- BBClist - maillist.psb.ugent.be

Programming for Evolutionary Biology Summer School, 10-27 Feb 2016, Leipzig, Germany
by Bert Overduin 06 Nov '15

06 Nov '15

Forwarding this on behalf of a friend. This is a very intensive course in which I have taught several times myself and that I can recommend very highly. Please feel free to forward this mail to anyone potentially interested. Cheers, Bert ********** Course on Programming for Evolutionary Biology When: February 10th - February 27th 2016 Location: Leipzig, Germany Application deadline: December 20th 2015 Detailed information about the course content and how to apply: http://evop.bioinf.uni-leipzig.de/ In this intensive 18 days course, students will learn how to survive in a Linux environment, get hands-on experience in two widely used programming languages (Python and R), and statistical data analysis. The classes will be given by experts in the field and consist of lectures and exercises with the computer. The aim of the course is to provide the students with the necessary background and skills to perform computational analyses with a focus on solving research questions related to genomics and evolution. The philosophy of the course will be “learning by doing”, which means that the computational skills will be taught using examples and real data from evolutionary biology for the exercises. During the course, students will also propose projects of their own interest and perform them as final projects in small groups under the supervision of a teaching assistant. This summer school is open for students from all countries and targeted toward PhD students and postdocs of evolutionary biology or related research fields with no or little programming experience who want to become proficient in computational evolutionary biology in a couple of weeks. The course takes place at the University of Leipzig. -- Dr. Katja Nowick Group Leader "TFome and Transcriptome Evolution" www.nowick-lab.info Universität Leipzig Härtelstrasse 16-18 04107 Leipzig Germany Phone 1: +49 341 97-16684 Phone 2: +49 341 97-16653 Fax: +49 341 97-16679 ********** -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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One-day symposium on in-silico drug design, Nov 30th 2015
by Marc Lensink 05 Nov '15

05 Nov '15

I should've specified the date: Nov 30th (it's on the website) cheers, marc ----- Forwarded message from Marc Lensink <marc.lensink(a)univ-lille1.fr> ----- Date: Thu, 5 Nov 2015 10:59:44 +0100 From: Marc Lensink <marc.lensink(a)univ-lille1.fr> To: BeNeLux bioinformatics forum <bbclist(a)psb.vib-ugent.be> Subject: [BBC] One-day symposium on in-silico drug design Dear colleagues, The Lille bioinformatics platform, bilille, is organizing a one-day symposium on the use of molecular modeling for computer-aided drug design. Recent years have seen a rapid development of molecular modeling and docking techniques in combination with high-throughput protein crystallography. These novel methods have allowed many a success story in the computer-assisted discovery of new drugs and has helped structure-based drug design to become increasingly effective in the development of target-based therapies. During this one-day symposium, a panel of experts will introduce, discuss and illustrate these techniques. The meeting will be held at the lecture hall of Campus CNRS Haute Borne in Villeneuve d'Ascq, next to Lille, France. Confirmed speakers are: * Martine Prevost - Université Libre de Bruxelles * Eric Henon - Université de Reims * Anna Gaulton - EMBL * Philippe Chavatte - Faculté de Pharmacie, Université de Lille * Henriette Willems - Takeda Cambridge * Jerome de Ruyck - UGSF, Université de Lille http://www.cristal.univ-lille.fr/~htouzet/bilille/drug_design.html There is no registration fee, but registration is required for participation. The number of places is limited. Lunch is offered. For more information, send an e-mail to any member of the organizing committee (marc.lensink, guillaume.brysbaert or helene.touzet, all @univ-lille1.fr) cheers, Marc -- Marc F Lensink, CR1, PhD marc.lensink(a)univ-lille1.fr University Lille, CNRS UMR8576 UGSF, FRABio FR 3688 Parc de la Haute Borne, 50 Avenue de Halley, BP 70478 F-59658 Villeneuve d'Ascq, France tel: +33 3 62 53 17 28 fax: +33 3 62 53 17 01 _______________________________________________ BBClist mailing list BBClist(a)psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/bbclist ----- End forwarded message ----- -- Marc F Lensink, CR1, PhD marc.lensink(a)univ-lille1.fr University Lille, CNRS UMR8576 UGSF, FRABio FR 3688 Parc de la Haute Borne, 50 Avenue de Halley, BP 70478 F-59658 Villeneuve d'Ascq, France tel: +33 3 62 53 17 28 fax: +33 3 62 53 17 01

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One-day symposium on in-silico drug design
by Marc Lensink 05 Nov '15

05 Nov '15

Dear colleagues, The Lille bioinformatics platform, bilille, is organizing a one-day symposium on the use of molecular modeling for computer-aided drug design. Recent years have seen a rapid development of molecular modeling and docking techniques in combination with high-throughput protein crystallography. These novel methods have allowed many a success story in the computer-assisted discovery of new drugs and has helped structure-based drug design to become increasingly effective in the development of target-based therapies. During this one-day symposium, a panel of experts will introduce, discuss and illustrate these techniques. The meeting will be held at the lecture hall of Campus CNRS Haute Borne in Villeneuve d'Ascq, next to Lille, France. Confirmed speakers are: * Martine Prevost - Université Libre de Bruxelles * Eric Henon - Université de Reims * Anna Gaulton - EMBL * Philippe Chavatte - Faculté de Pharmacie, Université de Lille * Henriette Willems - Takeda Cambridge * Jerome de Ruyck - UGSF, Université de Lille http://www.cristal.univ-lille.fr/~htouzet/bilille/drug_design.html There is no registration fee, but registration is required for participation. The number of places is limited. Lunch is offered. For more information, send an e-mail to any member of the organizing committee (marc.lensink, guillaume.brysbaert or helene.touzet, all @univ-lille1.fr) cheers, Marc -- Marc F Lensink, CR1, PhD marc.lensink(a)univ-lille1.fr University Lille, CNRS UMR8576 UGSF, FRABio FR 3688 Parc de la Haute Borne, 50 Avenue de Halley, BP 70478 F-59658 Villeneuve d'Ascq, France tel: +33 3 62 53 17 28 fax: +33 3 62 53 17 01

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[Gtpb] Corrected date: Introductory Bioinformatics Training Course IB15S - Announcement
by Pedro Fernandes 05 Nov '15

05 Nov '15

Dear all, Sorry for the mistake in our previous post. IB15F Introductory Bioinformatics our entry level course with a soft introduction to NGS data analysis Course date: December 14th - December 18th 2015 Now edited: The Applications for the Introductory Bioinformatics course, second instance in the 2015 Programme, are now OPEN. IMPORTANT DATES for this Course Deadline for applications: December 9th 2015 Latest notification of acceptance: December 10th 2015 Course date: December 14th - December 18th 2015 Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/IB15S/ This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. Important NOTE: This is one of our most popular courses. It usually gets full very quickly. Applications are approved and accepted in order of arrival and we only have 20 seats. 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 _______________________________________________ Research mailing list Research(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/research _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] Introductory Bioinformatics Training Course IB15S - Announcement
by Pedro Fernandes 04 Nov '15

04 Nov '15

Dear all, The Applications for the Introductory Bioinformatics course, second instance in the 2015 Programme, are now OPEN. IMPORTANT DATES for this Course Deadline for applications: December 9th 2015 Latest notification of acceptance: December 10th 2015 Course date: December 14th - April 18th 2015 Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/IB15S/ This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. Important NOTE: This is one of our most popular courses. It usually gets full very quickly. Applications are approved and accepted in order of arrival and we only have 20 seats. 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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Benelux Bioinformatics Conference 2015: last chance for early registration!
by Laukens Kris 02 Nov '15

02 Nov '15

- Benelux Bioinformatics Conference 2015 - 48 hours left for early registration - The University of Antwerp is proud to welcome you to the Benelux Bioinformatics Conference 2015 (BBC 2015). The BBC 2015 will take place at Elzenveld in the heart of Antwerp, on 7-8 December 2015. With this message we would like to inform you that the deadline for early registration is rapidly approaching: november 4. Register now at reduced rate! More information about registration: http://bbc2015.be/registration.html Abstract submission for oral presentations is closed. The list of accepted oral presentations is available at the program page. The full time schedule will be posted in a few days. http://bbc2015.be/programme.html We do however still accept late poster abstracts. To submit a late poster abstract, proceed to the submissions page and follow the instructions: http://bbc2015.be/submission.html See you in Antwerpen, 7 and 8 december! The organising committee. Gold sponsors: [cid:39348392-FFB5-410B-BD43-AC02AE426152@ua.ac.be][cid:A7C6CF3A-9AE4-4B83-A478-767908F6EA32@ua.ac.be]

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job opportunities: Bioinformatics Tool Developers
by Alexander Botzki | VIB | 31 Oct '15

31 Oct '15

Dear all, We are happy to announce the opening of two positions at VIB. Bioinformatics Tool Developers VIB is looking to expand its institute-wide bioinformatics platform, BITS<http://www.bits.vib.be/>, with two bioinformatics tool developers to enhance and integrate VIB's flagship bioinformatics tools such as PLAZA<http://plaza.psb.ugent.be/>, iceLogo<http://iomics.ugent.be/icelogoserver/index.html> and SNPEffect<http://snpeffect.switchlab.org/>. We are looking for dedicated individuals to join the BITS team in Ghent who will jointly work in projects for several Bioinformatics groups at VIB (http://www.vib.be/en/research/scientists/Pages/default.aspx?category=Bioinf…) The candidate needs to have outstanding communication skills to establish a close working relationship with the bioinformaticians and developers within the VIB departments and the staff of the BITS core facility. The candidate will split his/her time between various VIB BioIT groups and may be required to travel to all VIB sites (Ghent, Leuven, Brussels, Antwerp, and Hasselt). The close relationship within VIB's BioIT community will allow the integration of cutting edge bioinformatics solutions aiming at higher visibility of VIB's bioinformatics achievements. You will participate actively in computational aspects of VIB's research projects which focus on the molecular mechanisms that are responsible for the functioning of the human body, plants, and microorganisms. The responsibilities include: * continued development, maintenance, testing and evaluation of VIB's computational biology tools (often written in different programming environments) * enable relevant VIB software to be maintained long-term * make "developed @ VIB" a mark of excellence and reliability * provide an interface between BITS and the bioinformatics community at VIB More information on the BITS and the VIB Bio Community can be found at: https://corefacilities.vib.be/bits and https://www.bits.vib.be/bioit-at-vib Profile * Master in computer science, bioscience engineering or equivalent * Knowledgeable of W3C standards and best practices in web development * Experience in programming (e.g. Python, Perl, PHP, Javascript), version control * Good working knowledge of databases and SQL * High level of competency with Python is an asset * Experience of working with Linux/unix environments and scripting * Track record of relevant experience in software development would be an asset * Excellent communication skills * Interest in applied biological research is a must, experience an asset * Solution-oriented attitude, able to work independently as well as in a team * Fluent in English Benefits: * Start date: as soon as possible * Duration: 2 year, possibility to extend upon evaluation * International environment in an academic context * A challenging and stimulating work environment, at the edge of IT technologies and the latest research innovations Please apply online on this web site<http://www.vib.be/en/jobs/Pages/Bioinformatics-Tool-Developers.aspx>. Best regards, Alex Alexander Botzki Manager BITS Core Facility Training coordinator ELIXIR-BE VIB BITS http://www.bits.vib.be Rijvisschestraat 126 9052 Zwijnaarde Belgium

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TPNC 2015: posters deadline 8 November
by GRLMC 31 Oct '15

31 Oct '15

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* **************************************************************************************** The 4th International Conference on the Theory and Practice of Natural Computing (TPNC 2015) invites authors to submit poster presentations. TPNC 2015 will be held in Mieres (Spain) on 15-16 December, 2015. See http://grammars.grlmc.com/tpnc2015/ Poster presentations are intended to enhance informal interactions with the conference participants, at the same time allowing for in-depth discussion. TOPICS Authors are encouraged to submit presentations displaying novel work in progress on: - nature-inspired models of computation, - synthesizing nature by means of computation, - nature-inspired materials, - information processing in nature, - applications of natural computing. Posters do not need to show final research results. Work that might lead to new interesting developments is welcome. KEY DATES Submission deadline: November 8, 2015 Notification of poster acceptance or rejection: November 15, 2015 SUBMISSION Please submit a .pdf abstract through: https://www.easychair.org/conferences/?conf=tpnc2015 It should contain the title, author(s) and affiliation, and should not exceed 500 words. PRESENTATION Posters will be allocated 10 minutes each in the programme for oral presentation. Moreover, they will remain hanging out during the whole conference for discussion. PUBLICATION Posters will not appear in the LNCS proceedings volume of TPNC 2015. However, they will be eligible for submission to the post-conference journal special issue in Soft Computing (Springer). REGISTRATION At least one author of each accepted poster must register to the conference. Their registration fare is reduced: 225 Euro (appr. half of the cheapest fare for regular participants). Contributors of regular papers who in addition get a poster accepted must register for the latter too.

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ECCB 2016: Save the date & Call for workshops/SIGs and tutorials
by Femke Francissen 30 Oct '15

30 Oct '15

*-------------------------------------------------------------------------------------------------------* *15th European Conference on Computational Biology (ECCB 2016)* *3-7 September 2016* World Forum Convention Center The Hague, The Netherlands Website: http://www.eccb2016.org/ ------------------------------------------------------------------------------------------------------- *Save the date & Call for workshops and tutorials* We would like to invite you to the 15th edition of the European Conference on Computational Biology (ECCB 2016) that will be held on 3-7 September 2016 in the historic city of The Hague in the Netherlands. The venue will be the World Forum. ECCB 2016 is the main European computational biology and bioinformatics conference, gathering over 1,000 scientists from a broad range of disciplines: e.g. molecular biology, molecular medicine, biophysics, biostatistics, systems biology. *Call for workshops and tutorials* You can now submit a proposal for a workshop or a tutorial at the ECCB 2016. The workshops and tutorials are planned on September 3 and 4, 2016 in the World Forum in The Hague, immediately preceding the ECCB 2016. *Deadline for proposal submission is: January 13, 2016.* *Workshops / SIGs* The workshops are expected to provide participants with an informal setting to discuss technical issues, exchange research ideas, and to share practical experiences on a range of focused or emerging topics in bioinformatics. SIGs are workshops organized by a special interest group. Each workshop should provide an interesting perspective on the cutting edge of a selected research field. Workshops may include any form of presentation such as talks or panel discussions. Read more <http://www.eccb2016.org/calls/workshops/> *Tutorials* The purpose of the tutorial program is to provide participants with lectures and hands-on training covering topics relevant to the field of bioinformatics. Each tutorial will offer participants an opportunity to learn about new areas of bioinformatics research, to get an introduction to important established topics, or to develop advanced skills in areas they are already familiar with. This call is an invitation for scientists and professionals working in the fields of bioinformatics and computational biology to submit proposals for high quality tutorials for ECCB 2016. Read more <http://www.eccb2016.org/calls/tutorials/> *Keynote speaker* Our first confirmed keynote speaker is Professor Hans Clevers (Princess Maxima Center for pediatric oncology). He won several awards including the Dutch Spinoza Award (2001). From 2012-2015 he was President of the Royal Netherlands Academy of Arts and Sciences (KNAW). Read more <http://www.eccb2016.org/speakers/hans-clever/> *Sponsor options* Exclusive platinum sponsorship still available! The platinum sponsorship package (cost: 15,000 €) is the premier sponsorship package for the ECCB 2016 with exclusive sponsor opportunities. The sponsor logo will be featured prominently on all conference materials, and the Platinum Sponsor will be referred to in all communication prior to the event. This is an excellent way to ensure that your brand reaches thousands of scientists, policy makers and other stakeholders. *Special offer for startup companies* We offer startup companies the Startup Booth Package for only 600 €, it is the possibility to introduce your company to a wide audience from Europe and beyond. Have a look at the leaflet <http://www.eccb2016.org/wp-content/uploads/2015/10/Startup-Booth-leaflet.pdf> . *Original ways to sponsor ECCB 2016!* Your logo on chocolates during coffee breaks, or on t-shirts during the morning run? Have a look at our sponsor brochure for the sponsor options. Should you have an original idea that is not included in the brochure, we are open to suggestions so please feel free to get in touch with us! Read more <http://www.eccb2016.org/sponsoring/> The conference is hosted by: BioSB research school <http://www.biosb.nl>, Dutch Techcentre for Life Sciences <http://www.dtls.nl> and co-organised by: Vrije Universiteit Amsterdam, Delft University of Technology Contact: info(a)eccb2016.org

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BioSB Course Discovering Systems Biology Principles, 23-27 November 2015, Amsterdam
by Femke Francissen 30 Oct '15

30 Oct '15

*BioSB Course Discovering Systems Biology Principles, 23-27 November 2015, Amsterdam* *Website:* http://biosb.nl/education/course-portfolio-2/course-discovering-systems-bio… *Coordinators:* Frank Bruggeman (VU), Celia van Gelder (BioSB, celia.van.gelder(a)biosb.nl) *Registration: * http://biosb.nl/education/course-portfolio-2/course-discovering-systems-bio… . *Please note that this course is free of charge for PhDs who are or will become a member of the BioSB research school, and with a reduced fee for other researchers who are or will become a member of BioSB. *More information about the BioSB membership can be found here: http://biosb.nl/about/members/biosb-membership-information/ . *Course description* A large part of systems biology is concerned with studying how the molecular networks inside living cells function. What they do. How their molecular interactions, including feedback circuitry, give rise to cellular properties, such as sensing, adaptation, division and death, that transcend those of single molecules. This includes figuring out how gene mutations, causing changes in proteins, cause networks, and their cellular hosts, to malfunction. In order to do this, systems biology focusses on the dynamics of molecular networks, using quantitative experiments and mathematical modeling. Mathematical models help systems biologists to figure out: i. how molecular properties relate to the functional, systemic properties of molecular networks, and ii. how molecular networks assist in the survival and functioning of cells. This 1-week course serves as an introduction to mathematical modeling as it is used in systems biology. *Target audience* This course does not require any introductory reading or courses, it should be accessible to students with diverse backgrounds. *Course programme* We start from physical and chemical principles of molecules, cells and reactions. Next, you will learn how you can relate the changes in the concentrations of molecules over time to the activity of reactions and the underlying molecular properties. You will be introduced to enzyme kinetics and the dynamics of small enzyme systems, in metabolism and signal transduction. We also briefly deal with models of genetic circuits. We will illustrate a number of unexpected, functional properties of molecular networks that can be studied with simple mathematical models. You will make and analyse models yourself, on paper and with software. We will close the week with a short overview of some more advanced topics, to introduce you to approaches and concepts that you will often hear about in systems biology. The course material concerns a syllabus (with exercises and answers), handouts, and computer exercises. At the end of this 1-week course, you will have a good understanding how mathematical models are made, what biology they require and how you can use them in systems-biology research. *Course schedule* *Monday, Nov 23* 09:30-10:30 Diffusion 11:00-12:30 Diffusion 13:30-15:00 Mass balances and kinetics 15:30-17:00 Mass balances and kinetics *Tuesday, Nov 24* 09:30-10:30 Mathematica or JWS online, basics 11:00-12:30 Mathematica or JWS online, basics 13:30-15:00 Simulating differential equation models 15:30-17:00 Simulating differential equation models *Wednesday, Nov 25* 09:30-10:30 Enzyme kinetics 11:00-12:30 Enzyme kinetics 13:30-15:00 Rate characteristics 15:30-17:00 Supply demand theory and ultrasensitivity *Thursday, Nov 26* 09:30-12:30 Cool systems: kinetic proofreading, TF-DNA search, robustness, fold-change detection, optimal gene expression 13:30-17:00 Making models in JWS online or Mathematica *Friday, Nov 27* 09:30-10:30 Stoichiometric analysis, N, K, L 11:00-12:30 Flux balance analysis 13:30-15:00 Stability analysis, phase-plane analysis 15:30-17:00 Bistability and oscillations with JWS Online or Mathematica *BioSB Education Programme* This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl or via education(a)biosb.nl.

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