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[Gtpb] BFG12-Bioinformatics and Functional Genomics using R and Bioconductor
by Pedro Fernandes 24 May '12

24 May '12

Please excuse us for cross or duplicated messages ANNOUNCEMENT / REMINDER BFG12 Bioinformatics and Functional Genomics using R and Bioconductor with Javier de las Rivas and Celia Fontanillo from Universidad de Salamanca (USAL), Salamanca, ES and Consejo Superior de Investigaciones Científicas (CSIC) IMPORTANT DATES for this Course Deadline for applications: June 11th 2012 Notification of acceptance dates: EARLY: June 8th 2012 (on special request, see Application) NORMAL: June 14th 2012 Course date: June 18th to June 20th 2012 Course description: This is a practical course on Bioinformatics applied to analysis of Gene expression and Genomic data using mainly R and Bioconductor tools and algorithms. The course will focus in the use of robust methods to analyse microarray datasets âmainly from Affymetrix platform and from clinical-biomedical studies, integrating several strategies to achieve an optimum construction and analyses of gene expression profiles. The Course will be mostly practical using computers and prepared protocols. It will be divided in three major sessions: 1. Gene Expression Profiling. Microarrays genome-wide expression data integration, normalization, gene-based signal calculation, differential expression (using different algorithms: SAM, Bayesian and Limma) and clustering. Databases that integrate gene signatures. 2. Classification and Prediction using genomic data. Application of machine learning techniques to the analysis of gene expression data to allow classification of different states or different diseases subtypes. Error calculations. Class-prediction using de novo samples. 3. Gene Functional Enrichment. Gene list functional annotation using tools for statistical enrichment based on multiple concurrent annotation. Application of algorithms that measure outcome and response to assign specific functions to gene expression datasets. Target Audience Researchers in Biology and Biomedical areas (PhD students, PostDocs or Senior) working with genomic and gene expression data or with gene lists in general, that what to learn useful and powerful tools and methods for bioinformatic analysis. Course Pre-requisites Basic familiarity with genomic data and bioinformatics data resources. Minimum familiarity with R (although most scripts and command lines will be provided with written tutorials). Futher details, including application instructions available at http://gtpb.igc.gulbenkian.pt/bicourses/BFG12/ thank you for your interest Pedro Fernandes GTPB Coordinator -- Upcoming GTPB Courses BIG12, RNA12, MPA12, ADNMO12, BFG12, BPB12 Pedro Fernandes GTPB Coordinator 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

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PhD POSITION on BIOINFORMATICS METHODS FOR EPIGENOMICS (ULB, Brussels)
by Matthieu Defrance 22 May '12

22 May '12

PhD POSITION on BIOINFORMATICS METHODS FOR EPIGENOMICS (ULB, Brussels) Job description: PhD position is available in a joint project of the Laboratory of Cancer Epigenetics and the Machine Learning Group (Université Libre de Bruxelles) on bioinformatics approaches to transcriptomics and epigenomics in health and diseases. Given the strong interdisciplinary nature of the project the candidate is expected to share his/her time between the medical lab and the computer science unit. The research goal is to understand, study and develop a bioinformatics methodology to perform integrative analysis of high-throughput transcriptomics and epigenomics data sets generated using cutting edge next-generation sequencing platforms (available in the medical lab). Both fundamental and clinical aspects of human diseases will be addressed. The position is funded for 2 years, with a 2 years renewal. Screening of applications begins immediately and continues until an outstanding candidate is selected. Profile: The candidate should have a master degree in Bioinformatics, Bio-engineering, Biomedical Sciences, Engineering or Computer Sciences and demonstrate proficiency in programming (e.g. perl, python), computational statistics (e.g. R) and/or machine learning. Experience with sequence data, genome-wide data sets (ChIP-Seq, RNA-Seq, ...) or massive datasets analysis will be assets. The applicant should have good organizational skills, a taste for interdisciplinary research, excellent scientific writing and presenting skills and be able to work independently. How to apply? Informal enquiries, CV (+ ranking and grades during studies) and names of two referees should be send to: Dr. Matthieu Defrance (defrance(a)bigre.ulb.ac.be) Dr. François Fuks (ffuks(a)ulb.ac.be) Pr. Gianluca Bontempi (gbonte(a)ulb.ac.be)

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Professor Jack Leunissen
by Nijveen, Harm 19 May '12

19 May '12

It is with deep sadness I inform you that Jack Leunissen, Professor of Bioinformatics at Wageningen University, passed away Monday May 14 after a long illness at the age of 57. As a pioneer in bioinformatics he has made a great contribution to the development of the bioinformatics discipline. His enthousiasm and views have inspired generations of young researchers and students in the world. He was involved with his staff and students until the very end. His passion and knowledge of bioinformatics will remain an inspiration to us all. We wish Jack's family strength to cope with this loss. Harm Nijveen Laboratory of Bioinformatics, Wageningen University, The Netherlands. Funeral announcement card, in Dutch: http://www.bioinformatics.nl/rouwkaart-jack.pdf Condolences: http://www.condoleance.nl/13691/

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FSFLA 2012: 1st announcement
by GRLMC 18 May '12

18 May '12

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject* ********************************************************************* 2012 INTERNATIONAL FALL SCHOOL IN FORMAL LANGUAGES AND APPLICATIONS FSFLA 2012 (formerly International PhD School in Formal Languages and Applications) Tarragona, Spain October 29 November 2, 2012 Organized by: Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/fsfla2012/ ********************************************************************* AIM: FSFLA 2012 offers a broad and intensive series of lectures at different levels on selected topics in language and automata theory and their applications. The students choose their preferred courses according to their interests and background. Instructors are top names in their respective fields. The School intends to help students initiate and foster their research career. The previous event in this series was FSFLA 2011 ( <http://grammars.grlmc.com/fsfla2011/> http://grammars.grlmc.com/fsfla2011/) ADDRESSED TO: Graduate (and advanced undergraduate) students from around the world. Most appropriate degrees include: Computer Science and Mathematics. Other students (for instance, from Linguistics, Electrical Engineering, Molecular Biology or Logic) are welcome too provided they have a good background in discrete mathematics. The School is appropriate also for people more advanced in their career who want to keep themselves updated on developments in the field. There is no overlap in the class schedule. COURSES AND PROFESSORS: - Eric Allender (Rutgers), Circuit Complexity: Recent Progress in Lower Bounds [introductory/advanced, 8 hours] - Amihood Amir (Bar-Ilan), Periodicity and Approximate Periodicity in Pattern Matching [introductory, 6 hours] - Ahmed Bouajjani (Paris 7), Automated Verification of Concurrent Boolean Programs [introductory/advanced, 8 hours] - Bruno Courcelle (Bordeaux), Automata for Monadic Second-order Model Checking [intermediate, 8 hours] - Jörg Flum (Freiburg), The Halting Problem for Turing Machines [introductory/advanced, 6 hours] - Aart Middeldorp (Innsbruck), Termination of Rewrite Systems [introductory/intermediate, 8 hours] REGISTRATION: It has to be done on line at http://grammars.grlmc.com/fsfla2012/Registration.php FEES: They are variable, depending on the number of courses each student takes. The rule is: 1 hour = - 10 euros (for payments until June 2, 2012), - 12.50 euros (for payments between June 3 and August 15, 2012), - 15 euros (for payments after August 15, 2012). PAYMENT PROCEDURE: The fees must be paid to the School's bank account: Uno-e Bank banks address: Julian Camarillo 4 C, 28037 Madrid, Spain IBAN: ES3902270001820201823142 SWIFT/BIC code: UNOEESM1 account holder: Carlos Martin-Vide GRLMC account holders address: Av. Catalunya 35, 43002 Tarragona, Spain Please mention FSFLA 2012 and your name in the subject. A receipt will be provided on site. Remarks: - Bank transfers should not involve any expense for the School. - People claiming early registration will be requested to prove that the bank transfer order was carried out by the deadline. - Students may be refunded only in the case when a course gets cancelled due to the unavailability of the instructor. People registering on site at the beginning of the School must pay in cash. For the sake of local organization, however, it is much recommended to do it earlier. ACCOMMODATION: Information about accommodation is available on the website of the School. CERTIFICATE: Students will be delivered a certificate stating the courses attended, their contents, and their duration. IMPORTANT DATES: Announcement of the programme: March 24, 2012 Starting of the registration: March 24, 2012 Very early registration deadline: June 2, 2012 Early registration deadline: August 15, 2012 Starting of the School: October 29, 2012 End of the School: November 2, 2012 QUESTIONS AND FURTHER INFORMATION: Lilica Voicu: florentinalilica.voicu(a)urv.cat WEBSITE: http://grammars.grlmc.com/fsfla2012/ POSTAL ADDRESS: FSFLA 2012 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34-977-559543 Fax: +34-977-558386 ACKNOWLEDGEMENTS: Diputació de Tarragona Universitat Rovira i Virgili

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Practical Bionformatics course for Bench Scientsts: Protein Function Prediction
by Aidan Budd 14 May '12

14 May '12

Dear BBC-listers Together with several others I'm running an EMBO Practical Course in Berlin in September this year, that focuses on helping bench biologists use computational tools to analyse and predict protein function, with an emphasis on protein-protein interactions. More information is given below. If you'd ike to attend, then please apply - and/or if you know other scientists for whom it might be interesting e.g. those working in your institute/department, would be great if you could forward this announcement on to them. >From this page there's a link to the poster that you might also like to print and display at your workspace. http://events.embo.org/12-comp-ppi/index.html Thanks and best wishes, Aidan RE: Course on Computational Analysis of Protein-Protein Interactions for Bench Scientists 2-8.9.2012 EMBO Practical Course: Computational analysis of protein-protein interactions for bench biologists 2nd - 8th September 2012, MDC Berlin, Germany - How can bioinformatics help me predict/analyse my protein's interactions? - Which databases give information on existing experimental data on my protein's interactions? Focusing on these, and other related questions, this course aims to help bench scientists become more effective at exploiting the wide range of commonly-used bioinformatics tools that can be used to identify, understand, and predict protein-protein interactions (PPIs) by analysing their structure, sequences, and other features. The target group for the course are experimental scientists needing to analyse PPI data in their work, and who have limited experience using bioinformatics tools and resources that can help enhance their understanding and analysis of this, and related, data. The course covers analyses and tools that are applied **after** potential PPIs have been identified i.e. it does not cover analysis of the raw data from e.g. mass spectrometry using tools such as Mascot, PEAKS, SPIDER etc. Course trainers include developers of many commonly-used tools including Cytoscape, CLUSTALX, Pfam, IUPRED, STRING, STITCH, REFLECT, ScanSite, ELM, and PhosphoELM. In addition, many other key resources will be covered, for example BLAST, JalView, SMART, PyMOL, PISA and UniProt. Most tools used during the course are web-based and can be used, free of charge, by academic scientists worldwide. To apply for the course, fill in the online application form linked to from this page: http://events.embo.org/12-comp-ppi/application.html The registration deadline is Friday June 15th 2012. There is a course fee of 200 euros for academics, 1000 euros for scientists from industry. Places on the course are limited; applicants will be selected on the basis of the extent to which we expect their own work would benefit from attending the course. Thus, applicants are advised to highlight in their application both (i) clear examples of where they need to apply these methods in their current work and (ii) the extent of their previous experience using such approaches. Please contact the organisers (Miguel Andrade miguel.andrade(a)mdc-berlin.de; Aidan Budd aidan.budd(a)embl.de; Toby Gibson gibson(a)embl.de; Denis Shields denis.shields(a)ucd.ie) if you have questions on scientific aspects of the course, or Michaela Herzig (michaela.herzig(a)mdc-berlin.de) if you have questions concerning logistics/administration.

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Postdoctoral bioinformatics position in Edinburgh
by Francescatto, M. 11 May '12

11 May '12

The MRC Human Genetics Unit (http://www.hgu.mrc.ac.uk/) has an exciting opportunity for a Bioinformatician. This is a permanent position in a well-resourced MRC unit, embedded within a new University of Edinburgh institute: the MRC Institute of Genetics and Molecular Medicine (IGMM; http://www.igmm.ac.uk/) This new multi-disciplinary institute unites (~500) scientists across diverse fields from chromosome structure to cell and developmental biology, from model organism studies to human population and clinical genetics. The post holder will be expected to interact with members of the Bioinformatics staff, the wider computational community and HGU scientific staff, initiating and working on diverse collaborative projects independently. The IGMM hosts a variety of internationally competitive groups working on major problems in human genetics and disease with many opportunities for high impact collaborations with leading researchers. At the same time we encourage our computational biologists to develop their own research interests along IGMM research themes. Applicants should be able to demonstrate programming skills and possess published experience in the analysis of genome scale biological datasets, particularly high throughput sequencing data. We also envisage duties in the installation/maintenance of bioinformatics applications and provision of advice/training to users. This post would suit a biologist with good programming skills or a computer scientist with strong interests in biology/bioinformatics. Informal enquiries are welcome (Colin.Semple(a)igmm.ed.ac.uk) More details from: http://www.jobs.ed.ac.uk/vacancies/index.cfm?fuseaction=vacancies.detail&va…

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Postdoc or PhD fellowship
by Tim De Meyer 10 May '12

10 May '12

The Laboratory of Environmental Toxicology and Aquatic Ecology (Ghent University, Belgium) is urgently looking for someone to conduct research in (Epi)genomics and Bioinformatics in Ecotoxicology and Stress Ecology You will collaborate with a team of experienced ecotoxicologists and ecologists on several projects (in collaboration with bioinformatics experts at our faculty) to develop and apply methodologies that enable the use of epi(genomics) tools and datasets (including next generation sequencing) in ecotoxicology and stress ecology, in order to understand mechanistically and to predict how chemicals and other stressors interfere with normal biological functioning of ecosystems. For more details: see attachment. Prof. Colin Janssen & Prof. Karel De Schamphelaere (Principle Investigators) Laboratory of Environmental Toxicology and Aquatic Ecology Jozef Plateaustraat 22, B9000 Gent, Belgium Tel.: +32 9 264 89 19 www.ecotox.ugent.be

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ECCB2012 Basel - Workshop Bioinformatics Training for Life Scientists - Call for contributions
by Celia van Gelder 09 May '12

09 May '12

*Workshop Bioinformatics Training for Life Scientists: Showcases and Challenges from tutors' perspectives ** * *Call for contributions* September 9, 2012, Basel, Switzerland (a Satellite event of the European Conference on Computational Biology ECCB'12) This workshop represents a platform where those involved in bioinformatics training to life scientists can meet, confront and share experiences, as well as discuss future directions and collaboration in joint efforts. Topics will include: - Current state of the art and challenges in bioinformatics training for life scientists in the world. - Specific challenges for those delivering bioinformatics training -- organizers and teachers - and how we can address these. - Successful showcases of teaching bioinformatics to life science researchers. - Exchange views on the future of Bioinformatics Training, going global: building and strengthening networks of trainers, possible collaborations, international developments, and getting recognition for training efforts. *Abstract Submission* Participants can submit their contributions on one of the following topics: 1. Successful showcases of face-to-face bioinformatics teaching to life science researchers 2. Successful showcases of e-learning solutions for teaching bioinformatics to life science researchers The abstracts will be reviewed by the organisers and they will be selected for oral presentation according to the relevance to the sessions, innovation and country balance. Instructions for the abstracts submission can be found in the workshop website: http://www.eccb12.org/WS4 *Important dates* Submission Deadline: June 8, 2012 Author Notification: June 29, 2012 *Organisers* Patricia Palagi (SIB Swiss Institute of Bioinformatics, Patricia.Palagi(a)isb-sib.ch) Vicky Schneider (European Bioinformatics Institute, EBI, vicky(a)ebi.ac.uk) Allegra Via (Dept of Physics, Sapienza University of Rome, allegra.via(a)uniroma1.it ) Celia van Gelder (Netherlands Bioinformatics Centre, NBIC, celia.van.gelder(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 ____________

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Fwd: SeqAhead training school "Next generation sequencing data analysis with Chipster" 13.-15.6.2012, Finland
by Jacques van Helden 09 May '12

09 May '12

Begin forwarded message: From: Eija Korpelainen <Eija.Korpelainen(a)csc.fi> Date: 9 May 2012 13:44:11 CEST Cc: "erikbong(a)mac.com" <erikbong(a)mac.com> Subject: SeqAhead training school "Next generation sequencing data analysis with Chipster" 13.-15.6.2012, Finland Dear SeqAhead WG3 members, Could you please forward the following information about this COST training school to your user communities. The course is primarily targeted for biologists, but we can also organize separate sessions for developers if there is interest for that. Best regards, Eija ---------------------------------------------------------------------------------------------------- Next generation sequencing data analysis with Chipster 13.-15.6.2012, Helsinki, Finland This course covers several aspects of NGS data analysis and visualization, ranging from quality control, filtering and alignment to more specific tasks such as finding differentially expressed genes and detecting copy number aberrations, variants, methylation and ChIP-seq peaks. The course consists of lectures and hands-on exercises using the graphical Chipster software, so no prior knowledge of NGS analysis or unix is required. For more information and registration, please see http://www.csc.fi/english/csc/courses/archive/seqahead. The deadline for registration is 20.5.2012. The course is kindly sponsored by the SeqAhead COST Action (http://www.seqahead.eu/) which provides travel bursaries of 650 euros for 15 participants. Everybody who comes from the European union area and has no more than 8 years of research experience after obtaining PhD (COST definition for early stage researchers) can apply for a travel bursary. The user-friendly Chipster software (http://chipster.csc.fi/) integrates a comprehensive collection of analysis tools for high-throughput data such as NGS, microarrays and proteomics. For more information about the NGS functionality, please seehttp://chipster.csc.fi/manual/tools-ngs.html. Chipster also contains a built-in genome browser, allowing users to view reads and results in their genomic context. Users can save their analysis pipelines as reusable automatic workflows, and both workflows and analysis sessions can be shared with colleagues.

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PRIB 2012
by Dick de Ridder - EWI 09 May '12

09 May '12

------------------------------------------------------------------------------ PRIB2012 The 7th IAPR International Conference on Pattern Recognition in Bioinformatics ------------------------------------------------------------------------------ November 8-10 2012 Tokyo, Japan http://prib2012.org/ ----------------------------------------------------------------------------- =============== Call For Papers =============== In modern biology, high-throughput measurement devices allow scientists to gather data at unprecedented rates. To make sense of this data, computational biologists and system biologists construct quantitative models, many of which depend on pattern recognition techniques. Their application is challenging due to the large volumes of data and background information, noisy measurements and target outputs, highly diverse data types etc. The Pattern Recognition in Bioinformatics conference series aims to bring together researchers, practitioners, and students from around the world to present and discuss recent developments and applications of pattern recognition methods in current bioinformatics, computational biology, and systems biology. Authors are invited to submit full papers in relevant research areas, which include but are not limited to: - Bio-sequence analysis - Gene and protein expression analysis - Biomarker discovery - Protein structure and interaction prediction - Motifs and signal detection - Metabolic modeling and analysis - Systems and synthetic biology - Pathway and network analysis - Immuno- and chemo-informatics - Evolution and phylogeny - Bio-imaging - Biological databases, integration, and visualization Pattern recognition techniques of interest include: - Statistical, syntactic, and structural pattern recognition - Data mining and machine learning - Evolutionary computation - Bayesian networks and graphical models - Neural networks and fuzzy systems =========== Publication =========== Papers should be submitted electronically through the conference website (http://prib2012.org/) Accepted papers will be published in Springer's Lecture Notes in Bioinformatics (LNBI). =============== Important dates =============== Full paper submission deadline: May 28, 2012 Author notification of acceptance: July 31, 2012 Camera-ready paper deadline: August 23, 2012 Poster abstract submission : October 2, 2012

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