- BBClist - maillist.psb.ugent.be

[Gtpb] GTPB Course announcement - IB12A Introductory Bioinformatics (2nd course 2012)
by Pedro Fernandes 05 Nov '12

05 Nov '12

Course Announcement IB12A Introductory Bioinformatics http://gtpb.igc.gulbenkian.pt/bicourses/IB12A with David P. Judge, Phil Cunningham and Pedro Fernandes IMPORTANT DATES for this Course Deadline for applications: November 30th 2012 Latest notification of acceptance: December 3rd 2012 Course date: December 10th - 14th 2012 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Overview The course sets out to introduce an extensive range of computing facilities vital for molecular biological research. This will be achieved primarily through "hands on" exercises based around an investigation of a well documented human disease. How information can be obtained both by analysis of raw sequence data and by interrogation of information resources will be demonstrated. In order to enable the participants to perform sequence analysis on short read sequences, we will provide a short tutorial on NGS data analysis for beginners. Objectives The course is a user course. How to use the various tools is thus the prime objective. However, where it is useful, the operation of the programs will be discussed as far as is required. Participants will know how to set up the programs in an informed fashion, and to fully understand the output generated. On completion of this 5 day long training, they will also know how to implement this methodology elsehwere, using public domain software and data resources. The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations. Target Audience This course is intended for those wishing to investigate how they might begin to exploit the ever expanding abundance of computing resources for molecular biologists. Course Pre-requisites Basic understanding of molecular biology and no particular computing expertise will be assumed. Thank you for your interest! (deadline for applications Nov 30th) Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt ----- End forwarded message ----- _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

1 0

[Gtpb] GTPB Course announcement - BFB12 Biostatistical Foundations in Bioinformatics
by Pedro Fernandes 02 Nov '12

02 Nov '12

BFB12 Biostatistical Foundations in Bioinformatics IMPORTANT DATES for BFB12 Deadline for applications: November 17th 2012 <------------- Latest Notification of Acceptance: November 18th 2012 Course date: December 3rd - December 7th 2012 With Lisete Sousa and Carina Silva-Fortes We are proud to annouce the third edition of our Foundations course in BioStatistics. Led by the firm hand of two Statisticians that have their research work centered in the Life Sciences, participants go through a comprehensive set of short lectures and guided hands-on exercises. The course revisits concepts bottom-up from probability to classification, using an exclusive set of bioinformatics examples. It is a five day opportunity to put statistics back in shape, to acquire confidence in methods and to learn how to write small scripts using open source software (R). *Course description:* This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques used in Bioinformatics. Many analytical and inferential methods, regardless of their novelty, have their niches of application all over the place in Bioinformatics. Newer techniques such as the ones employed in high throughput data analysis are not different in this respect. We will be looking at statistical methods, digging into their inner workings, wearing the skins of professional statisticians. Attendees can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods, and extensive hands-on practice, exclusively based on biological examples. *Target Audience* Everybody using Bioinformatics methods is implicitly using statistical methods. Most people have had one or more semester courses in Statistics in their graduate education. For many, Statistics happened in their lives a long a time ago, and that makes it difficult to go back and manipulate the concepts with full confidence. Moreover, proper judgement of the results often calls for a deeper level of understanding than what is required to solve scholarly exercises. Attending this course is a chance of revisiting subjects like experimental design, hypothesis testing, inference and prediction in an intensive and systematic way. We will look into particular areas such as Bayesian Inference, Hidden Markov Chains and Multivariate methods with the attitude, eyes and brains of a statistician that wants to understand how the methods work. Methodology The course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from real world Bioinformatics practice. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. For more information, application procedures, etc. please visit http://gtpb.igc.gulbenkian.pt/bicourses/BFB12 Thank you for your interest! (deadlinefor applications Nov 17th) Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

1 0

Fwd: Bioinformatics position at ITB Milan
by Guy Bottu 25 Oct '12

25 Oct '12

-------- Original Message -------- Subject: Bioinformatics position at ITB Milan Date: Thu, 25 Oct 2012 10:20:12 +0200 From: Andreas Gisel <andreas.gisel(a)ba.itb.cnr.it> Reply-To: andreas.gisel(a)ba.itb.cnr.it To: emb-adm(a)embnet.org, Gianluca De Bellis <gianluca.debellis(a)itb.cnr.it> Dear EMBnetter Please, find attached the announcement for a bioinformatician position in ITB Milan. I would appreaciate if you could distribute this among your contacts. Best regards Andreas -- Italian EMBnet Node Institute for Biomedical Technologies - CNR Bioinformatics and Genomics Research Group Via Amendola 122/D 70126 Bari (Italy) Tel: +39 (0)80 5929662 Fax: +39 (0)80 5929690 e_mail:andreas.gisel@ba.itb.cnr.it http://www.ba.itb.cnr.it/ http://www.ba.itb.cnr.it/gisel/

1 0

NBIC PhD Course Pattern Recognition 21-25 January 2013, Amsterdam
by Celia van Gelder 19 Oct '12

19 Oct '12

*NBIC PhD Course Pattern Recognition (3rd edition)* Date: 21-25 January 2013 Location: Amsterdam Course Coordinator: Perry Moerland (AMC) Website: http://www.nbic.nl/education/nbic-phd-school/course-schedule/pattern-recogn…. <http://www.nbic.nl/education/nbic-phd-school/course-schedule/optimisation-t…> Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/ On Jan 21-25, 2013 the NBIC PhD School organises the third edition of the PhD Course 'Pattern Recognition' in Amsterdam. The course aims at PhD students with a background in bioinformatics, computer science or a related field. The course introduces basic techniques from the fields of pattern recognition and machine learning to solve bioinformatics problems. After having followed this course, a student should have an overview of basic pattern recognition techniques and be able to recognize what method is most applicable to classification problems (s)he encounters in bioinformatics applications. This course is part of the Education Programme of the NBIC PhD School. The PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on the NBIC website (www.nbic.nl <http://www.nbic.nl>-> Education -> NBIC PhD School). For more information about the course you can contact Celia van Gelder (NBIC Education) at education(a)nbic.nl -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

1 0

Last call for abstracts for BeNeLux Bioinformatics Conference (BBC12)
by Femke Francissen 17 Oct '12

17 Oct '12

*Last call for abstracts for BeNeLux Bioinformatics Conference (BBC12)* The 7th edition of the BBC12 will be organized in Nijmegen, the Netherlands on 10-11 December 2012. Key theme: "Bioinformatics at the interface". Abstracts can report research results in any area of bioinformatics, computational biology or related disciplines. Abstracts submission via: http://www.nbic.nl/about-nbic/events/bbc2012/abstract-submission/ *Submission deadline: Monday 22 October 2012* Conference website: http://www.nbic.nl/bbc2012 Registration via: http://www.nbic.nl/about-nbic/events/bbc2012/registration/ Contact: Barbara van Kampen (b.vankampen(a)cmbi.ru.nl<mailto:b.vankampen@cmbi.ru.nl>), Centre for Molecular and Biomolecular Informatics, UMC St Radboud Nijmegen Femke Francissen (femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>), Netherlands Bioinformatics Centre

1 0

status maillist
by Luc Van Wiemeersch 17 Oct '12

17 Oct '12

This maillist was unavailable due to maintenance, from 16 October till 17 October , 12h. Sorry for any incovenience --

1 0

Job Announcement: bioinformatician/developer
by Lieven Sterck 17 Oct '12

17 Oct '12

Dear Colleagues, I also apologize for some of you who are in several mailing lists and may receive this message several time. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Open position in Informatics/Bioinformatics Crop Development Centre University of Saskatchewan College of Agriculture and Bioresources September 7, 2012 A 2-years Engineer position in Informatics/Bioinformatics: This position is funded by a research grant administered by the University of Saskatchewan under the direction of Dr. C Pozniak, Crop Development Centre, College of Agriculture and Bioresources. Background In support of the international effort (IWGSC - http://www.wheatgenome.org/) to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline (http://www.clermont.inra.fr/triannot) Its modular architecture allows for the annotation and masking of transposable elements, the structural and functional annotation of protein-coding genes with an evidence-based quality indexing, and for identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in 26 hours. It is accessible through a web interface for small scale analyses (< 100 sequences of 3Mb max) or through a server for large scale annotations (thousands of scaffolds). The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 additional genes based on new biological evidence, increasing the percentage of perfect gene prediction to 63%. TriAnnot was designed specifically for complex genomes like wheat, and systematically showed a higher fitness than other annotation pipelines. TriAnnot is easily adaptable to the annotation of other plant genomes, and should become a useful resource for the annotation of large and complex genomes in the future. However, there is a need for further improvements: - Build a virtual machine of the TriAnnot pipeline; - Improve the Gene modeling process - definitely make a choice between two combiners: Eugene and Augustus; - Incorporate new, well trained ab initio gene prediction programs; - Develop tools to display splicing variants; - Implement a module for the discovery of SNP markers; - Develop and incorporate three new panels: o mapping the gene models on selected genome models o mapping the gene models within a pre-calculated phylogeny tree o mapping the gene models within a known biological pathways; o evaluate the possibility to develop a "bogas-like" interface for wheat manual curation (see http://bioinformatics.psb.ugent.be/webtools/bogas/) Building a virtual machine is a high priority as the improved TriAnnot pipeline will be installed as a mirror site to improve the informatics infrastructure in Canada. In this respect, we would develop a collaboration with iPlant to install the TriAnnot virtual machine (TriAnnot-VM) within the iPlant cyber infrastructure located in the USA. Collaborations are already underway with the CNRS at Roscoff (C. Caron) and the IBCP at Lyon (C. Blanchet) to work on these aspects. The engineer hired for this position will be in contact with these different centers to build the virtual machine. The development of the "bogas-like" interface will be made in close collaboration with the VIB in Ghent, Belgium. Research Groups The candidate will work under the direction of Dr. C. Pozniak, University of Saskatchewan. The successful candidate will spend the first year as a Visiting Scientist in the group "Structure, Function and Evolution of the Wheat Genome" led by C. Feuillet and located at the UMR INRA-UBP GDEC in Clermont-Ferrand (France). She/he will improve further the TriAnnot pipeline (see above) and build the TriAnnot-VM in direct collaboration with P. Leroy, the research engineer in charge of the TriAnnot project in the group. She/he will interact with researchers and graduate students that are users of the pipeline. She/he will also interact with other groups involved in Genetics, Bioinformatics and with other international laboratories developing similar activities. In the second year of the project, the candidate will work at the Crop Development Centre, University of Saskatchewan, Canada in the research group led by Dr. Pozniak. She/he will install and test the TriAnnot-VM within the informatics infrastructure available at the University of Saskatchewan and use it to annotate the sequence of wheat chromosomes being sequenced by that group. The second year of the project will involve interaction with iPlant to install the TriAnnot-VM within the iPlant cyber infrastructure in US. The successful candidate will also assist with writing and preparation of manuscripts for publication. Qualifications Required The candidate must have a minimum of a Master's degree in computer science or a related field with at least three years of bioinformatics experience. The candidate should have a good knowledge in Perl, python and Object Programming. Previous experience of Perl Object Oriented Programming is recommended. Candidate has to be familiar with parallel programming (Cluster) and Cloud computing. Research experience in plant genomics is desirable. Applicant must have a clear evidence of productivity, creativity and independence; excellent communication skills, and must be proficient in both reading and writing in the English language and an ability to work both independently and within a team. Candidates must have demonstrated report writing and publication capabilities. Salary: A competitive salary is available with full benefits (pension, health & dental, life insurance). Salary will be commensurate with experience. The University of Saskatchewan is committed to employment equity and applications from women, aboriginal peoples, visible minorities and persons with disabilities are encouraged. All qualified individuals are invited to apply, but Canadian citizens and permanent residents will be given priority. Contacts Parties interested in the position should provide by email a letter of application, Curriculum Vitae with a publication list, a brief statement of research and interests, and the names and contact information for at least three references, to: Chris Barker Genome Prairie Senior Project Manager Room 2E80, Agriculture Building Department of Plant Sciences University of Saskatchewan Saskatoon, Saskatchewan S7N 5A8 cbarker(a)genomeprairie.ca Review of applications will begin September 15th, 2012 and continue until the position is filled. All applicants will be notified shortly thereafter. The preferred start date for the position is November 1st, 2012. -- UMR 1095 INRA/UBP - Génétique, Diversité et Ecophysiologie des Céréales Group "Structure, Fonction & Evolution des Génomes de Blé" Philippe LEROY 234 Avenue du Brèzet 63100 CLERMONT-FERRAND - FRANCE Tel: +33 (0)4.73.62.43.37 Fax: +33 (0)4.73.62.44.53 Cellular : +33 (0)6.72.62.76.06 UMR 1095 : http://www.clermont.inra.fr/umr1095/ TriAnnot : http://www.clermont.inra.fr/triannot/ DE^CODAGE : http://www.inra.fr/decodage Curriculum Vitae : http://www.phleroy.fr/CV_PL.html

1 0

maillist status
by Luc Van Wiemeersch 17 Oct '12

17 Oct '12

This maillist was unavailable due to maintenance, from 16 October till 17 October , 11h. Sorry for any inconvenience --

1 0

Bioinformatician Job advert East Malling Research (UK)
by stephane Rombauts 17 Oct '12

17 Oct '12

FYI -------- Original Message -------- Subject: Job advert Date: Tue, 16 Oct 2012 14:10:46 +0000 From: Gerard Bishop (EMR) <Gerard.Bishop(a)emr.ac.uk> Would you kindly advertise the following Bioinformatician position I have on offer. See URLs below. If you can kindly send it out on any of your e-mail lists (e.g. ITAG or SGN etc) or if indeed you know of anyone that may be interested,.. I will be very grateful. http://www.jobs.ac.uk/job/AFG601/bioinformatician/ and http://www.nature.com/naturejobs/science/jobs/285995-Bioinformatician Many thanks in advance for all your help. Gerard Gerard Bishop Principal Research Scientist East Malling Research New Road, East Malling, Kent, ME19 6BJ, UK. Tel. (+44) (0)1732 523728 --East Malling Research registered office: New Road, East Malling, Kent ME19 6BJ. Tel. 01732-843833. Registered in England No. 5019373. Charity registration No.1102243. The information in this E-Mail and any attachments is confidential, may be legally privileged and is intended to be for the use of the intended recipient/s. If you are not the recipient named above please be aware that any disclosure, copying, distribution or use of the contents of this information is prohibited and may not represent the views of EMR. Activity and use of the East Malling Research E-mail system and any communications using it are monitored to secure its effective operation and for other lawful business purposes. -- ================================================================== Stephane Rombauts Principal Scientific staff Bioinformatics & Systems Biology Division Tel:+32 (0)9 331 38 21 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM strom(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ ==================================================================

1 0

Guest speakers NSBM Fall Meeting November 26 2012
by Barbara van Kampen 12 Oct '12

12 Oct '12

NETHERLANDS SOCIETY ON BIOMOLECULAR MODELLING Fall Meeting November 26th 2012 Venue: Academiegebouw Universiteit Utrecht Domplein 29 Utrecht the Netherlands The NSBM cordially invites you to visit its fall meeting 2012. Call for Abstracts (see attachment) As guest speakers, *Dr. Carlos Camacho* of Pittsburgh University, USA, will give a lecture on an "Interactive and efficient discovery tool of small molecule protein-protein interaction antagonists", *Prof Siewert-Jan Marrink*, Rijksuniversiteit Groningen, will present his data titled: "Large scale modeling of membrane protein self-assembly" and *Dr. Olivier Sperandio*, Inserm UMR-S973/MTi. Université Paris Diderot, France, will have a presentation titled: “Toward the design of focused chemical libraries to modulate Protein-Protein Interactions: A Chemoinformatics approach" Conference Chairs: *Prof. Dr. Alexandre Bonvin*, professor of Computational Structural Biology and *Dr. Gerry Nicolaes*, Cardiovascular Research Institute Maastricht -- Barbara van Kampen CMBI 260 Radboud University Nijmegen-Medical Centre / NCMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl

1 0