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Registration now open! - NBIC/BioSB course Comparative Genomics, 2-6 June 2014
by Femke Francissen 08 May '14

08 May '14

NBIC/BioSB Course Comparative Genomics: from evolution to function (2nd edition) - Registration open! Date: June 2 - June 6, 2014 Location: VU University, Amsterdam, the Netherlands Course coordinators: Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap Heringa (VU), Celia van Gelder (NBIC/BioSB, education(a)biosb.nl<mailto:education@biosb.nl>) Course website: http://biosb.nl/comparative-genomics-2014/ Registration: http://biosb.nl/education/enrollment-comparative-genomics/ More information: education(a)biosb.nl<mailto:education@biosb.nl> Course description Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology and orthology. Moreover it is important to know the assumptions and heuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why they fail (or misdetect) as a consequence of a variety of biological /evolutionary causes. The first two days of the course provide a basis for the course with the aim to move "beyond blast" in terms of more sensitive homology searches, domain level analysis of protein evolution as well as more fine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology).This foundation is used to discuss in the three following days in more detail three topics: (1) the study of functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements. Target audience The course is intended for PhD students and master students in bioinformatics, especially those interested in evolution and/or those who want to compare various genomics data between species. Participants are expected to have some hands on experience with blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains. Programme Monday June 2: Distant homology and protein domains (lecturer Jaap Heringa) Topics & Tools: Divergent and convergent evolution, (multiple) sequence alignment, psiblast, hhsearch, pfam, homology and function, undetected orthology from failure to detect homology, paralogs and function specificity prediction Tuesday June 3: Comparative Interactomics (lecturers Jaap Heringa, Martijn Huynen/John van Dam) Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration, neofunctionalization vs subfunctionalization Wednesday June 4: Small scale orthology and large scale databases (lecturers Martijn Huynen, Berend Snel) Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission Thursday June 5: Genome duplications (lecturer Berend Snel) Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart Friday June 6: Finding functional elements in DNA and RNA sequences, Biased gene conversion (lecturer Martijn Huynen) Topics & Tools: phylogenetic footprinting, (phylogeny aware) gibbs sampling, RNA secondary structure prediction based on sequences and on experimental data, biased gene conversion & positive selection. BioSB Course Programme The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology Research School (BioSB). The Education Portfolio of BioSB can be found at http://biosb.nl/education/course-portfolio/. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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[Gtpb] REMINDER, new deadline. Structural Modeling for Large Macromolecular Complexes - SMLMC14 in Oeiras, Portugal
by Pedro Fernandes 07 May '14

07 May '14

GTPB Reminder Applications are open for another Bioinformatics Training course: SMLMC14 Structural Modeling for Large Macromolecular Complexes with Joanna Kasprzak and Grzegorz Chojnowski IMPORTANT DATES for this Course Deadline for applications: May 20th 2014 < New deadline Latest notification of acceptance: May 17th 2014 Course date: June 11th - June 13th 2014 For a reference about the use of the methodology: http://dx.doi.org/10.1016/j.ymeth.2013.09.014 *Computational modeling of proteinRNA complex structures* Irina Tuszynska, Dorota Matelska, Marcin Magnus, Grzegorz Chojnowski, Joanna M. Kasprzak, Lukasz P. Kozlowski, Stanislaw Dunin-Horkawicz, Janusz M. Bujnicki Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland *********************************************************************** Course description One of the major challenges in structural biology is to determine the structures of macromolecular complexes and to understand their function and mechanism of action. However, structural characterisation of macromolecular assemblies is very difficult. To begin addressing this problem, we have developed PyRy3D. In a nutshell, PyRy3D employs a hybrid computational approach that incorporates spatial information from a variety of experimental methods into the modelling procedure to build low-resolution models of large macromolecular complexes. The PyRy3D model building procedure uses a Monte Carlo approach to sample the solutions-space. It uses spatial restraints to define components interacting with each other, and a simple scoring function is applied to pack them tightly into contours of the entire complex (e.g. cryoEM density maps). More details at http://gtpb.igc.gulbenkian.pt/bicourses/SMLMC14/ Thank you for your interest! Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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3rd RSG Belgium seminar - reminder
by Jurgen CLAESEN 06 May '14

06 May '14

Dear all, We are very pleased to invite submissions for talks at the third RSG Belgium seminar. For more information about RSG Belgium, please have a look at the following link: http://www.iscbsc.org/rsg/rsg-belgium The goal of this seminar day is to allow PhD students from different research groups around Belgium to present their work and interact with each other. It will take place in *Antwerp* on Wednesday, the 28th of May 2014 from 14h to 17h. We will be accepting the first four submitted talks for this session. So don't wait too long to submit. The featured talks will have 20 minutes to present followed by about 10 minutes of questions. To submit a talk proposal, simply email rsg-belgium(a)iscbsc.org with the title of the talk and the name of the presenter. The submission deadline is Monday, the 19th of May. Please diffuse this call to anyone who might also be interested in joining. Hope to see you there! Best Regards, RSG Belgium committee

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REMINDER submit your abstract for ISCS2014!
by ISCBSC announcement 06 May '14

06 May '14

*ISCB Student Council Symposium 2014, Boston, USA.* Dear Colleagues, We are pleased to announce that the call is now open for the submission of abstracts to the 10th ISCB Student Council Symposium, to be held on the 11 of July 2014 in Boston, USA, as a satellite meeting of the International Conference on Intelligent Systems for Molecular Biology (ISMB). The Student Council Symposium is a forum for students, post docs, and young researchers in the fields of Computational Biology and Bioinformatics. Participants will have the opportunity to present their work to an international audience of young scientists, build a network within the computational biology community and develop important soft skills in an environment that fosters exchange of ideas and knowledge. We encourage you to submit an abstract to showcase your work at the Symposium’s poster session. As the central part of our symposium, 10 abstracts will be selected for an oral presentation. Awards will be given to outstanding posters and presentations. Travel fellowships will be available and candidates with accepted abstracts will be invited to apply. *Important Dates:* May 9, 2014: Abstract submission deadline May 16, 2014: Acceptance notifications May 23, 2014: Travel fellowship deadline June 4, 2014: Travel fellowship acceptance notification July 11, 2014: Student Council Symposium Submit your work at http://scs2014.iscbsc.org/scs14-call . For updates and news, keep an eye on symposium website http://scs2014.iscbsc.org/ . We look forward to receiving your abstract. On behalf of the SCS organizers, Farzana Rahman (Chair) Tomás Di Domenico (Co-Chair)

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[Gtpb] IBSTAT14 Introductory Biostatistics - Training course announcement
by Pedro Fernandes 01 May '14

01 May '14

GTPB Course Announcement IMPORTANT DATES for this Course Deadline for applications: May 15th 2014 Course date: June 2nd - June 6th 2014 This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques in Biostatistics. Participants can expect to go through a set of exercises that are based on biomedical problems. These exercises are preceded by short lectures that are simple to follow. The lectures are designed to provide the conceptual framework that is needed to release the training power of the exercises, not to flood the participants with formality, which will be kept to a minimum. We will make use of a highly interactive methodology, taking advantage of our well equipped Bioinformatics training room. With this approach, we expect to bring the participants to a high degree of usage independence in using the methods that we cover. Main topics: Descriptive Statistics; Probability; Statistical Inference; Design of Experiments. More information, including instructions for applicants Thank you for your interest! Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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[ECCB'14] Call for abstracts: Workshop on Disease Comorbidity
by BAUDOT Anaïs 29 Apr '14

29 Apr '14

We are pleased to announce the ECCB'14 satellite workshop dedicated to "Computational and Systems Biology for Disease Comorbidities" that will take place Sunday, 7th September, 2014, in Strasbourg, France. The workshop will be organized around 3 sessions scoping the discovery, the interpretation and the exploitation of disease comorbidities. Key invited speakers will introduce each session and speakers selected from abstract submissions will broaden the overview of the science currently developed in this field. We deeply encourage you to submit abstracts to the workshop here: https://www.easychair.org/conferences/?conf=csbdc2014 Informations on the workshop can be found here: http://www.eccb14.org/program/workshops/csbdc Keydates Abstract submission deadline: 15th, May 2014 Workshop: 7th, September 2014 Looking forward to seeing you in Strasbourg, Anaïs Baudot & Alfonso Valencia ############# Workshop Description Disease comorbidity – or multimorbidity – exists if 2 or more disorders affect the same individuals more often than expected by chance. Such co-occurrence of diseases are the rule rather than the exception, in particular in ageing populations. Disease comorbidities hence represent a major burden in public health, and greatly affect disease costs and outcomes. But the recent expansion of large-scale biomedical databases and post-genomics disease-related datasets are now offering an unprecedented avenue for the investigations on comorbidities between human disorders. And Computational and Systems Biology are undeniable actors of such investigations. Session 1: Discovering Disease Comorbidities The first session of the workshop will be dedicated to the different approaches that can lead to the detection of comorbidities between disorders, such as the parsing of clinical and epidemiological data. Confirmed speakers: Søren Brunak, CBS, Copenhague, Denmark Maria Martinez, INSERM, Toulouse, France Session 2: Interpreting Disease Comorbidities The second session of the workshop will be dedicated to the network-based approaches developed to interpret at the molecular levels the comorbidities between human disorders. Many data and multi-scale approaches studying the entangled molecular relationships between proteins, diseases and/or phenotypes rely on network representations. Phenotypes proximities between diseases can arise from mutations in functionally similar genes, for instance genes coding for proteins involved in the same pathways that are close in a protein interaction network. Confirmed speaker: Ioannis Xenarios, SBI, Lausanne, Switzerland Session 3: Exploiting Disease Comorbidities A major interest for the study of disease comorbidities lies in the therapeutic road of drug repurposing (or repositioning). The knowledge on disease comorbidities could drive drug repositioning in a more effective way than systematic screenings. This assumption is the rationale of the last session. Confirmed speaker: Patrick Aloy, IRB, Barcelona, Spain Organizers : Anaïs Baudot, CNRS, Marseille, France. Contact: anais.baudot [at] univ-amu.fr Alfonso Valencia, CNIO, Madrid, Spain

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[Gtpb] REMINDER Structural Modeling for Large Macromolecular Complexes - SMLMC14 in Oeiras, Portugal
by Pedro Fernandes 29 Apr '14

29 Apr '14

GTPB Reminder Applications are open for another Bioinformatics Training course: SMLMC14 Structural Modeling for Large Macromolecular Complexes with Joanna Kasprzak and Grzegorz Chojnowski IMPORTANT DATES for this Course Deadline for applications: May 15th 2014 Latest notification of acceptance: May 17th 2014 Course date: June 11th - June 13th 2014 Course description One of the major challenges in structural biology is to determine the structures of macromolecular complexes and to understand their function and mechanism of action. However, structural characterisation of macromolecular assemblies is very difficult. To begin addressing this problem, we have developed PyRy3D. In a nutshell, PyRy3D employs a hybrid computational approach that incorporates spatial information from a variety of experimental methods into the modelling procedure to build low-resolution models of large macromolecular complexes. The PyRy3D model building procedure uses a Monte Carlo approach to sample the solutions-space. It uses spatial restraints to define components interacting with each other, and a simple scoring function is applied to pack them tightly into contours of the entire complex (e.g. cryoEM density maps). More details at http://gtpb.igc.gulbenkian.pt/bicourses/SMLMC14/ Thank you for your interest! Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt

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From NGS to mutation to structural interpretation - Course 3-4 June Nijmegen, the Netherlands
by Celia.vanGelder＠radboudumc.nl 27 Apr '14

27 Apr '14

The effects of a mutation on protein structure and function >From NGS to mutation to structural interpretation Date: June 3-4, 2014 Location: CMBI, UMC Radboud, Nijmegen, the Netherlands Course teachers: Gert Vriend (CMBI), Hanka Venselaar (CMBI) Course website & registration: http://swift.cmbi.ru.nl/gv/NGS . More information: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.nl> Course description Much research in NGS human DNA diagnostics labs is aimed at determining mutations causal for disease states. Many journals these days do no longer publish such studies unless accompanied from at least a computational prediction of what the mutation does to the protein in terms of its structure and function. This two day course aims at generating a level of understanding of the relation between protein structures, amino acids, and function. After the course the participants will be able to understand the output of compute servers that predict the structural and functional effects of mutations in proteins with known structure (or for which the structure can be predicted with homology modelling). The users will also be able to perform elementary visual inspections of protein structures with and without mutations using the YASARA software (that is free and runs on all computers). During the course we will work with the YASARA visualizer and the HOPE mutation effect prediction software (http://www.cmbi.ru.nl/hope/ ). The educational material and the seminars will be sufficiently general, though, to be applicable to other computational tools too. Target audience The course is meant for novices in the protein structure field. As prior knowledge we expect that people have some minimal knowledge about amino acids, have an idea about how to operate BLAST, and can use a browser. Course programme The course website, including the full course programme, can be found at : http://swift.cmbi.ru.nl/gv/NGS Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<http://www.biosb.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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NBIC/BioSB course RNAseq data analysis course (4th edition), 7-9 July 2014
by Celia.vanGelder＠radboudumc.nl 27 Apr '14

27 Apr '14

NBIC/BioSB RNA- seq data analysis course (4th edition) Date: 7-9 July, 2014 Location: Leiden, the Netherlands Course coordinators: Peter-Bram 't Hoen (LUMC), Jan Oosting (LUMC), Andrew Stubbs (ErasmusMC), Celia van Gelder (NBIC/BioSB, education(a)biosb.nl<mailto:education@biosb.nl> ) Course website: http://biosb.nl/education/course-portfolio/rna-seq/ . Registration: Registration is not yet open. You can express your interest in the course by filling out the pre-registration form at http://biosb.nl/education/enrollment/pre-registration-courses/ . More information: education(a)biosb.nl<mailto:education@biosb.nl> Course description BioSB/NBIC and partners LUMC and ErasmusMC are organizing a 3-day course on RNA-seq. This is an expert course for people with experience in NGS and a follow-up course on the general NBIC NGS data analysis course (coordinator Jeroen Laros, LUMC). The course will consist of seminars and hands-on command line, Galaxy and R practicals and will focus on data preprocessing, quality control, alignment, visualization and statistics for differential transcript expression. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects. Course topics RNA-seq experimental approaches Alignment and de novo assembly Statistics for differential gene expression eQTL analysis and allele specific expression Variant calling and RNA editing Small RNA profiling Software for RNA-seq data analysis Target audience Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded project RD-Connect and Marie Curie European Training Network TranCYST. BioSB Course Programme The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology Research School (BioSB). The Education Portfolio of BioSB can be found at http://biosb.nl/education/course-portfolio/. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<http://www.biosb.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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NBIC/BioSB Course Algorithms for Biological Networks (3th edition)
by Celia.vanGelder＠radboudumc.nl 27 Apr '14

27 Apr '14

NBIC/BioSB Course Algorithms for Biological Networks (3rd edition) Date: 30 June - 4 July, 2014 Course coordinators: Dick de Ridder (WUR), Jeroen de Ridder (TUD), Celia van Gelder (NBIC/BioSB) Location: Delft University of Technology (TUD), Delft, the Netherlands Website: : http://biosb.nl/education/course-portfolio/bioinformatics-portfolio/course-… Registration: Registration is not yet open. You can express your interest in the course by filling out the pre-registration form at http://biosb.nl/education/enrollment/pre-registration-courses/. More information: education(a)biosb.nl<mailto:education@biosb.nl> Target audience PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. Course Description In the third edition of this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring networks from observed measurement data and of integrating various data sources and databases to refine networks. Once networks are derived they often serve as the cornerstone in the visualization, analysis and interpretation of high-throughput data; we will discuss a number of methods in this area. As an alternative to static networks, a number of alternative dynamic network models more suited for high-level simulation of cellular behaviour for will be introduced. Finally, we will give some examples of algorithms exploiting the networks found to learn about biology, specifically for inspecting protein interaction networks and for finding active sub networks. Course programme The course website, including full course programme, can be found at http://helix.ewi.tudelft.nl/nbic/abn/ . BioSB Course Programme The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology Research School (BioSB). The Education Portfolio of BioSB can be found at http://biosb.nl/education/course-portfolio/. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC/BioSB tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<http://www.biosb.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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