- BBClist - maillist.psb.ugent.be

Fwd: help me to find a good bioinformatician
by Stephane Rombauts 18 May '17

18 May '17

> From: "Walter Sanseverino" <wsanseverino(a)sequentiabiotech.com> > Sent: Wednesday, May 17, 2017 5:02:54 PM > Subject: help me to find a good bioinformatician > Hi guys, > I hope to find you well. > Please help me, we are looking a talented young bioinformatician. > thank you > Walter > Walter Sanseverino, PhD > Executive Director, Sequentia Biotech > Parc Cientific de Barcelona > Torre R 02A6/A7 > c/ Baldiri Reixac 4-8 > 08028 Barcelona > +34930107368 > [ http://www.sequentiabiotech.com/ | www.sequentiabiotech.com ] > LinkedIn: Follow Sequentia [ > https://www.linkedin.com/company/3068832?trk=tyah&trkInfo=tarId:14116362001… > | here ] > This message is intended exclusively for its addressee and may contain > information considered CONFIDENTIAL and protected by professional privilege. If > you are not the intended recipient you are hereby notified that any > dissemination, copy or disclosure of this communication is strictly prohibited > by law. If this message has been mistakenly received, please immediately notify > us via e-mail and delete it. > La información contenida en la presente transmisión es confidencial y su uso > únicamente está permitido a su(s) destinatario(s). Si Ud. no es la persona > destinataria de la presente transmisión, rogamos nos lo comunique de manera > inmediata por teléfono +34 935636600 y destruya cualquier copia de la misma > (tanto digitales como en papel). De conformidad con la Ley 15/99 Sequentia > Biotech S.L. le informa que los datos personales que facilite serán > incorporados a ficheros del que somos responsables y destinatarios y que tienen > por finalidad mantener las relaciones con Vd. Puede ejercer sus derechos de > acceso, rectificación, cancelación y oposición por e-mail [ > mailto:info@esario.com | info(a)sequentiabiotech.com ] incluyendo la palabra > PROTECCIÓN DE DATOS en el cuerpo del mensaje o bien en las dependencias sitas > en nuestras oficinas.

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BioSB Course Quantitative and Predictive Modelling, 26-30 June 2017 in Wageningen
by Femke Francissen 15 May '17

15 May '17

BioSB Course Quantitative and Predictive Modelling Date: 26-30 June, 2017 Location: Wageningen Course Coordinators: Natal van Riel (TUE) & Jaap Molenaar (WUR) Website: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Registration: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Please note that this course is free of charge for PhDs who are or become a member of the BioSB research school <http://biosb.nl/about/members/biosb-membership-information/>. Description On June 26-30 2017, BioSB organises the second edition of the course Quantitative and Predictive Modelling (QPM). In this course the participants learn how to describe the dynamic behaviour of biological systems and to integrate experimental data. Concepts of modelling in terms of differential equations are introduced via a great variety of case studies taken from diverse practices. The course offers a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. The emphasis is on providing an introduction into modelling approaches rather than an in-depth treatment of a few techniques and aims as such at a broad audience. The course is a mixture of theory sessions and computer practicals. During the practicals most of the time Matlab will be used. Participants not acquainted with Matlab will get an introduction. The course has to be completed with assignments in the form of practical exercises as homework afterwards. Target audience and learning objectives This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences, Bioinformatics, Systems Biology or Biomedical Engineering. Participants from the private sector are also welcome. Participants are expected to have some experience in modelling with differential equations. The students will be provided with a theoretical basis, a variety of methods and a computational hands-on experience to handle differential equation modelling, parameter estimation and uncertainty analysis. In the course the students will learn: - How to set-up a dynamic model to represent biological networks using different interaction mechanisms - To implement, simulate and analyse dynamic network models in different software tools - To understand the common ground and the differences for applications in metabolic, regulatory, signalling, population and multi-scale biological processes - To integrate experimental data in modelling, estimate model parameters and assess the accuracy of parameter estimates and model predictions This course is part of the Education Programme of BioSB <http://biosb.nl/education/course-portfolio-2/>, 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. Beste regards, Femke Francissen ** ** *Femke Francissen* Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: femke.francissen(a)biosb.nl Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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Workshop GATK Best Practices for Variant Discovery, 17-19 July 2017 - Registration open (second announcement)
by Bert Overduin 15 May '17

15 May '17

Dear all, I am happy to announce that for the third year in a row we have been able to get three members of the GATK team of the Broad Institute ( https://software.broadinstitute.org/gatk/) over to Edinburgh for a few days to teach a workshop on GATK Best Practices for Variant Discovery. Details of the workshop can be found below. With kind regards, Bert ********** GATK BEST PRACTICES FOR VARIANT DISCOVERY DATE: Monday 17 - Wednesday 19 July 2017 VENUE: The King's Buildings,The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 3 July 2017 CANCELLATION DEADLINE: Monday 10 July 2017 PLACES: 85 (lectures), 30 (hands-on sessions) (first come, first served) REGISTRATION FEE: £70 for the lectures, £35 for each half-day hands-on session (includes coffee/tea, but no lunch) INFORMATION: Bert Overduin (bert.overduin(a)ed.ac.uk) TO REGISTER: http://genomics.ed.ac.uk/services/gatk-best- practices-variant-discovery This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq-specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery, and we demonstrate the use of pipelining tools to assemble and execute GATK workflows. "Excellent opportunity to learn from world-renowned experts!" (April 2016) INSTRUCTORS GATK staff (The Broad Institute, Cambridge, MA, United States) WORKSHOP FORMAT The workshop is composed of one day of lectures (including many opportunities for Q&A) and two optional days of hands-on training, structured as follows: Lectures (day 1): Rationale, theory and application of the GATK Best Practices for Variant Discovery in high-throughput sequencing data. Hands-on 1 (day 2 am): Germline variant discovery (SNPs + Indels) Hands-on 2 (day 2 pm): Germline variant filtering (SNPs + Indels) Hands-on 3 (day 3 am): Somatic variant discovery (SNPs + Indels + CNV) Hands-on 4 (day 3 pm): Pipelining on the cloud with WDL Please note that the lectures part is mandatory. It is not possible to attend any of the hands-on sessions without attending the lectures. In the three optional hands-on sessions focused on analysis, we walk attendees through exercises that teach them how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to common use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK and Picard tools, dealing with problems, and using third-party tools such as Samtools, IGV, RStudio and RTG Tools. In the optional hands-on session on pipelining, we walk attendees through exercises that teach them to write workflow scripts using WDL, the Broad's new Workflow Description Language, and to execute these workflows locally as well as through publicly available cloud-based services. Please note that this workshop is focused on human data analysis. The majority of the materials presented applies equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points. WHO SHOULD ATTEND The lecture-based component of the workshop is aimed at a mixed audience of people who are new to the topic of variant discovery or to GATK, seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. Attendees should already be familiar with the basic terms and concepts of genetics and genomics. The hands-on component is aimed at novice to intermediate users who are seeking detailed guidance with GATK and related tools. Basic familiarity with the command line environment is required. Please note that for the hands-on sessions attendees will be expected to bring their own laptops with software preinstalled (detailed instructions will be posted two weeks before the workshop). Supported systems are Mac and Unix/Linux systems. MS Windows is not supported. COVERED TOPICS Lectures Introduction to variant discovery analysis and GATK Best Practices Marking Duplicates Indel Realignment Base Recalibration Variant Calling and Joint Genotyping Filtering variants with VQSR Genotype Refinement Workflow Callset Evaluation Somatic variant discovery with MuTect2 Preview of CNV discovery with GATK4 Hands-on 1 Germline variant discovery (SNPs + Indels) Hands-on 2 Germline variant filtering (SNPs + Indels) Hands-on 3 Somatic variant discovery (SNPs + Indels + CNV) Hands-on 4 Pipelining on the cloud with WDL -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 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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Researcher meeting on the Dutch "National Plan Open Science"
by Egon Willighagen 13 May '17

13 May '17

(as indicated below, the meeting is aimed at *Dutch* researchers, but I believe it is relevant for the other BBC countries to be aware of the meeting.) During the its EU presidency last year, the Dutch government pushed to further Open Science as a European level. This has led to various activities, and at a local level in a "National Plan Open Science" (https://www.openscience.nl/) to enact the European "Amsterdam Call for Action on Open Science" (see [0]). On May 29, this National Plan will be discussed directly with researchers for the first time at a national meeting aimed at Dutch scientists. Besides some top down information with speakers like Sander Dekker (government) and Wim van den Doel (NWO), the meeting will be by researchers and for researchers: https://www.openscience.nl/nationaal-plan For example, during the lunch break researchers can present their own Open Science work or shop around and see how others are using Open Science in their research. This is organized as a Knowledge Commons session. After this 1.5h Open Science galore, there will be break out sessions where you can learn about various themes and discuss the issues you are facing. Mind you, this is the time to let the Dutch government hear your researcher voice and needs! Importantly, the meeting is for anyone doing research, whether at a university, a HBO, an institute, but even at home as a citizen scientist. After all, it's about Open Science and our European future. Also, it's not only about natural sciences, but also linguistics, humanities, social sciences, law, etc. With kind regards, Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/u/egonwillighagen

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RSG Student Symposium 2017 - Gent
by Daniele Parisi 10 May '17

10 May '17

RSG Belgium, the network that connects PhD students and young postdocs working in Bioinformatics, is proud to announce their 2017 Bioinformatics Symposium. Date: THURSDAY 8TH JUNE Abstract submission deadline: 31th MAY Place: GHENT UNIVERSITY, scientific park Keynote Speaker: YVES VAN DE PEER http://bioinformatics.psb.ugent.be/pe.../profile/yvesvandepeer [1] The RSG STUDENT SYMPOSIUM will be an half day of PRESENTATIONS, DISCUSSION AND NETWORKING from and for PhD students in Bioinformatics. The goal of this symposium is to give PhD students and young postdocs the opportunity to present their research as well as broaden their network. Please SUBSCRIBE AND SUBMIT YOUR ABSTRACT HERE, BEFORE MAY 31TH: https://docs.google.com/forms/d/e/1FAIpQLScjrKKk7DXi_aQv5E1PUCOt5bDw5gyLada… [2] You can also FIND US ON FACEBOOK: https://www.facebook.com/RSGBelgium/ [3] A NETWORK DINNER in the centre of the city follows the symposium (soon more information) -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Board member of PhD Leuven society Kasteelpark Arenberg 10 - box 2446 3001 Leuven, Belgium Tel: +32488794394 Links: ------ [1] https://l.facebook.com/l.php?u=http%3A%2F%2Fbioinformatics.psb.ugent.be%2Fp… [2] https://docs.google.com/forms/d/e/1FAIpQLScjrKKk7DXi_aQv5E1PUCOt5bDw5gyLada… [3] https://www.facebook.com/RSGBelgium/

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Reminder: BioSB Course Kick start R (4th edition), May 19, 2017, Amsterdam
by Femke Francissen 10 May '17

10 May '17

*BioSB Course Kick start R (4th edition) * *Date: May 19, 2017* *Location: Amsterdam* *Course Coordinator: Douwe Molenaar (VU)* *Website*, including course programme: http://biosb.nl/edu cation/course-portfolio/course-kick-start-r/ *Registration: * http://biosb.nl/education/course-portfolio/co urse-kick-start-r/enrollment-kick-start-r-course-4th-edition/ On May 19, 2017, BioSB organises the fourth edition of the Kick Start R course in Amsterdam. *Goal* The goal of this kick-start course is to: - Introduce the structure and philosophy behind the R-language. - Introduce a number of tools to work with R. - Give hands-on experience in solving data problems from the lab This is an introductory course to speed up the study of R. *Target audience* Primarily targeting researchers from academia, but participants from the private sector are also welcome. *Description* This is a one-day introduction to 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. We will start with a lecture in which the philosophy behind the R-language will be explained. An understanding of the data structures in R allows you to work more efficiently with R. We will show some of the advanced possibilities of R as well as where to find tutorials if you want to know more about those techniques. Most of the day will be devoted to a hands-on tutorial. The tutorial contains material from an introductory master course that is taught at the VU University. The manual contains material and references to material for self-study. Topics that we will discuss: R language basics, installing R and R-packages, finding help, using R-studio, making dynamic reports, model fitting, reading/writing data from/to files, making publication-ready graphs, books and tutorials on the use of R. Participants will get a certificate after successfully completing this course. Read more <http://biosb.nl/education/course-portfolio/course-kick-start-r/> & Register via the registration form <http://biosb.nl/education/course-portfolio/course-kick-start-r/enrollment-k…> Best regards, ** ** *Femke Francissen* Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: femke.francissen(a)biosb.nl Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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Reminder: 13th Student Council Symposium
by ISCBSC announcement 10 May '17

10 May '17

Dear All, The ISCB Student Council is excited to announce the *13th Student Council Symposium (SCS)* which will be hosted, preceding *ISMB/ECCB 2017*, at the Prague Congress Centre in Czech Republic on July 21, 2017. The SCS is an annual student-organized event, with a goal to highlight latest research from a wide variety of subfields of bioinformatics and computational biology. The SCS 2017 will include keynote talks, contributed talks, poster session, and a social event in the evening. The symposium is a great opportunity to hear talks from an international group of students, learn about latest advances in computational biology, and build a worldwide scientific network. We are also pleased to announce our keynote speakers: *Professor Christine Orengo* from University College London (UCL), and *Dr. Johannes Söding *from the Max Planck Institute for Biophysical Chemistry. Prof. Orengo is an expert in bioinformatics and her research group, at UCL, focuses on understanding how protein domains are conserved over evolutionary time and developing methods to predict protein function. Dr. Söding is specialized in the development of statistical methods for the detection of distant evolutionary relationships on protein sequences. Additional keynote information can be found online <http://symposium.iscbsc.org/scs2017-keynotes>. Please *submit your abstract soon *for poster and/or an oral presentation! The deadline is approaching fast (*May 14, 2017*). *Key Dates:* May 14, 2017 Abstract Call Closes May 14, 2017 Travel Fellowship Call Closes *July 21, 2017 13th Annual Student Council Symposium* You can help us spread the word by sharing the event flyer (please find it attached) and using the hashtag *#SCS17* on social media. We look forward to welcome you in Prague this summer! The SCS2017 Organizing Committee <http://www.ectmih2017.be/> Disclaimer <http://www.itg.be/disclaimer> Directions to our location(s) <http://g.co/maps/ua89b>

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PhD position in Leuven
by Karoline Faust 10 May '17

10 May '17

?The Laboratory of Microbial Systems Biology (http://tinyurl.com/MicrobialSysBio) is looking for a motivated PhD candidate who is ?interested in the development of a platform that builds and analyses networks from microbial sequencing data. The young lab, started in 2016, is part of the Molecular Bacteriology unit at the Rega institute. In general, the lab's research projects aim at improving our understanding of microbial community structure and dynamics. Project An increasing number of large-scale sequencing projects studies the composition of microbial communities in environments ranging from the open ocean to the human gut. These projects often yield abundance estimates for thousands of operating taxonomic units over hundreds of samples and are accompanied by rich metadata on the environment and the sequencing protocol. Previously, a number of network construction techniques was developed and applied to these data sets to explore microbial community structure. However, these techniques often result in large networks, so-called "hairballs", which need to be further analyzed to better understand the community under study. In this project, we will develop, implement and benchmark novel approaches to visualize, analyze and interpret these "hairballs", in order to gain biological insights from these challenging data sets. Profile Two types of profiles are acceptable: Background in informatics · good knowledge of an object-oriented programming language, integrated development environment and modern version control system · at least basic knowledge of microbiology or ecology · strong interest in microbial ecology Background in biology · good knowledge of microbiology or ecology · at least basic knowledge of an object-oriented programming language · strong motivation to improve programming skills The PhD candidate is expected to apply for an FWO PhD fellowship and should therefore meet the eligibility criteria (http://www.fwo.be/en/fellowships-funding/phd-fellowships/phd-fellowship/) Proficiency in English is required, knowledge of graph theory, Cytoscape or R is a plus. The PhD candidate should obtain a Master degree end of September 2017 at the latest. Offer · full-time 2-year contract, with the possibility of an extension · enrolment at one of the top universities in Europe · exciting research environment · competitive salary Interested? Please submit a cover letter, a CV including obtained grades, and a list with at least two references (with name, function, email, address, phone number) through the online application tool: https://icts.kuleuven.be/apps/jobsite/vacatures/54023741 The starting date is the first September 2017. For more information please contact Karoline Faust at: karoline.faust(a)kuleuven.be

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Genome 10K and Genome Science 2017, Norwich, UK - 29 August to 1 September 2017
by Bert Overduin 05 May '17

05 May '17

FYI ********** Dear Colleague, You are invited to the Genome 10K and Genome Science 2017 conference, hosted by Earlham Institute, Norwich from 29 August to 1 September 2017. Registrations are now open <http://www.earlham.ac.uk/genome-10k-and-genome-science>. Note that early bird registration has been extended to May 31st! This conference combines the biannual Genome 10K conference with the annual UK Genome Science Meeting, offering fantastic opportunities to hear from an even more diverse range of internationally renowned speakers and giving you greater networking opportunities. Please feel free to send this invitation on to colleagues for wider dissemination – we appreciate your support! *About the event* Earlham Institute are proud to host two prestigious conferences in one – The Genome 10K biannual conference for the Genome 10K project – assembling a genomic zoo to capture genetic diversity of vertebrate species to support worldwide conservation efforts – and the Genome Science meeting – a successful annual meeting exploring advances in genomic technologies and computational biology and their applications across the biomedical sciences. We have an exciting programme packed full of renowned speakers, current hot topics for discussion, continuing professional development and training sessions. On top of this there will be ample networking opportunities, such as the conference dinner and social mixer events to really help bring together these fantastic communities of leading researchers. *Dr Emily Angiolini* *Scientific Training and Education Team Manager* [image: ei-as-signature-4] [image: email-banner-31-may] <http://www.earlham.ac.uk/genome-10k-and-genome-science> -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 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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Data Manipulation and Visualisation with Python and Advanced Python for Biologists, Edinburgh, July 2017
by Bert Overduin 02 May '17

02 May '17

Dear all, In July Edinburgh Genomics will be offering the following two 5-day Python workshops, taught by Dr. Martin Jones of Python for Biologists ( http://pythonforbiologists.com) DATA MANIPULATION AND VISUALISATION WITH PYTHON, 10-14 July 2017: For details and to register: http://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-python ADVANCED PYTHON FOR BIOLOGISTS, 24-28 July 2017: For details and to register: http://genomics.ed.ac.uk/services/advanced-python-biologists The Advanced course is aimed at people who want to develop bigger or more complicated programs in Python, or to learn more about the language, or to explore different approaches (object-oriented, functional) to programming. The material covered is very general purpose and can be applied to any kind of problem. The Dataviz course is about using a set of Python libraries that are specifically designed for data exploration and visualisation. In the Dataviz course, we're going to concentrate on using these tools to explore patterns in data, but the actual code that we write will be very simple - mostly we will be calling the functions and methods in these libraries. To summarise: if you want to learn more about the language, build more complicated programs, or need to work with existing complicated programs, attend the Advanced course. If you want to explore datasets, find patterns, produce figures and charts, attend the Dataviz course. For both workshops knowledge at the level of the Edinburgh Genomics workshop INTRODUCTION TO PYTHON FOR BIOLOGISTS ( http://genomics.ed.ac.uk/services/introduction-python-biologists) is sufficient. Please don't hesitate to contact me in case you have any questions. With kind regards, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 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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