March 2015 - BBClist - maillist.psb.ugent.be

6 Months internship position at Schneider Lab - University of Luxembourg - call extended until March 29
by ISCBSC announcement 21 Mar '15

21 Mar '15

*Internship at University of Luxembourg: Developing web resource for enzymes of unknown function.* The ISCB Student Council is pleased to announce a 6-month internship position with the Schneider group at Bioinformatics Core, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg. The internship is expected to start in October and it is available to Masters and PhD students in computational biology or related areas from developing nations. *About the group* Bioinformatics Core at (LCSB) facilitates efficient data flow between experimental theoretical and medical groups which involves handling, storing, categorizing huge amount of data as well as developing techniques for cost and time efficient data analysis. Composed of computer scientists and biologists covering a broad spectrum of disciplines, the group aims to provide new insights and to generate new hypotheses regarding the functioning of complex biological systems. *Stipend / Accommodation / Visa Information* A stipend of 850 Euros/month will be provided to the selected intern. The student is going to be responsible for covering the travel and accommodation expenses. University of Luxembourg accommodation service can provide guidance on finding accomodation. Visa information will be provided at the time of interviews. *Eligibility Criteria* The student should be a citizen of a developing country and pursue a degree program in a university located in a developing country (if you are not sure of your country classification, please check the IMF website available at this link: http://www.imf.org/external/pubs/ft/weo/2009/02/weodata/groups.htm#oem) Look under “Emerging and Developing Economies” to see if your country is listed here. The applicant should be either doing or have finished a Masters degree in computational biology or related disciplines and should be able to provide proof of her/his enrollment status. *Prerequisite skills:* - Exposure to different life science databases - Experience with scripting languages like Perl ot Python - Proficient in use of Linux OS - Knowledge of MySQL, Oracle, PostgreSQL - Good communication skills in English *How to Apply* Send all the following documents as a single zip file attachment to mailto: internships(a)iscbsc.org(we accept files in txt,PDF or .doc/.docx format): 1. *Resume or curriculum vitae.* Please include citizenship, programming languages known and programming experience, courses taken, research experience and publications if any. 2. *Statement of Purpose (max 500 words).* It is expected that the student briefly talks about his/her past experience in computational biology showcasing the skills he/she has learned and their relevance to the advertised position. Either the candidate should have a computational background with sound knowledge of molecular/cellular biology concepts or biological background with programming experience. 3. *Proof of enrollment, such as a letter from university or department.* The letter should be on the official University letterhead and should clearly state that the student is enrolled as a full time student in the University and will continue to maintain the same status during the period of the internship. 4. *One recommendation letter.* We accept files in txt, PDF or .doc/.docx format. *Selection process* Applications will be reviewed by volunteers of the ISCB Student Council Symposium and four students will be selected for phone interviews (Skype) with the group offering the position, that will have the final choice in selecting the successful candidate. *Applications will be accepted until March 29, 2015.* The candidates selected for an INTERVIEW will be contacted by April 20, 2015. If you have any questions, please contact us at mailto: internships(a)iscbsc.org ISCB Student Council Education and Internships Committee

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BioSB 2015 - Extended abstract submission deadline: March 26, 2015!
by Femke Francissen 20 Mar '15

20 Mar '15

*Netherlands Bioinformatics & Systems Biology Conference 2015 - BioSB 2015* Date: 20-21 May 2015 Venue: De Werelt, Lunteren, the Netherlands Website: http://www.aanmelder.nl/biosb2015 Registration: https://www.aanmelder.nl/biosb2015/subscribe *Abstract submission - extended submission deadline: March 26!* We have decided to extend the submission deadline for abstracts for the BioSB 2015 conference programme with one week, to March 26, 2015! Abstracts can be submitted for the following topics / topical tracks: - Metabolism - Gene regulation - Networks & Data integration - Next Generation Sequencing - Bioinf & SysBio in practice: industrial and medical applications (industry track) (May 20) - Statistics & modeling - Genotype/phenotype & disease - Proteomics - Whole-cell modeling / multi-scale modeling / genome-scale modeling - Metagenomics topical track (May 20) - NSBM Spring meeting 2015 (biomolecular modelling track) (May 21) You can submit an abstract for a lecture in one of the parallel sessions, a poster presentation or for a demo in the application showcase. Read more about the abstract submission here: https://www.aanmelder.nl/biosb2015/wiki/93751/abstracts. *Extended abstract submission deadline: March 26, 2015*, Extended notification date: April 14, 2015. *Nominations for BioSB Young Investigator Award 2015* Young researchers can now be nominated for the BioSB Young Investigator Award 2015. The winner will present an honorary lecture at the conference (May 20) and will receive an award provided by the BioSB research school <http://www.biosb.nl>. You can now submit your nominations via: https://www.aanmelder.nl/biosb2015/wiki/93721/biosb%20young%20investigator%…. *Nomination deadline: April 10, 2015*. *BioSB 2015: Merging two research fields* BioSB 2015 will be the first in a series of yearly organised Dutch Bioinformatics & Systems Biology (BioSB) conferences focusing on both bioinformatics and systems biology research. The BioSB 2015 combines the annual Netherlands Bioinformatics Conference (NBIC) and the annual Systems Biology Symposium (SB@NL). Because of the success of the NBIC conference format in the past, the BioSB conference will be organised in the familiar style: a 2-day conference at Congrescentrum De Werelt in Lunteren. The BioSB 2015 will be co-organised by the BioSB research school <http://www.biosb.nl> and the Utrecht Bioinformatics Center <http://ubc.uu.nl/>. *Subscribe to the BioSB newsletter* to stay up to date about the BioSB 2015 conference and the BioSB research school activities. Subscribe here <http://biosb.nl/newsletter/>.

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Registration Open: BioSB Course Kick start R (3rd edition) , April 24 2015, Amsterdam
by Celia.vanGelder＠radboudumc.nl 18 Mar '15

18 Mar '15

BioSB Course Kick start R (3rd edition) Date: April 24, 2015 Location: Amsterdam Course Coordinator: Douwe Molenaar (VU) Website: http://biosb.nl/education/course-portfolio/course-kick-start-r-3rd-edition/ Registration: http://biosb.nl/education/course-portfolio/enrollment-kick-start-r-course-3… On April 24, 2015, BioSB organises the third edition of the Kick Start R course in Amsterdam. This is a one-day introduction course for researchers about the possibilities of the statistical calculation environment R for those who would like to use it, or have already started using R for statistical data analysis but would like to obtain a bit more background. The main goal is to provide the participant with a kick-start in R. Clearly, good and practically applicable knowledge of R will only be gained by subsequent self-study. A kick start is achieved through the following sub-goals: 1. The participant will become acquainted with the structure and philosophy behind the R-language. The participant will thereby be able to gain a quicker understanding of the R-language compared to the "immediate problem solving" approach taken by most (online) manuals. 2. The participant will become acquainted with a number of tools specific to the R-language. This will help the participant to start using R quickly in a professional manner This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl>. Best regards Celia van Gelder Dr. Celia W.G. van Gelder Education Manager NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre 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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PhD Position at Wageningen UR
by Dijk, Aalt-Jan van 17 Mar '15

17 Mar '15

We are looking for a PhD student for a project on prediction and identification of key determinants of protein-protein interaction specificity. You will develop novel bioinformatics methods, based on machine learning, to predict which domains and amino acids specify protein-protein interaction potential. You will apply these methods in particular to study MADS domain transcription factors, which regulate transcription patterns underlying major plant developmental processes. You will be part of a team that includes wet lab scientists from the Immink group with ample experience on plant developmental biology and computational scientists from the Bioinformatics group, experts in machine learning and data integration. The Immink group investigates the transcriptional regulation of plant developmental processes, such as flowering time control, floral organ development and leaf and floral organ growth, with special interest in the role of protein-protein interactions. The Bioinformatics group focuses on fundamental and applied bioinformatics research in the green life sciences. The group has a strong track record in genomics, algorithm development and tool construction. For more information, see: http://www.wageningenur.nl/en/Jobs/Vacancies/Show/PhD-position-Prediction-a… The deadline for application is April 15, 2015. Best regards, Aalt-Jan van Dijk

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Mini-symposium Thu. 2 April (10.30-14.10 h, VU) on Modeling complex protein-ligand interactions and drug action
by Barbara.vanKampen＠radboudumc.nl 17 Mar '15

17 Mar '15

You are cordially invited to attend the mini-symposium "Modeling complex protein-ligand interactions and drug action" on Thursday 2 April (10.30 - 14.10 h, VU University Main building, sixth floor, room HG-06A05), preceding Ruben Vosmeer's thesis defense and with the following speakers: Chris Oostenbrink (BOKU, Vienna, Austria) Gerhard F. Ecker (University of Vienna, Austria) Alan E. Mark (University of Queensland, Brisbane, Australia) Scott Boyer (Swedish Toxicology Sciences Research Center, Södertälje, Sweden) For the program, see attached flyer (or http://aimms.vu.nl/en/news-events/events/2015/2015-04-02-mini-symposium-mod… ). Lunch will be served and participation is free, but registration is required until 29 March via https://fd7.formdesk.com/vuamsterdam/modeling_complex_protein_ligand_intera… Kind regards, Daan Geerke 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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Computational Single Cell analysis position at Janssen
by Ceulemans, Hugo [JRDBE] 17 Mar '15

17 Mar '15

Dear all, Please find the description of an exciting computational biology position at Janssen R&D attached. Kind regards, Hugo Ceulemans

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[Gtpb] [GTPB] New course - Structural Modelling for Large Macromolecular Complexe, applications s now OPEN
by Pedro Fernandes 15 Mar '15

15 Mar '15

Dear all, Applications for the "Structural Modelling for Large Macromolecular Complexes" training course are now OPEN IMPORTANT DATES for this Course Deadline for applications: April 10th 2015 Latest notification of acceptance: April 15th 2015 Course date: April 27th - April 30th 2015 With Joanna Kasprzak and Mateusz Dobrychlop http://gtpb.igc.gulbenkian.pt/bicourses/SMLMC15/ Description We will present a range of techniques to generate, analyse, and optimise models of proteins, RNA, and their complexes. We will talk about new approaches to structure determination of macromolecules and macromolecular complexes. During the practical sessions participants will learn how to use methods for modelling protein and RNA 3D structures such as Modeller and ModeRNA. Also we will focus on methods dedicated to protein-RNA complexes modelling, e.g. by combining data from low-resolution density maps, SAXS and biochemistry. In particular, we will present how to use PyRy3D, a computational tool to build models of macromolecular complexes based on data from various sources. Participants will be able to bring-in specific biological questions and/or their on data to work with during the course. Target Audience The course has been designed for molecular and structural biologists, bioinformaticians and biotechnologists and other scientists interested in modelling of biological complexes. The content is suitable for researchers, both at the graduate and post-graduate levels. 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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[Gtpb] [GTPB] "Promoter hunting and systems modelling of cellular pathways" - reminder
by Pedro Fernandes 15 Mar '15

15 Mar '15

Dear all, The Applications for the PHSMCP15 course, "Promoter hunting and systems modelling of cellular pathways", are now OPEN. IMPORTANT DATES for this Course Deadline for applications: April 2nd 2015 Latest notification of acceptance: April 3rd 2015 Course date: April 22nd - April 24th 2015 With Alexander Kel and Christoph Wierling Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/PHSMCP15/ In short: Learn how to find promoters in NGS data an how to use genes and promoters to produce inferences at the pathway and system levels. Full description: Overview This course starts by reviewing basic principles of gene regulation and how information is encoded in the huge part of genome - it's so called "non-coding" part. Bioinformatics plays a huge role in exploring how gene regulation works. We will introduce mathematical modelling of cellular pathways and address the interplay between feedback and feed-forward loops of regulation. We will see how a range of modelling techniques can help us to: - find master regulators - understand disease mechanisms - build models for use in precision medicine - design novel systems for biotechnology Starting from techniques for the computational prediction of promoters and distant enhancers, we will deal with the analysis of the structure of regulatory regions by identifying binding sites for transcription factors. A complete annotation of a newly sequenced genome has to address the identification of these regions in addition to the classical task of finding genes in terms of coding regions. Regulatory regions determine where, under which conditions and when genes become active. Thus, they are a fundamental part of the definition of the function of a gene. We will have a chance to introduce and acquire *hands-on* practice in next generation sequencing (NGS) techniques for genome-wide epigenetic analyses such as ChIP-seq. Then we will approach the analysis and modelling of biological systems from several practical angles. Systems biology and modelling are approched here from the interaction and network-based perspectives. We will introduce several pathway databases, such as Reactome, KEGG, TRANSPATH, TRANSFAC, ConsensusPathDB and use these information resources to perform pathway analysis. Next, we will use modelling of biological systems to look at different mathematical modelling strategies, such as Boolean networks and ordinary differential equation systems (ODEs). We will describe computational tools, like Cytoscape and CellDesigner, for the set-up and development of model prototypes and show further tools, such as Copasi, BioUML and PyBioS that can be used for parameter-fitting and sensitivity analysis. We will follow-on by looking at methods for reconstructing gene regulatory networks from gene expression data. The application of such methods can reveal key nodes in networks as potential biomarkers or drug targets. Dynamic systems modelling will be used to check the consistency of target and biomarker predictions. We will show real examples of application of these methods for identification of disease related biomarkers, drug discovery and personalized medicine. Special attention will be given to the application of the above mentioned methods in designing novel biological systems, in the growing field of Synthetic Biology. Methods Participants will learn about several techniques of finding promoters and enhancers and the principles on which these methods are based on. In the hands-on exercises, several analytical tools will be introduced and the results critically evaluated to assess their reliability. The course sessions will consist of lectures that lay out the conceptual framework as needed, and hands-on exercises, which will provide the practical insight on the use of the methods, gradually, in order to produce skills that can be used with a relatively high degree of independence. Participants will learn how to set-up some of the programs, and use publicly available servers for more complex analytical jobs, in an informed fashion, so that they fully understand the output generated and how their quality can be assessed. Participants will also learn the novel principles of organization of gene regulatory regions, which will help them to interpret their results of genomic and transcriptomic studies. The course will provide sufficient skills for the participants to address problems using open source software and freely accessible data resources. It will also be a chance to use commercially licensed resources such as TRANSFAC or the geneXplain integrated analytic platform for specific purposes. Target Audience The course was designed for researchers in biology, bioinformatics, biochemistry and medicine that have an interest in gene regulation and related topics. Course Pre-requisites Basic biochemistry. Elementary computing skills. Background knowledge in bioinformatics is not absolutely necessary, but may be instrumentally useful. Best wishes 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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Fwd: BioNetVisA workshop at ICSB2015: abstract submission deadline on April 1st
by m.michaut＠nki.nl 12 Mar '15

12 Mar '15

========================================================= BioNetVisA 2015 workshop: From biological network reconstruction to data visualization and analysis in molecular biology and medicine. ABSTRACT SUBMISSION DEADLINE: April 1st Check http://www.2015icsb.com/page.asp?call=Workshop and https://sysbio.curie.fr/bionetvisa Venue: The workshop will take place in Shanghai, China on August 25th, 2015 as part of the 16th International Conference on System Biology (ICSB’15). http://www.2015icsb.com<http://www.2015icsb.com/> Topics: Graphical representation of biological knowledge Comprehensive signaling networks Molecular interaction and pathway databases Networks annotation and curation High-throughput data visualization, analysis and interpretation in the context of networks Network modeling Basic research and clinical application of networks Audience: The workshop is suitable for wide audience as database providers, networks creators, computational and experimental biologists, clinicians and anyone who is interested to be ex posed to the different paradigms of network biology and the latest achievements in the field. Confirmed speakers: Lodewyk Wessels (Netherlands Cancer Institute, Amsterdam, Netherlands) Samik Ghosh (Systems Biology Institute, Tokyo, Japan) Andrei Zinovyev (Institut Curie, Paris, France) Mariko Okada ((RIKEN Center for Integrative Medical Sciences Yokohama, Japan) Yoshiyuki Asai (The Okinawa Institute of Science and Technology, Okinawa, Japan) BioNetVisA organizing committee: Inna Kuperstein (Institut Curie, France) Emmanuel Barillot (Institut Curie, France) Andrei Zinovyev (Institut Curie, France) Hiroaki Kitano (Okinawa Institute of Science and Technology Graduate University, RIKEN Center for Integrative Medical Sciences, Japan) Nicolas Le Novère (Babraham Institute, UK) Robin Haw (Ontario Institute for Cancer Research, Canada) Alfonso Valencia (Spanish National Bioinformatics Institute, Madrid, Stain) http://sysbio.curie.fr/bionetvisa

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Course: Intro to R (June 10-12, 2015), Maastricht University
by Viechtbauer Wolfgang (STAT) 11 Mar '15

11 Mar '15

Course: Introduction to R (June 10-12, 2015) Three-day course on R, covering the following topics: * History and Introduction to R * Data Structures, Functions, Basic Arithmetic, Data Manipulation * Working with Data and Command Files * Data Inspection and Summary Statistics * Graphs, Plots, and Tabulations * Statistical Methods: Continuous Data * Statistical Methods: Categorical and Time-to-Event Data * Finding, Installing, and Loading Additional Packages * Programming Structures and Flow Control * Generating Random Data and Monte Carlo Simulations * Generic, Method, and User-Written Functions * Advanced and Miscellaneous Topics The course is aimed at researchers, (Master and PhD level) students, data analysts/scientists, and essentially anybody interested in learning how to work with R. We use a mixture of lectures and hands-on exercises that provide ample opportunities for practicing the concepts taught. Course Dates: June 10-12, 2015 Course Location: Maastricht, The Netherlands (see course website for details) Registration Deadline: June 3, 2015 Course Fee: 600 Euros Please see the course website (http://www.wvbauer.com/course_r) for more details on the course location, instructors, schedule, and registration information. -- Wolfgang Viechtbauer, Ph.D., Statistician 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 +31 (43) 388-4170 | http://www.wvbauer.com

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