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VIB Upcoming Bioinformatics Training Sessions
by Alexander Botzki | VIB | 01 Oct '15

01 Oct '15

[VIB] [VIB] VIB Bioinformatics Training November sessions IN THIS ISSUE * Basic statistics in R, part II * Linux for bioinformatics * Mass spectrometry data processing Basic statistics in R, part II This training builds further on the Basic statistics in R<http://bits.cmail2.com/t/r-l-zldijdy-tylylroud-d/> training, showing you how to do statistical analyses in R. This training gives you a full overview of statistical analyses in R including: * distributions * plots * confidence intervals * regression * hypothesis testing: two sample tests, ANOVA.... . Required skills: Basic knowledge of R: data types, graphics... Date: 9 and 23 November, 9h30-17h00 Location: Fiers-Schell-Van Montagu building, Gent Trainer: Veronique Storme More information and registration: VIB website<http://bits.cmail2.com/t/r-l-zldijdy-tylylroud-h/> Linux for bioinformatics After this training you will: * feel comfortable using Linux * know how software works on Linux and how to use it * use bash to execute commands in Linux and know your way around the file system * have an overview of Linux tools that are extremely useful for bioinformatics Date: 13 and 16 November, 9h30-17h00 Location: Fiers-Schell-Van Montagu building, Gent Trainer: Joachim Jacob More information and registration: VIB website<http://bits.cmail2.com/t/r-l-zldijdy-tylylroud-k/> Mass spectrometry data processing During this training you will: * Obtain a good understanding of the origins and properties of mass spec data * Obtain an understanding of the processing of mass spec data, aimed at identifying peptides and proteins * Gain sufficient understanding of the software tools and database used, and of the issues and caveats involved, to critically analyse and assess results from mass spectrometry based proteomics experiments Required skills: Basic understanding of mass spectrometry as applied to peptides and proteins Date: 19 and 20 November, 9h30-17h00 Location: Fiers-Schell-Van Montagu building, Gent Trainers: Lennart Martens and Niels Hulstaert More information and registration: VIB website<http://bits.cmail2.com/t/r-l-zldijdy-tylylroud-u/> You receive this email because you work at VIB or you have expressed interest in our Bioinformatics training sessions. Feel free to forward this email to interested colleagues. If you do not want to receive this email anymore, you can unsubscribe here<http://bits.cmail2.com/t/r/u/zldijdy/tylylroud/r/>. -- _______________________________________________________ Gert Van Isterdael IRC Flow Core Facility Manager Unit of Immunoregulation and Mucosal Immunology VIB Inflammation Research Center, UGent 'Fiers-Schell-Van Montagu' building Technologiepark 927 B-9052 Ghent, Belgium Tel : +32-(0)93313754 or +32-(0)93313578 Fax : +32-(0)93313609 E-mail : gert.vanisterdael(a)irc.vib-ugent.be<mailto:gert.vanisterdael@irc.vib-ugent.be> URL : http://www.irc.UGent.be/ Twitter: @IRCFlowCore _______________________________________________________

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Benelux Bioinformatics Conference 2015 - Abstract submission deadline extended!
by Meysman Pieter 01 Oct '15

01 Oct '15

- Benelux Bioinformatics Conference 2015 - Abstract submission deadline extended due to popular demand! Abstract submission for oral and poster presentations is now open until October 7th, 2015. Follow the instructions provided here: http://bbc2015.be/submission.html Main conference Date: 7 - 8 december, 2015 Venue: Elzenveld, Lange Gasthuisstraat 45, Antwerpen, Belgium For more details on the program, check the website http://www.bbc2015.be. Register now at a reduced rate for the tenth anniversary edition of the Benelux Bioinformatics Conference in Antwerpen! http://bbc2015.be/registration.html Additionally you can register for the gala dinner on Monday December 7th, evening. This 4-course dinner takes place in the medieval basement of Pelgrom (http://www.pelgrom.be/) at walking distance from the conference venue and close to public transportation. BBC2015 Student Symposium RSG Belgium, RSG Netherlands, RSG Luxembourg and RSG France (JeBiF) are organising the adjacent BBC2015 Student Symposium on the 6th of December (the day before the BBC) in the Institute for Tropical Medicine in Antwerp. For more information on registration and abstract submission for this event: http://bbc2015.be/ss_about.html Key dates - 07/10/2015: Abstract submission deadline - 30/10/2015: Abstract acceptance notification - 04/11/2015: Early conference registration deadline - 30/11/2015: Late conference registration deadline - 06/12/2015: BBC Student Symposium - 07/12/2015 - 08/12/2015: Main conference takes place More information - website: www.bbc2015.be<http://www.bbc2015.be> - Twitter: @BBC2015AN - social media hashtag: #BBC2015AN - Linkedin group: http://linkd.in/1a4Gv1T - conference email: info(a)bbc2015.be<mailto:info@bbc2015.be> Gold sponsors [cid:39348392-FFB5-410B-BD43-AC02AE426152@ua.ac.be][cid:A7C6CF3A-9AE4-4B83-A478-767908F6EA32@ua.ac.be]

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The LUMC offers a position for a Scientific programmer/Senior sequence data analyst.
by J.F.J. Laros 29 Sep '15

29 Sep '15

Scientific programmer/Senior sequence data analyst Department : Department of Human Genetics Vacancy number : D.15.GJ.MV.18 Appointment : 36 hours per week Starting date : as soon as possible Educational requirements : bachelor Maximum salary : according to CLA for University Hospitals Closing date for applications : until the position is filled The position As a scientific programmer / (senior) sequence data analyst, you will conduct biomedical and clinical research in the LUMC by the analysis and interpretation of Next Generation Sequencing (NGS) data. You will develop and apply various analysis pipelines on large genome, exome and transcriptome data sets produced using advanced NGS technologies. You will contribute to the analysis and interpretation of data generated by novel NGS technologies such as Pacific Biosciences RSII single-molecule long read sequencing. Such projects can vary from characterizing full-length mRNA sequences to de novo characterization of fully phased variants in disease genes or de novo assembly and characterization of complex genomes or genomic regions. Other responsibilities include the integration of various omics datasets, such as exome-, transcriptome and chromatin immunoprecipitation sequencing data. This position will require and promote close collaboration with scientists from various fields. For more information, see the full description on the LUMC website [1]. References: [1] https://www.lumc.nl/over-het-lumc/werken-bij/vacatures-solliciteren/researc…

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Invitation to participate in the Life Sciences with Industry 2015 Lorentz workshop
by Celia.vanGelder＠radboudumc.nl 29 Sep '15

29 Sep '15

Invitation to participate in the Life Sciences with Industry 2015 Lorentz workshop Leiden, November 16 - 20, 2015 We invite PhD students and postdocs from all branches of the life sciences that like to participate in the one-week Life Sciences with Industry 2015 Lorentz workshop in Leiden: November 16 – 20, 2015. During the workshop, the about 40 participants tackle in groups of eight six scientifically challenging and commercially important problems formulated by six companies. The workshop will take place in Leiden in the building of the Lorentz Center, an organisation that is specialised in organising scientific workshops (http://www.lorentzcenter.nl/) To create multi-disciplinary teams, participants will be selected based on their (i) specific background in the life sciences, (ii) motivation to participate, and (iii) date of registration. Registration on the workshop website: http://www.lorentzcenter.nl/lc/web/2015/762/info.php3?wsid=762&venue=Oort Deadline: Sunday October 18, 2015. Participation is free of charge, including hotel accommodation during the workshop. Also lunches and two workshop dinners are covered. The workshop is sponsored by the Lorentz Center, the Research School BioSB (http://biosb.nl/) STW (http://www.stw.nl/) and the companies involved. Need more information? Contact Yousra Jaddour at the Lorentz Center: jaddour(a)lorentzcenter.nl<mailto:jaddour@lorentzcenter.nl> or +31-71-527 5578. The organisers Dr. Ellen Feddes (STW) Dr. Gökhan Ertaylan (MaCSBio, Maastricht University) Dr. Jurgen R. Haanstra (VU University Amsterdam) prof. em. Dr. Roel van Driel (University of Amsterdam) ********************************************************************* Six industrial challenges Life Sciences with Industry 2015 1. New possibilities for developing disease-resistant plants Bejo Zaden B.V. (www.bejo.nl<http://www.bejo.nl>) 2. Technologies to modulate galactosylation and fucosylation in human antibodies production in clonal cell lines Bioceros B.V. (www.bioceros.com<http://www.bioceros.com>) 3. Isolation of phospholipids from fresh cow milk Nutricia Danone (www.nutricia.nl/<http://www.nutricia.nl/>) 4. Applications of a novel low-cost/disposable high resolution and sensitive detector in health and biotechnology NXP Semiconductors B.V. (www.nxp.com<http://www.nxp.com>) 5. Quantifying the quality of light for human-centric lighting solutions: how to objectively measure (visual) comfort and well-being Philips Research (www.research.philips.com<http://www.research.philips.com>) 6. Automated 3D imaging and analysis systems to measure plant volume and other critical parameters of seed germination and seedling establishment Syngenta (www3.syngenta.com/country/nl/nl/Pages/home.aspx<http://www3.syngenta.com/country/nl/nl/Pages/home.aspx>) 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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The NIOO-KNAW offers a post-doc position for a Bioinformatician / Quantitative Ecologist
by Mattias de Hollander 28 Sep '15

28 Sep '15

The NIOO-KNAW offers a position for a *Bioinformatician / Quantitative Ecologist – post-doc* *Project description* The key question this project addresses is to what extend open access data, now often required by journals to be deposited in data repositories such as Dryad, can be used in meta-analysis. What are the pitfalls and what are the advantages over traditional meta-analysis? To explore this question the post-doc will closely collaborate with a number of researchers from all four departments at the NIOO. These researchers will carry out meta-analyses to answer a range of ecological questions (such as “How do richness patterns relate to environmental C:N:P stoichiometry across kingdoms and ecosystems?”, “Is rarity (type) phylogenetically conserved among microbes?” and “Does additive genetic variation in traits, and thereby the potential for evolutionary responses, vary with environmental conditions?”). The post-doc will support these analyses and use the experiences as input to address the key-question of this project, which should result in a methodological paper. The post-doc will thus play a central role in a small group of enthusiastic ecologists to explore a potentially new ‘niche’ in ecological research methods. *Requirements* We are looking for a highly motivated and enthusiastic person with a PhD in bioinformatics or ecology and experienced in working with large datasets (‘big data’) and preferably with meta-analysis. Affinity with ecological research is a pre-requisite, as well as the ability to work in a team. More info: https://nioo.knaw.nl/nl/vacatures/bioinformatician-quantitative-ecologist-%…

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TPNC 2015: call for posters
by GRLMC 25 Sep '15

25 Sep '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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matlab cursus in Wageningen
by Stigter, Hans 25 Sep '15

25 Sep '15

Beste, Onderstaand wil ik graag aankondigen via de bbc mailing list. Met dank alvast + vriendelijke groet, Hans Stigter (Biometris, Wageningen UR). BioSB Course Matlab, 20 October 2015, Wageningen Website: http://biosb.nl/education/course-portfolio-2/course-matlab/ . Coordinators: Hans Stigter (WUR), Celia van Gelder (BioSB, celia.van.gelder(a)biosb.nl<mailto:celia.van.gelder@biosb.nl>) Registration: http://biosb.nl/education/course-portfolio-2/course-matlab/enrollment-cours… Please note that if you are (or become) a member of BioSB this course is free of charge for PhD students and with reduced fee for other researchers! Goal The main goal of this course is to get acquainted with Matlab software for use within Systems Biology. After this introductory course you will have gained the basic knowledge to pursue further use via self-study of Matlab in order to apply more advanced programming techniques within Matlab in your own research. In summary, the sub-goals are: 1. To learn the philosophy behind Matlab and its syntax 2. To program simple Systems Biology models in Matlab (in ordinary differential equation format) and to solve these differential equations with Matlab Programme 09:45 Coffee/Tea 10:00 Welcome 10:05 Introduction Matlab Basics (functions, variables, matrices, etc) 10:45 Advanced Programming (vectorised thinking, solving dynamic ordinary differential equation models in Matlab, parameter estimation for ODE-models) 12:00 Afternoon: Solving basic and advanced problems in Matlab - hands-on experience on a PC. Exercises will be provided, but you can also bring your own problems that you have encountered in your own research. 12:30 Lunch 15:00 Coffee/tea 16:30 End Target audience Primarily targeting researchers from academia, but participants from the private sector are also welcome. The course focusses on the use of Matlab for building dynamic Systems Biology Models in terms of ordinary differential equations. Course Description This is a one-day introduction to the possibilities of Matlab as a programming environment for simulation and analysis of biological models. We will start with a simple introduction of the basics of Matlab (matrices, vectors, manipulation of matrices and presentation of data). Having obtained some basic programming knowledge (writing of simple scripts and functions in Matlab), we will move on to more advanced topics. These include programming and solving ordinary differential equation models (ODEs) and the concept of "vectorized thinking" while writing Matlab-code. Finally, calibration of parameters in ODE type of models using measured data will be discussed and examples will be given. The course also includes the basics of presenting your results (graphing) in various types of plots that can easily be drawn in Matlab. Participants will, of course, get hands-on experience with Matlab and write code themselves in a practical. 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<http://www.biosb.nl/> or via education(a)biosb.nl<mailto:education@biosb.nl>.

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Software developers / sys admins
by Anna Leinfelt 24 Sep '15

24 Sep '15

Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology Are you looking for a position where your work makes life-changing, real-world impact? We are now looking for 1-2 software developers / sys admins who can help us bring genomics-based technologies to routine clinical use in Sweden. The *Clinical Genomics *unit is a national research infrastructure at SciLifeLab in Stockholm. Together with caregivers in Sweden, we aim to make advanced clinical tests based on massively parallel DNA sequencing an integrated part of the routine diagnostics in the healthcare sector. Our mission is to ensure that the diagnostics offered in Sweden is at the international forefront. Clinical Genomics today consists of 12 employees and works in close collaboration with other researchers at SciLifeLab and with the healthcare system. We have a technical state-of-the-art capability to carry out NGS, including MiSeq, HiSeq 2500 and HiSeq X instrumentation and an automated library preparation capability. We are now looking for talented, highly motivated bioinformaticians to join the team. Those appointed will be expected to work with clinicians, geneticists, software developers, programmers and molecular biologists. We can offer a creative environment where the mission is to improve the patient management by moving towards personalised medicine, exciting work tasks, and a team spirit aiding us to more quickly achieve our common goals. On the technical level our work is highly competitive at the international level; we actively work to test the boundaries and develop our bioinformatic tools and services further. You are a careful and detail oriented person, not afraid of taking responsibility, and you appreciate working with the latest technology in a rapidly developing field. You have a strong desire to further develop the service offerings and solve problems where and when they arise. Primary duties - Automation and surveillance of data transfers and analysis pipelines - Development and maintenance of internal information databases - Development and maintenance of solutions for visualizations of processes and results - Development of tools supporting clinical decision making General qualifications (software developers and sys admins) - Excellent programming skills in foremost Python - Git and version control - Solid UNIX competency, Bash - Familiar with databases, both SQL and alternatives - Fluency in English - Personal qualifications that enhance collaboration internally and externally / team spirit, excellent communication skills Additional meriting qualifications for software development position - Familiar with software testing, meriting if continuous integration, Travis CI - Web development, HTML5 including JS, REST APIs. Meriting if Bootstrap, Flask experience - Agile development, pair programming - Open source development experience Additional meriting qualifications for sys admin position - Cluster management, highly meriting if SLURM - Hardware acquisition - Automation of data transfers and analysis pipelines - Ansible provisioning - Interest in Docker/container technologies - Functional languages, low level languages, Java Application deadline is Oct 30, 2015. Please apply early; interviews will be held throughout the application period. The positions are full time. A probationary period of 6 months will be applied. The application is to be submitted through the MyNetwork system. In your application letter, please also clearly explain your motivation for applying for one of the positions. The position will formally be at the Department of Microbiology, Tumour and Cell biology at KI. All work is carried out at SciLifeLab. Science for Life Laboratory (SciLifeLab) is a national center for large-scale life science research. Our aim is to enable researchers in Sweden to decipher molecular mechanisms relating to health and environment. Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 per cent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. Pursuant to the regulations of the Swedish National Archives, applications are kept on file for two years after the appointment has gained legal force. The regulations do not apply to attachments that have been printed or otherwise published. Karolinska Institutet strives to provide a workplace that has approximately the same number of women and men, is free of discrimination and offers equal opportunity to everyone. For temp agencies and recruiters, and to salespersons: We politely, yet firmly, decline direct contact with temp agencies and recruiters, as well as those selling additional job announcements. Type of employmentProbationary periodWorking hoursFull timeFirst day of employmentAccording to agreementSalaryMonthly salaryNumber of positions1Working hours100%CitySolnaCountyStockholms länCountrySwedenReference number 2-3386/2015Contact - Valtteri Wirta, valtteri.wirta(a)scilifelab.se Union representative - Cecilia Björkdahl, SACO , 08-524 872 65 - Torbjörn Laggar, OFR, 08-524 862 12 - Gunnar Stenberg, SEKO, 08-524 880 75 Published23.Sep.2015Last application date30.Oct.2015 11:59 PM CET

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Bioinformaticians
by Anna Leinfelt 24 Sep '15

24 Sep '15

Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology Are you looking for a position where your work makes life-changing, real-world impact? We are now looking for 1-2 bioinformaticians who can help us bring genomics-based technologies to routine clinical use in Sweden. The *Clinical Genomics *unit is a national research infrastructure at SciLifeLab in Stockholm. Together with caregivers in Sweden, we aim to make advanced clinical tests based on massively parallel DNA sequencing an integrated part of the routine diagnostics in the healthcare sector. Our mission is to ensure that the diagnostics offered in Sweden is at the international forefront. Clinical Genomics today consists of 12 employees and works in close collaboration with other researchers at SciLifeLab and with the healthcare system. We have a technical state-of-the-art capability to carry out NGS, including MiSeq, HiSeq 2500 and HiSeq X instrumentation and an automated library preparation capability. We are now looking for talented, highly motivated bioinformaticians to join the team. Those appointed will be expected to work with clinicians, geneticists, software developers, programmers and molecular biologists. We can offer a creative environment where the mission is to improve the patient management by moving towards personalised medicine, exciting work tasks, and a team spirit aiding us to more quickly achieve our common goals. On the technical level our work is highly competitive at the international level; we actively work to test the boundaries and develop our bioinformatic tools and services further. You are a careful and detail oriented person, not afraid of taking responsibility, and you appreciate working with the latest technology in a rapidly developing field. You have a strong desire to further develop the service offerings and solve problems where and when they arise. Primary duties - Development of analysis tools and strategies for clinical NGS data - Establish and continuously improve analysis pipelines - Engage in discussions with scientists and health care professionals for translating NGS into routine clinical use Qualifications - M.Sc. degree in a field related to the position (eg maths, physics or computer-science) or comparable documented experience - Excellent programming skills in foremost Python - Experience of using Linux/UNIX systems - Experience using version control software, such as git - Fluency in English Experience (meriting) - Familiar with NGS data and analysis of biological data - Software development - Bash, Java and other programming languages - Experience with databases - Personal qualifications that enhance collaboration internally and externally / team spirit, excellent communication skills Application deadline is Oct 30, 2015. Please apply early; interviews will be held throughout the application period. Both positions are full time. A probationary period of 6 months will be applied. The application is to be submitted through the MyNetwork system. In your application letter, please also clearly explain your motivation for applying for one of the positions. The position will formally be at the Department of Microbiology, Tumour and Cell biology at KI. All work is carried out at SciLifeLab. Science for Life Laboratory (SciLifeLab) is a national center for large-scale life science research. Our aim is to enable researchers in Sweden to decipher molecular mechanisms relating to health and environment. Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 per cent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. Pursuant to the regulations of the Swedish National Archives, applications are kept on file for two years after the appointment has gained legal force. The regulations do not apply to attachments that have been printed or otherwise published. Karolinska Institutet strives to provide a workplace that has approximately the same number of women and men, is free of discrimination and offers equal opportunity to everyone. For temp agencies and recruiters, and to salespersons: We politely, yet firmly, decline direct contact with temp agencies and recruiters, as well as those selling additional job announcements. Type of employmentProbationary periodWorking hoursFull timeFirst day of employmentAccording to agreementSalaryMonthly salaryNumber of positions1Working hours100%CitySolnaCountyStockholms länCountrySwedenReference number 2-3384/2015Contact - Valtteri Wirta, valtteri.wirta(a)scilifelab.se Union representative - Cecilia Björkdahl, SACO , 08-524 872 65 - Torbjörn Laggar, OFR, 08-524 862 12 - Gunnar Stenberg, SEKO, 08-524 880 75 Published23.Sep.2015Last application date30.Oct.2015 11:59 PM CET

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AIMMS post-graduate course 19-23 Oct 2015 Biomolecular Modelling at VU University
by Barbara.vanKampen＠radboudumc.nl 24 Sep '15

24 Sep '15

>From 19 - 23 October 2015, the AIMMS postgraduate "Practical Course in Biomolecular Modelling" will run, with hands-on tutorials and morning lectures by Wilfred van Gunsteren, Sereina Riniker, Daan Geerke and Chris de Graaf. Please check out further information and the programme at http://www.aimms.vu.nl/en/news-events/events/2015/2015-10-19-aimms-post-gra… ; registration via the website is still possible (until 29 September). Sincerely, Nico Vermeulen, Director AIMMS (Amsterdam Institute for Molecules, Medicines and Systems) Ellen Langemeijer, Managing director Email: info(a)aimms.vu.nl<mailto:info@aimms.vu.nl> Website: www.aimms.vu.nl<http://td35.tripolis.com/public/r/xHth1K_uUUd0pgJA4ZKciA/-/-> _________________________________________________________________________________________________________________________________________________________________________________ This message is sent to you via the NSBM mailinglist 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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