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Registration - Multiscale Modeling of Biomolecular Systems - 28 November 2014
by Sanne Abeln 24 Sep '14

24 Sep '14

You are cordially invited to the Multiscale Modeling of Biomolecular Systems (MMBS) symposium on Friday 28 November 2014. This meeting is jointly organized by the Amsterdam Center for Multiscale Modeling (ACMM) and the Netherlands Society for Biomolecular Modeling (NSBM). The meeting aims to bridge multiple levels of modeling, from structural bioinformatics to biomolecular simulation at various scales. You are now able to register at: https://www.aanmelder.nl/79914/subscribe?survey_id=59573 The deadline for registration is 31 October 2014. Scope: The meeting will focus on multiscale and multilevel modeling of biomolecular systems including proteins, DNA or RNA. Topics will cover (but are not limited to): bioinformatics sequence analysis, structure analysis, structure prediction methods (including docking), coarse grained simulations, full atomistic classical force field simulations, combined QM/MM, ab initio and/or DFT calculations, and enhanced sampling methods. Keynote Speakers: Prof. David Jones (UCL, UK) Prof. Ursula Roethlisberger (EPFL, Switzerland) Date: 28 November 2014 - 11:00 - 18:00 Location: VU University, De Boelelaan 1081, Amsterdam, the Netherlands Registration & posters: https://www.aanmelder.nl/79914/subscribe?survey_id=59573 Program Committee: Jocelyne Vreede (UvA), Paola Gori-Giorgi (VU) Daan Geerke (VU), Sanne Abeln (VU) Advisory board (NSBM+ACMM): Gerry Nicolaes (UM), Gert Vriend (UMCN) Peter Bolhuis (UvA), Evert Jan Meijer (UvA) Matthias Bickelhaupt (VU), Luuk Visscher (VU) Best regards, Jocelyne Vreede, Paola Gori-Giorgi, Daan Geerke, Sanne Abeln -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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PhD Position at Maastricht University: Identification of gene-environment interactions in the development of psychosis
by Viechtbauer Wolfgang (STAT) 23 Sep '14

23 Sep '14

Subject: PhD Position at Maastricht University Project: Identification of gene-environment interactions in the development of psychosis [Project] A psychotic disorder is a psychiatric condition characterized by delusions, hallucinations, and social and emotional problems. Various environmental factors, such as the use of cannabis and experiencing traumatic events, increase the risk of a psychosis, but the risk-increasing effects of these factors are much higher in people with a pre-existing genetic vulnerability. This phenomenon is also called gene-environment interaction. New technical possibilities in modern genetics, such as genome-wide genotyping, now make it possible to systematically investigate the genes that make people more susceptible to such environmental factors and the biological pathways to which these genes belong. In 2010, a major European study on the importance of gene-environment interactions in the etiology of psychotic disorders was launched. Now that the data collection phase is close to completion, there is an open position for a doctoral student to examine the genome-wide data from this study for gene-environment interactions in a systematic way. [Tasks] Your task is to identify genes and biological systems that interact in a plausible manner with relevant environmental factors. For this purpose, you derive sets of genes linked together in a biologically plausible way and analyze whether they can explain sensitivity to environmental factors. You work on large data sets that have already been collected. The development of new and/or the application of advanced statistical methods to analyze such data, in consultation with a statistician, is an important ambition of the project. [Requirements] Graduated in bioinformatics or a related discipline. Good communication skills, fluent in English, and some affinity for research on psychiatric disorders. Demonstrated interest in clinical research. Some research experience is recommended. [Conditions of employment] The terms of employment of Maastricht University are set out in the Collective Labour Agreement of Dutch Universities (CAO). Furthermore, local UM provisions also apply (see http://www.maastrichtuniversity.nl/web/Main/Employees/AZ.htm) This is a temporary employment for 4 years. Your salary would be € 2.083,-- gross per month in the first year up to € 2.664,-- gross per month in the fourth year according to the PhD-student salary scale. Each year an evaluation will take place. [Organization] Maastricht University (http://www.maastrichtuniversity.nl/) is renowned for its unique, innovative, problem-based learning system, which is characterized by a small-scale and student-oriented approach. Research at UM is characterized by a multidisciplinary and thematic approach, and is concentrated in research institutes and schools. Maastricht University has around 15,000 students and 4,000 employees. Reflecting the university's strong international profile, a fair amount of both students and staff are from abroad. The university hosts 6 faculties: Faculty of Health, Medicine and Life Sciences, Faculty of Law, School of Business and Economics, Faculty of Humanities and Sciences, Faculty of Arts and Social Sciences, Faculty of Psychology and Neuroscience. The School for Mental Health and Neuroscience (http://mhens.unimaas.nl/) is one of the internationally leading institutes on neuroscience research, and aims at advancing our understanding of brain-behavior relationships by adopting an integrated approach between the various disciplines in neuro- and behavioral science, medicine, and the life sciences. The project is embedded in Division 2, Cognitive Neuropsychiatry & Clinical Neuroscience. The mission of Division 2 is to generate new insights into the neurocognitive and neurobehavioral mechanisms in order to improve treatment and care for people with cognitive disorders and other neurological disorders. [Contact] For more information about this position and/or to submit your application materials (CV, letter of motivation, and contact information for two references), please contact Dr. Ruud van Winkel at: ruud.vanwinkel(a)maastrichtuniversity.nl Dr. Ruud van Winkel Dr. Wolfgang Viechtbauer Department of Psychiatry and Psychology School for Mental Health and Neuroscience Faculty of Health, Medicine, and Life Sciences Maastricht University, P.O. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands

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FW: vacature nexsplorer.iph
by Katrijn Vannerum 23 Sep '14

23 Sep '14

Dear, The WIV/ISP has a vacant PhD position for the project 'Development of next generation sequencing data analysis tools in support of a fast response for public health and food chain safety'. Best regards, Katrijn Vannerum Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01CFD737.B4E567A0]

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[Gtpb] REMINDER: TA-AFADM14 - Bioinformatics Training Course
by Pedro Fernandes 23 Sep '14

23 Sep '14

Dear GTPB mailing list member Please allow me to remind you that this hands-on training course joins together of two connected subjects - RNAseq using open source tools - Automatic Functional Annotation using Blast2GO In the feedblack collected in previous editions, this course is considered highly efficient in skills transfer If you have not yet done so, please consider applying or indicating the course to a colleague or collaborator. The published deadline is Sept 26th. Thank ,Pedro Fernaandes GTPB Coodinator REMINDER IMPORTANT DATES for TA-AFADM14 Deadline for applications: September 26th 2014 <================= Notification of acceptance dates: EARLY: Sept 19th 2014 (on special request, see Application) NORMAL: September 26th 2014 Course date: October 6th - October 9th 2014 The Gulbenkian Training Programme in Bioinformatics is pleased to announce that the applications for the hands-on Bioinformatics training course TA-AFADM14 Transcriptome Assembly, Automatic Annotation and Data Mining are now OPEN. Please have a look at our website here: http://gtpb.igc.gulbenkian.pt/bicourses/TA-AFADM14/ Course duration: 4 days Course fee: Euro 320.00 We will have Stefan Goetz and Riccardo Alese Cigliano as instructors. This course has already been run here several times with a great deal of success, as revealed by very positive feedback reports and subsequent recruitment by word of mouth by satisfied attendees. Course description: This is a combined course in RNA-seq and functional annotation aimed at scientists working in next generation sequencing transcriptomics who want to extract the best possible information from their data. The course covers all aspects of RNA-seq analysis, from quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNA-seq data both in the presence and absence of a reference genome. The second part of the course is a practical workshop on Blast2GO, the most popular framework for functional annotation of sequence data. Participants will learn how to generate de novo functional labels, such as GO terms and KEGG pathways, for their sequence data and how to extract relevant information from these annotations, i.e. visualisation and enrichment analysis using the Gene Ontology. This part will be based on the use of the Blast2GO application and will mainly comprise exercises and practical cases. Participants may bring their own data. Who should attend? Experimentalists and bioinformaticians working on EST, NextGeneration Sequencing and microarray design projects, specially (but not exclusively) of non-model species. No programming knowledge is required. Thank you for your continued interest P.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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PhD opportunity at Wageningen Univeristy
by Besten, Heidy den 19 Sep '14

19 Sep '14

Dear sir/madam, Please find below the links to a PhD vacancy in the Food Science Domain of Wageningen University. We are looking for a MSc student with a genuine interest in bioinformatics and (food)microbiology. I would be grateful if you can please pass this information on to relevant contacts/people that may be interested in applying. http://www.wageningenur.nl/en/Jobs/Vacancies/Show/PhD-Food-Safety-System-Dy… https://www.academictransfer.com/employer/WUR/vacancy/23158/lang/en/ Thanks in advance, Heidy den Besten dr. ir. H. M. W. den Besten (Heidy) Assistant Professor in Food Microbiology Wageningen University Laboratory of Food Microbiology Postal address: PO Box 17, 6700 AA Wageningen, The Netherlands Visiting address: Building 118 (Axis-X office 3.10B), Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands T: +31-317-483213 E-mail: heidy.denbesten(a)wur.nl<mailto:heidy.denbesten@wur.nl> I: www.fhm.wur.nl<http://www.fhm.wur.nl/>

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[Gtpb] REMINDER: TA-AFADM14 - Bioinformatics Training Course
by Pedro Fernandes 19 Sep '14

19 Sep '14

REMINDER IMPORTANT DATES for TA-AFADM14 Deadline for applications: September 26th 2014 <================= Notification of acceptance dates: EARLY: Sept 19th 2014 (on special request, see Application) NORMAL: September 26th 2014 Course date: October 6th - October 9th 2014 The Gulbenkian Training Programme in Bioinformatics is pleased to announce that the applications for the hands-on Bioinformatics training course TA-AFADM14 Transcriptome Assembly, Automatic Annotation and Data Mining are now OPEN. Please have a look at our website here: http://gtpb.igc.gulbenkian.pt/bicourses/TA-AFADM14/ Course duration: 4 days Course fee: Euro 320.00 We will have Stefan Goetz and Riccardo Alese Cigliano as instructors. This course has already been run here several times with a great deal of success, as revealed by very positive feedback reports and subsequent recruitment by word of mouth by satisfied attendees. Course description: This is a combined course in RNA-seq and functional annotation aimed at scientists working in next generation sequencing transcriptomics who want to extract the best possible information from their data. The course covers all aspects of RNA-seq analysis, from quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNA-seq data both in the presence and absence of a reference genome. The second part of the course is a practical workshop on Blast2GO, the most popular framework for functional annotation of sequence data. Participants will learn how to generate de novo functional labels, such as GO terms and KEGG pathways, for their sequence data and how to extract relevant information from these annotations, i.e. visualisation and enrichment analysis using the Gene Ontology. This part will be based on the use of the Blast2GO application and will mainly comprise exercises and practical cases. Participants may bring their own data. Who should attend? Experimentalists and bioinformaticians working on EST, NextGeneration Sequencing and microarray design projects, specially (but not exclusively) of non-model species. No programming knowledge is required. Thank you for your continued interest P.Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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

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FW: SEMINAR on 18/9 by Vanessa Didelez on Causal Models for Optimal Dynamic Treatments with Survival Outcomes
by Katrijn Vannerum 16 Sep '14

16 Sep '14

-----Original Message----- From: Stijn Vansteelandt [mailto:stijn.vansteelandt@ugent.be] Sent: dinsdag 16 september 2014 13:33 To: Olivier Thas Cc: Ann Vanreusel; Beatrijs Moerkerke; Carlos De Wagter; Dirk De Bacquer; Dirk Van den Poel; Els Goetghebeur; Georges Van Maele; Georges De Moor; Gino Verleye; Hubert De Saedeleer; Jean-Pierre Ottoy; Jo Demeester; Luc Duchateau; Marc Van Meirvenne; Maria.Ysebaert Ysebaert; Nele De Belie; René Boel; Ronan Van Rossem; Stefan Van Aelst; Thierry Marchant; Yves Rosseel; Tom Loeys; Lieven Clement; Lieven Clement; Karel Vermeulen; Machteld Varewyck; Bart Jacobs; Johan Steen; Bart Van Rompaye; Tim De Craecker; Kristof De Beuf; Holger Cevallos Valdiviezo; Kristof Vansteelandt; Ludger Goeminne; Sjouke Vandenberghe; Arnout Van Messem; Dominik Sznajder; Joris Meys; Dries Benoit; Gerdie Everaert; Dieter Fiems; Herman Van Oyen; An Vandebosch; Peter Dawyndt; Veronique Storme; Jan De Neve Subject: SEMINAR on 18/9 by Vanessa Didelez on Causal Models for Optimal Dynamic Treatments with Survival Outcomes Dear all, You are cordially invited to the following seminar, which will take place on Thursday September 18 at 12h in Room A3 (De Sterre, S9). Vanessa Didelez, University of Bristol, U.K. Causal Models for Optimal Dynamic Treatments with Survival Outcomes A dynamic treatment is a set of rules that assigns for each time point when a treatment decision needs to be made what this should be, given the patient's history so far. An example in the context of HIV studies is "start treatment when CD4 count first drops below 600". An optimal dynamic treatment is such a set of rules that optimises a criterion reflecting better health for the patient. I will give an overview of the main methods in this context (based on structural models), with particular attention to the case of survival outcomes. For instance we may use the g-computation approach or dynamic marginal structural models - the latter are becoming popular for HIV studies as mentioned above. The particular difficulty with survival outcomes is that marginal and conditional models are typically not compatible. I will discuss and compare approaches, as well as the issue of simulating from structural models; this (hopefully) leads to additional insight and understanding of the models used in this context. Best wishes, Stijn.

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Computational microbiome postdoc positions at Broad Institute
by Katrijn Vannerum 16 Sep '14

16 Sep '14

The microbiome field is at an important and exciting crossroad: numerous associations have been made that connect the microbes living in and on our bodies with diseases such as inflammatory bowel disease, type 1 diabetes, obesity, and many others, but how these organisms impact the host in health and disease remains largely unknown. We are expanding our team that is broadly engaged in multiple collaborative studies of the roles of the human microbiome in health and disease. The focus of these position(s) is on computational methods to characterize biomolecular functions within these microbial communities and their interactions with host immunity and genetics. We are part of the vibrant research community at the Broad Institute, the Harvard Medical School, Massachusetts General Hospital, and Harvard School of Public Health, and the broader Boston biomedical and life sciences communities, resulting in a rich environment for quantitative, computational, and laboratory collaborations. The successful candidate will perform computational analysis of population-scale metagenomic data, the largest datasets of its kind in the world. Specifically, we seek to determine A) links between microbial membership and metabolic function in the gut microbiota; B) causal or correlative changes in the human microbiota during disease onset and treatment; and C) potential biomolecular interactors between the gut microbial community and the host immune system. The candidate will be responsible for computational methods development and/or applications, should be conversant with bioinformatic techniques for genomic data analysis, and will collaborate closely with experimental laboratories in order to validate computational results and their translation to the clinic. The position will be located within the Broad Institute, and work closely with the Xavier and Huttenhower labs. The Broad Institute is a new kind of deeply collaborative research institution that is transforming medicine and human health by performing experimental research and analyzing scientific data on an unprecedented scale. We will consider candidates with a doctoral degree in Computer Science, Bioinformatics, Biostatistics, Biology, or a related field; familiarity with functional genomic and/or metagenomic data, as indicated by publication record; proficiency in one or more scripting languages appropriate for scalable data analysis; ability to communicate scientific material; Candidates should be resourceful, self-motivated, and possess a proven record of scientific advances leading to high quality publications. Must be capable of working in a collaborative and fast-paced team environment and working on self-directed research projects within broader goals set by group. If you are interested in applying, please send a cover letter and your CV to Dirk Gevers (dgevers(a)broadinstitute.org) If you would like more information about the microbiome program at Broad Institute, visit http://www.broadinstitute.org/blog/new-phase-microbiome Dirk Gevers Via Dr. Katrijn Vannerum Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01CFD197.A8E572B0]

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Fwd: Position open: Scientific programmer, Genome Variation, Algorithms Development, TGAC, UK
by Frederik Coppens 15 Sep '14

15 Sep '14

Begin forwarded message: > From: "Bernardo Clavijo (TGAC)" <Bernardo.Clavijo(a)tgac.ac.uk> > Subject: Position open: Scientific programmer, Genome Variation, Algorithms Development, TGAC, UK > Date: 15 Sep 2014 11:27:30 GMT+2 > To: "Bernardo Clavijo (TGAC)" <Bernardo.Clavijo(a)tgac.ac.uk> > > Hi all, > I just wanted to ask you a favour. I have an opening in my Algorithms Development at TGAC for a scientific programmer/postdoc. Would you please spread the word among the people that could be interested? > Work area will be mainly variant analysis on genomes (challenging genomes, such as a variety of plants), with a focus going from tool evaluation and pipeline design to algorithm development, depending on the profile of the successful candidate. There is a couple of directions we want to expand our research into, so there will be freedom to choose among those and purse the candidate’s own research ideas. > The ideal candidate should have a good CS/math/stats background, and some experience on NGS, but the main thing I am looking for is someone with a lot of enthusiasm to learn and develop new techniques. > More details available on the website: http://jobs.tgac.ac.uk/Details.asp?vacancyID=8119 and obviously for any other questions, simply write me an e-mail. > > Thank you! > > Best, > > > Bernardo J. Clavijo > > Project Leader > Bioinformatics Algorithms Development > The Genome Analysis Centre, Norwich, UK ================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics Tel: 32 (0)9 3313692 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM frcop(a)psb.ugent.be http://www.psb.ugent.be/abb ==================================================================

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MG-RAST workshop (17-18 Sept 2014)
by Katrijn Vannerum 13 Sep '14

13 Sep '14

MG-RAST workshop (17-18 Sept 2014) MG-RAST (the Metagenomics RAST; http://metagenomics.anl.gov<http://www.google.com/url?q=http%3A%2F%2Fmetagenomics.anl.gov&sa=D&sntz=1&u…>) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples. This 2-day workshop will offer researchers opportunities to analyze shotgun metagenomics high-throughput sequencing datasets with MG-RAST, understand the user interface, provide metadata and perform analysis. Special attention will be paid to the API and the R interface, together with general tips and trick for data processing. Sample data will be provided for hands-on analysis. This workshop will acquaint researchers with MG-RAST sequence analysis tools, enable them to implement their research with MG-RAST, provide hands-on training with real sequence data and offer opportunities to discuss analysis strategies directly with the MG-RAST developers. Instructors Folker Meyer (Argonne National Laboratory and University of Chicago) Andreas Wilke (Argonne National Laboratory and University of Chicago) Schedule day1: Wednesday September 17, 2014, 9:00-17:30 1. MG-RAST overview and user interface * browse and search public data * understanding the pipeline and its limitations * understanding the overview page (a first glance at your data) * check primer/probe coverage in Probe Match 2. Analysis and comparison with the web interface * review concepts (abundance profile) * adjusting parameters * comparison of multiple samples * exporting data day2: Thursday September 18, 2014, 9:00-17:30 1. R Interface (matR) and the API * using R * the MG-RAST API * simple script examples using the API * exporting from MG-RAST to other software 2. Metadata GSC --- Standards and Data Submission * GSC genome standards * Entering metadata with MetaZen 3. Specialist topics * sequence pathology --- common problems with NGS and how to find them * to assemble or not to assemble? * details on the pipeline * scripting with MG-RAST Venue The course will be organised in the multimedia room of the Information and Communication Technology Department (DICT) at Ghent University, as this facilty has laptop computers for participants that cannot bring their own. Participants that work on their own laptop computer are invited to install a recent version of Firefox. This venue will be made freely available by DICT, with coffee and soda drinks free of charge for all participants. Organizing committee Prof. Dr. Peter Dawyndt (Ghent University) Prof. Dr. Anne Willems (Ghent University) ir. Bart Mesuere (Ghent University) ir. Caroline De Tender (Institute for Agricultural and Fisheries Research; ILVO) Contact Prof. Dr. Peter Dawyndt Department of Applied Mathematics, Computer Science and Statistics Ghent University phone: +32 9 264 4779 email: Peter.Dawyndt(a)UGent.be<mailto:Peter.Dawyndt@UGent.be> Please fill up this form<https://docs.google.com/forms/d/1_4awjkASXBa52s1ckdfEv4pcZMIO9MraHerFIlpxEr…> to register your participation to this workshop. -- ------------------------------------------------------------------------- Prof. Dr. Peter Dawyndt Ghent University Department of Applied Mathematics, Computer Science and Statistics (WE02) Krijgslaan 281 (S9) B-9000 Ghent Belgium Tel: (32)9.264.47.79 Fax: (32)9.264.49.95 Email: Peter.Dawyndt(a)UGent.be<mailto:Peter.Dawyndt@UGent.be> -------------------------------------------------------------------------

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