and groups focusing on the representation and reasoning of knowledge that can be derived from this data. ? Encouragement of interaction between life science and computational research groups. For more information and registration details please see: http://www.sbforum.org/events.php?e_id=93 *** Programme to follow shortly *** Thank you for your time, we look forward to seeing you on 18th June. -- 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 jeedward at yahoo.com Fri May 14 21:12:07 2010 From: jeedward at yahoo.com (John Edward) Date: Fri, 14 May 2010 13:12:07 -0700 (PDT) Subject: [Sbforum-general] Call for papers: BCBGC-10, USA, July 2010 Message-ID: <133062.81188.qm@web45906.mail.sp1.yahoo.com> It would be highly appreciated if you could share this announcement with your colleagues, students and individuals whose research is in bioinformatics, computational biology, genomics, data-mining, and related areas. Call for papers: BCBGC-10, USA, July 2010 The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org ) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) ? International Conference on Automation, Robotics and Control Systems (ARCS-10) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) ? International Conference on Computer Communications and Networks (CCN-10) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) ? International Conference on High Performance Computing Systems (HPCS-10) ? International Conference on Information Security and Privacy (ISP-10) ? International Conference on Image and Video Processing and Computer Vision (IVPCV-10) ? International Conference on Software Engineering Theory and Practice (SETP-10) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) MULTICONF-10 will be held at Imperial Swan Hotel and Suites. It is a full-service resort that puts you in the middle of the fun! Located 1/2 block south of the famed International Drive, the hotel is just minutes from great entertainment like Walt Disney World? Resort, Universal Studios and Sea World Orlando. Guests can enjoy free scheduled transportation to these theme parks, as well as spacious accommodations, outdoor pools and on-site dining ? all situated on 10 tropically landscaped acres. Here, guests can experience a full-service resort with discount hotel pricing in Orlando. We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward -------------- next part -------------- An HTML attachment was scrubbed... URL: From dan.bolser at gmail.com Thu May 20 03:04:07 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 20 May 2010 03:04:07 +0100 Subject: [Sbforum-general] SOL2010 meeting in Dundee! Message-ID: Dear Colleague We are writing to invite you to register, submit abstracts and book accommodation for SOL2010, to be held in Dundee, Scotland, and jointly hosted and organised by SCRI and UK-SOL. http://www.sol2010.org/ Online registration for the conference is available now?? please register soon as the ?early bird? rate is available only until May 31st. https://reg.istrations.com/delegate/events/DNDSOL2010 Abstract submission can be found on this link: http://www.sol2010.org/Abstracts Accommodation Special rates have been arranged for conference guests at the conference hotel, the Apex City Quay and Spa, Dundee. Online Accommodation booking is available via this link: https://www.conferencebookings.co.uk/delegate/DNDSOL2010 We look forward to welcoming you to Dundee in September. Glenn Bryan Gerard Bishop Graham Seymour ?and the rest of the SOL2010 team Please contact Anne Rendall if you have any enquiries email: SOL2010 at scri.ac.uk Tel: +44 1382562317 Mob: 07745178132 From sandra.borthwick at sbforum.org Thu May 20 16:42:23 2010 From: sandra.borthwick at sbforum.org (Sandra Borthwick) Date: Thu, 20 May 2010 16:42:23 +0100 Subject: [Sbforum-general] Invitation to participate workshop on data abstraction Message-ID: <4bf5583a.22a0100a.39fc.018c@mx.google.com> Dear All We are organising a joint workshop with SICSA on data abstraction, under the title of "Biomedical and E-Health Abstractions and Modelling: Engineering and Research," to be held in the RSE on 18th June. What we mean by abstraction is data representation and processing for down-stream analysis. We are trying bring together those who generate biological data with those who are interested in abstraction from the computing science aspect. Details are available here: http://www.sbforum.org/events.php?e_id=93 The keynote from the life science side will be given by Rainer Breitling, SULSA professor for systems biology. We are still looking for a few short presentations (15min) from biologists, covering the types of data that they generate/ need to analyse. If you think that you would like to contribute, or can suggest someone who you think would be good, we would like to hear from you. All expenses will be covered. I look forward to your replies. 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 ces at cs.stir.ac.uk Wed May 26 21:51:52 2010 From: ces at cs.stir.ac.uk (Carron Shankland) Date: Wed, 26 May 2010 21:51:52 +0100 Subject: [Sbforum-general] Second call for participation: Multi-scale modelling of Biological Systems Message-ID: <4BFD89E8.6090600@cs.stir.ac.uk> Second Call for Participation (note extended deadline for abstracts below) MULTI_SCALE MODELLING OF BIOLOGICAL SYSTEMS 5-6th July 2010 University of Stirling Sponsored by EPSRC IMPORTANT DATES Abstract submission deadline: 5 June, 2010 Notification of programme: 7 June, 2010 Registration deadline 5 June, 2010 Computational and mathematical modelling of biological systems is now commonplace and indeed essential to many projects. A particular problem faced by modellers is that of choosing the most appropriate scale, or level of abstraction, for their model, especially given that there may be different important features at each scale. For example, in an epidemiological model, we might wish to describe the way in which individuals interact. Alternatively, we might be more interested in the analysis of population level features, making ordinary differential equations more appropriate. The aim of the workshop is to bring together researchers working on techniques which allow exploration of models spanning a range of scales, especially those in which the different scales are rigorously related. At Stirling, we are interested in modelling techniques such as Process Algebra that allow large scale properties to emerge from small scale behaviour. We would welcome contributions using other techniques. We also particularly welcome biologists interested in how this sort of modelling across scales can help them understand their system. CONFIRMED INVITED SPEAKERS Modelling and analysis of biological systems using process calculi Federica Ciochetta (The Microsoft Research - University of Trento Center for Computational and Systems Biology) Data Driven Network Modelling for Epidemiology Eiko Yoneki (Computer Laboratory, University of Cambridge) LOCATION The workshop will be held at the Stirling Management Centre, in central Scotland. The Centre is part of the University of Stirling campus, and is easy to reach from most places in the UK. International connections are available via nearby Glasgow and Edinburgh airports. http://www.smc.stir.ac.uk/ REGISTRATION Registration is now open via Eventbrite: http://mmbs2010.eventbrite.com The password for the event is "models". Workshop Fees (including lunch both days, and dinner on the 5th) Early Bird: (first 40) free! Standard (non-student): ?100 Standard (student): ?80 Research students: There are 10 bursaries to support attendance, covering conference fee, travel and accommodation costs. These will be allocated on a first come, first served basis. ACCOMMODATION We have reserved accommodation at the Stirling Management Centre. Please contact them directly, quoting ref: 48122, after you have registered to book. SMC rooms: Bed and Breakfast at ?35 per person per night. Double en-suite bedroom (no single supplement). Visit their web site: http://www.smc.stir.ac.uk/content/default.asp?page=s7, or call the sales office (Mon-Fri 0900-1700) 01786 451712 Alternatively there are some slightly cheaper rooms in other campus accommodation: Bed and Breakfast at ?26.35 per person per night. Single standard bedroom, with access to shared toilet and shower facilities. A short walk from the conference venue. Please mail the organisers (mmbs2010 at cs.stir.ac.uk) to book these rooms stating your arrival date, and departure date. CONTRIBUTED TALKS Participants are encouraged to present a contributed talk (30 minute slots). Please submit an abstract when you register. Please forward this message on to anyone who you think may be interested. Many thanks and looking forward to seeing you there Organisers: Carron Shankland and Rachel Norman. -- The Sunday Times Scottish University of the Year 2009/2010 The University of Stirling is a charity registered in Scotland, number SC 011159. -------------- next part -------------- An HTML attachment was scrubbed... URL: From john.davey at ed.ac.uk Thu May 27 10:35:02 2010 From: john.davey at ed.ac.uk (John Davey) Date: Thu, 27 May 2010 10:35:02 +0100 Subject: [Sbforum-general] 2nd UK RAD Sequencing Meeting, Edinburgh, 31st August Message-ID: * * * * * * * * * * * * * * * * * * * 2nd UK RAD Sequencing Meeting 31st August 2010, 9:00 am - 5:00 pm Edinburgh University http://www.nesc.ac.uk/esi/events/1090/ * * * * * * * * * * * * * * * * * * * Dear all, The 2nd UK meeting on RAD (Restriction-site Associated DNA) Sequencing, a new method for SNP discovery and genetic mapping by sequencing thousands of markers in multiple individuals using next generation DNA sequencing, will be held in Edinburgh on August 31st. The meeting is intended to bring together UK and European researchers who are implementing or are interested in RAD sequencing. There is no charge for attendance. Dr Paul Hohenlohe from the University of Oregon, co-author on a recent major paper on RAD Sequencing (http://dx.doi.org/10.1371/journal.pgen.1000862), will be attending the meeting to talk about his work, using RAD Sequencing to study population genomics of threespine stickleback. The meeting will cover the use of RAD Sequencing for genotyping, linkage mapping, genome scaffolding and population genomics. A range of ongoing projects will be presented and there will be opportunity to discuss the wet lab and bioinformatics aspects of the method. If you would like to attend, please register online at http://www.nesc.ac.uk/esi/events/1090/. If you have any queries, please contact me at john.davey at ed.ac.uk. Please feel free to forward this message on to anyone you think may be interested. Best wishes, John Davey Background to RAD Sequencing method: By cutting genomic DNA with a restriction enzyme, it is possible to sequence thousands of markers with high coverage in a single individual using next generation sequencing. By adding a short DNA identifying sequence to the fragments for one individual, it is possible to pool multiple individuals together, sequence them all on one lane of an Illumina Genome Analyzer run, and separate out the sequences for each individual bioinformatically by examining the identifiers. Because each fragment can be sequenced with high coverage, and the fragments from a particular restriction enzyme site can be easily aligned, it is easy to call SNPs in these sequences. If a reference genome is present, it is also easy to identify recombination regions and so produce genetic maps for the sequenced individuals. -- Dr. John Davey Bioinformatics Researcher and Support Provider Institute of Evolutionary Biology University of Edinburgh Post : Room 354 Ashworth Laboratories King's Buildings West Mains Road Edinburgh EH9 3JT UK Email : john.davey at ed.ac.uk Phone : +44 (0) 131 650 7403 Web : genepool.bio.ed.ac.uk www.nematodes.org -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From kemp at chalmers.se Thu May 27 15:08:48 2010 From: kemp at chalmers.se (Graham Kemp) Date: Thu, 27 May 2010 16:08:48 +0200 (CEST) Subject: [Sbforum-general] DILS, Call for Posters and Demos Message-ID: ----------------------------------- CALL FOR POSTERS AND DEMONSTRATIONS ----------------------------------- Seventh International Conference on Data Integration in the Life Sciences (DILS 2010) 25-27 August, 2010 Gothenburg, Sweden http://www.chalmers.se/cse/dils2010/ The development and increasingly widespread deployment of high throughput experimental methods in the life sciences is giving rise to numerous large, complex and valuable data resources. This foundation of experimental data underpins the systematic study of organisms and diseases, which increasingly depend on the development of models of biological systems. The development of these models often requires integration of diverse experimental data resources; once constructed, the models themselves become data and present new integration challenges for tasks such as interpretation, validation and comparison. Topics of Interest ------------------ The DILS conference provides a forum for the discussion of emerging challenges for data integration in the life sciences, and the techniques that seek to address them. Topics of interest include, but are not limited to: - Architectures and data management techniques for the life sciences - Query processing and optimization for biological data - Biological Data sharing and update propagation - Query formulation assistance for scientists - Modeling of life sciences data - Biological Metadata management - Annotation in scientific data integration - Provenance modeling and management for the life sciences - Scientific Workflows and analysis pipelines - Laboratory information management systems in biology - Biological data quality and data cleaning - Life sciences ontologies - Semantic web for the life sciences - Mining integrated life sciences data - Text mining in the life science literature - Machine learning in data integration in the life sciences - Grid Computing and Grid technologies for the life sciences - System prototypes for biology - Commercial solutions in the life sciences - Integration challenges presented by new kinds of biological data - Scientific results arising from innovative data integration solutions Submission Guidelines --------------------- Authors are invited to submit poster and system demonstration papers (2-4 pages in the LNCS format) by 1 July 2010. Selected poster and system demonstration papers papers will be included in CEUR Workshop Proceedings, pending approval. Please submit your paper using the DILS 2010 EasyChair site: http://www.easychair.org/conferences/?conf=dils2010