April 2017 - BBClist - maillist.psb.ugent.be

Bioinformatics position available at the Erasmus MC Cancer Computational Biology Center
by Harmen van de Werken 04 Oct '19

04 Oct '19

A bioinformatics position is currently available at the Erasmus MC Cancer Computational Biology Center. http://www.erasmusmc.nl/vacature/?num=21578 Please apply, if you are enthusiastic and eager to improve our knowledge on cancer biology. Harmen van de Werken

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Vacancy in Amsterdam
by Dorsman, JC 28 Apr '17

28 Apr '17

Dear all, We are looking for a PhD student Applied Cancer Bioinformatics: Advanced Profiling of Retinoblastoma (36 hrs) in Amsterdam, The Netherlands. Due to the multidisciplinary environment, you are expected to develop proficiencies that are equally relevant to academia and industry. See attachment for more details. Best wishes, Josephine Dorsman. Dr. Josephine Dorsman, PI Oncogenetic labs Department of Clinical Genetics Cancer Center Amsterdam De Boelelaan 1118 1081 HV Amsterdam The Netherlands Office 2-28 Tel. 31-020-4448424 / 31-06-22513387 Email: JC.Dorsman(a)vumc.nl

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Fw: Open PhD position in computational (bio)science (FI/BE). Application DL May 26, 2017.
by Karoline Faust 27 Apr '17

27 Apr '17

________________________________ From: Leo Lahti <leo.lahti(a)utu.fi> Sent: Thursday, April 27, 2017 4:10 PM To: Karoline Faust; sudarshan.shetty(a)wur.nl; gerben.hermes(a)wur.nl Subject: Open PhD position in computational (bio)science (FI/BE). Application DL May 26, 2017. Hi, for circulation if you know suitable candidates / channels. / Leo --------- Open PhD student position / Project Researcher / Research Assistant in high-throughput biomedical data analysis (Finland / Belgium) 1.7.2017 – 30.6.2019 **A position is open for a PhD candidate on high-throughput biomedical data analysis** in the research team of Dr. Leo Lahti http://www.iki.fi/Leo.Lahti in University of Turku, Finland. The project provides a unique opportunity to gain widely applicable data analytical skills and make pioneering work in a rapidly emerging, data-intensive biomedical research area; a particular focus of the project is on computational analysis and modeling of the human microbiome and its individuality, dynamics, and function in large population cohorts. **Project** The position is intended for full-time research including moderate contributions to university teaching and other supporting tasks. The project aims at a holistic characterization of the organization and dynamics of the human microbiome and its associations with host lifestyle and health, with the ultimate aim to improve fundamental understanding and applications of human biology and personalized medicine. A particular focus will be on the development of statistical techniques and data science tools for biomedical research, blending approaches from statistical machine learning, ecology, bioinformatics, and related fields. You will join the Turku biomedical research community and work in close collaboration with key partners in Finland and abroad. The project starts with a 6-12 month mobility period in the research group of Prof. Jeroen Raes http://www.vib.be/en/research/scientists/Pages/Jeroen-Raes-Lab.aspx at VIB/KU Leuven, Belgium. **Qualifications** We are looking for outstanding candidates with a high level of independence as well as good collaboration skills and analytical capabilities. An ideal candidate would have a solid background in mathematics and/or statistics, familiarity with statistical programming (e.g. R/Python/Matlab/Julia) and bioinformatics, and ability to work in multidisciplinary environment. Fluent communication skills in English are essential. The doctoral candidate should hold a MSc degree in a relevant research field. Strong candidates who are willing to make MSc thesis as part of the project are also encouraged to apply. The new doctoral student must pass the standard enrollment process. **Salary** The salary depends on the stage of the studies and is based on the University salary system for research personnel and will allow full-time focus on the doctoral studies. The position has a trial period of 4 months. **Host institute** University of Turku is a world-class research university with an active biomedical research community. The research team of Dr. Lahti at the Department of Mathematics and Statistics http://www.utu.fi/en/units/sci/units/math/Pages/home.aspx focuses on the theory and applications of modern data analytics with a stimulating multidisciplinary research environment and international collaboration networks. The working language is English, and support for international staff is available. The project will start with a 6-12 month mobility period in the research group of Prof. Jeroen Raes at VIB/KU Leuven, Belgium. The city of Turku is a vivid, middle-sized student city with 180,000 inhabitants, beautiful natural surroundings and ample opportunities for free-time activities. **Application** Applications must be submitted no later than Friday, May 26, 2017 via the electronic application form of the University of Turku. For further details, you can contact Dr Leo Lahti. Contact information and the link to the application system can be found from the University of Turku recruitment page https://www.utu.fi/fi/Yliopisto/yliopisto-tyonantajana/avoimet-tehtavat/Siv… (ID 3662). A direct link to the application form: https://rekry.saima.fi/certiahome/open_job_view.html?id=00003662&did=5600&l…

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Last chance to submit your abstract for SCS2017 Prague
by ISCBSC announcement 26 Apr '17

26 Apr '17

Last chance to submit your abstract for SCS2017 Prague 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. SCS 2017 will bring an exciting program that includes 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). 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. Professor Johannes Söding from the Max Planck Institute for Biophysical Chemistry. ). Prof. Söding is specialized in the development of statistical methods for the detection of distant evolutionary relationships on protein sequences, improving multiple sequence alignments and protein structure prediction. Additional keynote information can be found online. You still can submit an abstract for an oral presentation and/or poster, however the deadline is approaching fast (April 30,2017). Key Dates: April 30, 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 (attached to this e-mail) or using the hashtag #SCS17 on social media. We look forward to welcome you in Prague this summer! The SCS2017 Organizing Committee

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Last chance to submit your abstract for SCS2017 Prague
by Cuypers Bart 26 Apr '17

26 Apr '17

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. SCS 2017 will bring an exciting program that includes 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). 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. Professor Johannes Söding from the Max Planck Institute for Biophysical Chemistry. ). Prof. Söding is specialized in the development of statistical methods for the detection of distant evolutionary relationships on protein sequences, improving multiple sequence alignments and protein structure prediction. Additional keynote information can be found online<http://symposium.iscbsc.org/scs2017-keynotes>. You still can submit an abstract for an oral presentation and/or poster, however the deadline is approaching fast (April 30,2017). Key Dates: April 30, 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 (attached to this e-mail) or using the hashtag #SCS17 on social media. We look forward to welcome you in Prague this summer! The SCS2017 Organizing Committee

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[Gtpb] Fwd: Subject: GTPB Entry Level Bioinformatics - applications are OPEN
by Pedro L. Fernandes 26 Apr '17

26 Apr '17

REMINDER Applications for the Entry Level Bioinformatics training course are still open. Deadline: May 1st 2017 (Monday) We have a few seats still available. http://gtpb.igc.gulbenkian.pt/bicourses/ELB17F with David P. Judge, Pedro Fernandes and Daniel Sobral IMPORTANT DATES for this Course Deadline for applications: May 1st 2017 <========= ! Course date: May 8th - May 12th 2017 This is our Entry Level course. It is the best way to start working with sequence data, gently introduced to participants with no experience. You just need to have minimal knowledge in Biochemistry and Molecular Biology and minimal computer usage skills. The course will take you to a level where you understand how to use NGS data as well. We aim at training the participants to gain independence in basic usage of bioinformatic tools and data resources. The course covers a very wide range of subjects. A successful participant will be able to do perform a great deal of bioinformatics tasks by him/herself. He/she will also to easily engage in most of our more specialised or advanced training courses. Above all, he/she will have a good understanding of how to work with data to support research activities, integrating wet lab research l research with data analytical tasks in a coherent framework. NOTE: 1) Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. 2) This course is often fully booked. Please do not delay your application if you are interested. Best wishes Pedro Fernandes -- Pedro Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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Extra Workshop: R2 - Genomics analysis and visualization platform
by r2-support 25 Apr '17

25 Apr '17

Dear Researcher, Since the next R2 workshop on May 2nd is overbooked, we are organising another R2 introduction workshop on Monday the 19th of June 2017 (09:30-17:00). R2 is a free, publicly accessible web-based genomics analysis and visualization platform (http://r2.amc.nl) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. The workshop will cover the essentials of working with genomics data in R2 and will be an excellent opportunity to learn how to use this versatile tool. If you are: Studying a specific pathway in disease Trying to find biomarkers in specific tissue Investigating the function of a specific protein Involved in any kind of molecular biology Then this workshop may be of interest to you. Every participant will receive a printed tutorial book. Coffee / tea and a simple lunch will be provided during the workshop. If you are interested in participating in the workshop then please visit the R2 website for more information and registration (http://hgserver1.amc.nl/cgi-bin/r2/main.cgi?option=about_intro_workshop ). The workshop is provided free of charge, however, we will have to charge 25 euro (for administation, lunch, printing costs) in case of a no show on the workshop. Best regards, R2-support r2-support(a)amc.nl Department of Oncogenomics, M1-132 Academic Medical Center University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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Data Scientist position Janssen Pharmaceuticals (Beerse, Antwerp)
by Tim Van den Bulcke 24 Apr '17

24 Apr '17

Our Data Sciences group is expanding further. We are looking for entrepreneurial data scientists with a strong track record that want to move healthcare forward in a young and dynamic group within Janssen Pharmaceuticals. Please find the job description below, you can contact me directly for applications (motivation letter + resume) or use the link below. *Tim Van den Bulcke, PhD* Senior Data Scientist Data Sciences, Pharma IT Janssen Pharmaceutica (Johnson & Johnson) Antwerpseweg 15-17 2340 Beerse Belgium email tvande38(a)its.jnj.com Data Scientist Job description ‘Caring for the world, one person at a time’... inspires and unites the people of Johnson & Johnson. We embrace research and science - bringing innovative ideas, products and services to advance the health and well-being of people. Employees of the Johnson & Johnson Family of Companies work with partners in health care to touch the lives of over a billion people every day, throughout the world. Janssen Pharmaceutica joined the Johnson & Johnson group in 1961. Today, Janssen Pharmaceutica is one of the most innovative pharmaceutical companies in the world. Our research and development centre develops products for a wide range of disease areas, such as mental disorders, neurological problems, infectious diseases, immunological disorders, cancer, and cardiovascular and metabolic conditions. The Data Sciences department within Janssen Pharmaceutica is looking for an outstanding Scientist who is interested in designing, developing, and fielding data mining solutions that have direct impact to Patients and Janssen. Our department spans across the entire value chain at Janssen Pharmaceuticals from discovery to after launch and supply chain. This will enable the scientist to work with various business units to help identify viable data mining opportunities and then conceive, develop and implement end to end data analytical solutions. There are many ways to explore and analyze data, and this drives the excitement and passion of data scientists at Janssen as many business units are eager to leverage the data to create business value. The Scientist will be someone who stays on the cutting edge of data mining research by doing novel research to influence decisions at various levels in the organization. The role requires both a broad knowledge of existing data mining algorithms and creativity to invent and customize when necessary. The Scientist, Data Sciences will be part of a dynamic, accomplished informatics team that will support multiple R&D therapeutic areas in the discovery and development of innovative medicines. The Scientist will partner with colleagues in Research, Development, Commercial, Supply Chain and Informatics to develop, implement, and apply state-of-the art scientific algorithms and methods for key J&J business functions. Will invent and implement creative solutions that go beyond current tools to deliver best solutions to the problems. Will participate in project teams, elicit needs, and act in a primary role as a trusted primary business and scientific partner. Will conceive and develop end to end data mining solutions to support Janssen’s business units and initiatives. Thriving on a diverse company culture, celebrating the uniqueness of our employees and committed to inclusion. Proud to be an equal opportunity employer. Qualifications - Ph.D degree in Computer Sciences, Statistics, Machine Learning & Artificial Intelligence, Physics, Molecular Biology, Bioinformatics, Computational Informatics, Medical Informatics, Computational Biology or a related discipline is required. - Strong understanding of drug discovery and development processes is preferred. - Strong working knowledge of data mining algorithms including machine learning techniques such as decision trees, probability networks, association rules, clustering, regression, neural networks, Bayesian models is required. - Familiarity with large datasets, handling of biomedical datasets and understanding of data analysis workflows is required. Experience in the handling and analysis of real world evidence data is preferred. - Proficient with one or more programming language such as .net, Java, Perl, C++ is required. - Experience with informatics, analysis and visualization software/tools such as R, MatLab, SAS, Python, Spotfire, Pipeline Pilot or other analytical tools is required. What’s in it for you…? “Caring for the world, one person at a time…” As an employee we consider you as our most valuable asset. We take your career seriously. As part of a global team in an innovative environment your development is key and our day-to-day responsibility. Through e-university, on the job training, various projects and programs, we ensure your personal growth. Our benefits make sure we care for you and your family now and in the future. -- Link to job posting: https://jobs.jnj.com/jobs/1600135271W/Data+Scientist

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BioSB Course Kick start R (4th edition), May 19, 2017, Amsterdam
by Femke Francissen 21 Apr '17

21 Apr '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 now 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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Galaxy Community Conference (GCC2017) deadline extended
by Dave Clements 20 Apr '17

20 Apr '17

2017 Galaxy Community Conference (GCC2017) 26-30 June 2017 Montpellier, France https://gcc2017.sciencesconf.org/ -- *The deadline for submitting oral presentation abstracts for the 2017 Galaxy Community Conference <https://gcc2017.sciencesconf.org/> has been extended to 29 April.* If you work in data intensive life science research then GCC2017 is an ideal opportunity to present your work. Posters and computer demonstration submission closes on 27 May and the lightning talk submission deadline is 23 June. The 2017 Galaxy Community Conference will bring together several hundred researchers working in and supporting data intensive life science research. There is no better place to share your work and learn from others that are addressing diverse questions and facing common challenges in data intensive biology. GCC participants work across the tree of life, come from around the world, and represent universities, research organizations, industry, medical schools and research hospitals. GCC2017 will be in Montpellier, France, 26-30 June and will feature two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups, all about data-intensive biology and the tools that support it. GCC2017 also includes data and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>, and two days of training <https://gcc2017.sched.com/overview/type/Training> covering 16 different topics. GCC2017 will be held at Le Corum Conference Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart of Montpellier <https://gcc2017.sciencesconf.org/resource/page/id/2>, just 10km from the Mediterranean. Early registration <https://gcc2017.sciencesconf.org/resource/page/id/6> is now open and starts at less than 55€ / day for post-docs and students. You can also book low cost conference housing when you register. Travel fellowships are being offered by the Galaxy Community Fund for early career researchers that are travelling from afar. *About Galaxy* Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on public and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. We hope to see you this summer in Montpellier! Au revoir, The GCC2017 Organising Committee -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

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