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Summer School on Rare Disease and Orphan Drug Registries including BYOD - Sep 10-14 2018 - Rome, Italy
by Celia van Gelder 02 Jun '18

02 Jun '18

COURSE ANNOUNCEMENT Please circulate this email to those who might be interested. The National Centre for Rare Diseases, Istituto Superiore di Sanità (Rome, Italy), in collaboration with ELIXIR-IIB, ELIXIR-NL, RD-Connect, EURORDIS, Orphanet, EuRRECa, European Reference Networks, EPIRARE and ICORD, is pleased to announce the "6th International Summer School on Rare Disease and Orphan Drug Registries", including Bring Your Own Data Registries. COURSE DESCRIPTION: Registries are key resources in order to increase timely and accurate diagnosis, improve patients management, tailor treatments, facilitate clinical trials, support healthcare planning and speed up research. The course will provide participants with useful tools and methodologies for establish a registry, the quality of the data collected and how a registry is turned into a FAIR resource. It intends: i) to promote the establishment of Findable, Accessible, Interoperable, Reusable (FAIR) registries in compliance with IRDiRC and EU Recommendations; ii) to support cooperation among different registry stakeholders and coordination with registries that are developed within European Reference Networks and National Plans in the EU. The course is organized in two training modules with the following objectives: * the first one (“Rare Disease Registries”, September 10-12, 2018) will provide participants with useful tools and methodologies to plan, establish and manage the registry activities. * the second one (“Bring Your Own Data - BYOD”, September 13-14, 2018) will be a hands-on experience (Bring Your Own Data), where the attendees work with FAIR data experts to make their data FAIR and linked to other data that has been made FAIR before. The "6th International Summer School on Rare Disease and Orphan Drug Registries" is open to health professionals, researchers, medical specialists, registry curators, database managers and representatives of patients’ associations involved in or intend to establish a rare disease registry, including ERN registries. Registration is possible for: - the first training module (Rare Disease Registries, Sept. 10-12, 2018) - the second training module (Bring Your Own Data- BYOD, Sept. 13-14, 2018) - or both (Rare Disease Registries and BYOD, Sept. 10-14, 2018). FEE: Registration is free of charge. Please, note that travel, subsistence and other costs incurred by the participants to attend the event are not covered by the organisers. VENUE: Aula Rossi, Istituto Superiore di Sanità, Via Giano della Bella, 34 - Rome, Italy. IMPORTANT DATES: Deadline for applications: 16 June 2018 Course date: 10-14 September 2018 Full details at: <http://old.iss.it/cnmr/?lang=1&id=2795&tipo=3> http://old.iss.it/cnmr/?lang=1&id=2795&tipo=3 Should you have any question, do not hesitate to contact the Organisers at <mailto:rareregistries-school@iss.it> rareregistries-school(a)iss.it We apologise for cross-posting. Please, email us back with the word REMOVE as the subject line, if you don't want to receive messages from ELIXIR-IIB Training anymore. Kind regards, the Organisers. -- ELIXIR-IIB Training https://elixir-iib-training.github.io/website/ <https://docs.google.com/uc?export=download&id=0B0c7_C2GRNsQTEpVMXRDeDBiQnM&…> _______________________________________________ Training-coordinators mailing list Training-coordinators(a)elixir-europe.org <mailto:Training-coordinators@elixir-europe.org>

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Register now for BioSB course: Algorithms for Biological Networks - June 25-29, Wageningen
by Femke Francissen 31 May '18

31 May '18

BioSB Course: Algorithms for Biological Networks (5th edition)Course coordinators: dr. Maria Suarez Diez (WUR), prof. dr. Dick de Ridder (WUR), dr. Jeroen de Ridder (UMCU) *Date:* June 25-29, 2018 *Location:* Wageningen University & Research *Website:* link to course page <https://www.biosb.nl/education/course-portfolio/course-algorithms-for-biolo…> *Registration:* link to registration form <https://www.biosb.nl/education/course-portfolio/course-algorithms-for-biolo…> Course description Molecular biology is concerned with the study of the presence of and interactions between molecules, at the cellular and sub-cellular level. In bioinformatics and systems biology, algorithms and tools are developed to model these interactions, with various goals: predicting yet unobserved interactions, assigning functions to yet unknown molecules through their relations with known molecules; predicting certain phenotypes such as diseases; or just to build up biological knowledge in a structured way. Such interaction models are often best modelled as networks or graphs, which opens up the possibility of using a large number of readily available algorithms for inferring networks, performing simulations of biology, optimising paths or flows through networks, graph-based data integration and graph mining. Many of these algorithms can be applied (sometimes with slight alterations) to solve a particular biological problem, such as modeling transcriptional regulation or predicting protein interaction/complex formation, but also to derive systems behaviour by breaking down networks into modules or motifs with certain characteristics. In this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring these from observed measurement data. A number of alternative network models more suited for high-level simulation of cellular behaviour will also be introduced. Building on the network inference methods, a number of ways of integrating various data sources and databases to refine biological networks will be discussed, with specific attention to the use of sequence information to refine interaction and transcription regulation networks. Finally, we will give some examples of algorithms exploiting the networks found to learn about biology, specifically for inspecting protein interaction networks. Course programme The tentative course programme and course materials can be found here <http://www.bioinformatics.nl/courses/BioSB-AfBN/>. Target audience The course is aimed at PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. The BioSB course “Pattern recognition” <https://www.biosb.nl/education/course-portfolio/pattern-recognition/> and the ASCI course “Advanced pattern recognition” (a1) discuss many of the tools used in this course, but it is not required to have followed these. Prior knowledge of molecular biology is a bonus, but also not strictly required. BioSB research school 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.

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Fwd: Tenure track in Amsterdam on Multiscale Scientific Computing
by Sanne Abeln 30 May '18

30 May '18

See the link below for a tenure track position in Amsterdam, the closing date is 30 June. http://www.uva.nl/en/content/vacancies/2018/05/18-294-assistant-professor-m… -- Computational Science <http://uva.computationalscience.nl> Lab <http://uva.computationalscience.nl> Master Programme Computational Science <http://www.uva.nl/en/shared-content/subsites/graduate-school-of-sciences/en…> -- -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln <http://www.few.vu.nl/%7Eabeln> -- -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln <http://www.few.vu.nl/%7Eabeln>

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Upcoming training workshops at Edinburgh Genomics: Linux for Genomics and Intro to RNAseq Analysis
by DUNBAR Donald 29 May '18

29 May '18

Hello all, we have some new dates for our popular Edinburgh Genomics training workshops<https://genomics.ed.ac.uk/services/training>. We now offer registration, on a first come first served basis, to our Linux for Genomics and Introduction to RNAseq Data Analysis workshops developed and taught by our Edinburgh Genomics Bioinformaticians. 1. Introduction to RNAseq Data Analysis, Tuesday 19th to Wednesday 20th June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/6QQVF7D> 2. Introduction to RNAseq Data Analysis, Thursday 21st to Friday 22nd June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/ZKG5F8N> 3. Linux for Genomics, Monday 25th June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/Z8RYF8T> 4. Linux for Genomics, Tuesday 26th June 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/Z86GFSH> Please use the links provided above to register for a place. These workshops are very popular and have limited places, so please do register as early as you can. We also have a few remaining places on our Advanced Python for Biologists workshop, taught by Dr Martin Jones, founder of Python for Biologists<https://pythonforbiologists.com/>. 1. Advanced Python for Biologists, Monday 9th to Friday 13th July 2018 REGISTER NOW<https://www.surveymonkey.co.uk/r/NDSGYHL> * https://genomics.ed.ac.uk/services/training * https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis * https://genomics.ed.ac.uk/services/linux-genomics * https://genomics.ed.ac.uk/services/advanced-python-biologists Please let me know if you have any questions or comments. Feel free to share with colleagues and contacts. With best wishes and we look forward to welcoming you to Edinburgh Genomics. Donald --- Dr Donald Dunbar Bioinformatics Operations Manager Edinburgh Genomics, Genome Science Ashworth Labs, The King's Buildings The University of Edinburgh donald.dunbar(a)ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Job vacancy Cluster Leader Applied Bioinformatics
by Warris, Sven 24 May '18

24 May '18

Dear reader, Our cluster Applied Bioinformatics of Wageningen University and Research is looking for a new cluster leader. For more information about the job vacancy and on how to apply, please visit: https://www.wur.nl/en/Jobs/Vacancies/Show/Cluster-leader-Applied-Bioinforma… Kind regards, Sven Warris

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+++ TRAVEL FELLOWSHIPS - ESCS2018 +++
by Daniele Parisi 24 May '18

24 May '18

Dear colleagues in bioinformatics and computational biology, In order to provide as many people as possible with the opportunity to attend the ESCS 2018 (European student council symposium of bioinformatics and computational biology), we are happy to announce there will be 3 travel fellowship available. The value of the travel fellowship will depend on the distance the recipient has to travel; please note the travel fellowship may not cover all your travel and/or hotel expenses. ELIGIBILITY In order to be eligible for the travel fellowship your abstract should be accepted for presentation at the symposium. Should you be awarded a travel fellowship by ECCB 2018, the ESCS travel fellowship will be withdrawn. HOW TO APPLY Please provide a PDF document containing * The abstract you have submitted * A copy of your curriculum vitae (CV) * A brief motivation describing why you would like to attend the ESCS and why you require a travel fellowship to do so Please send your application to escs(a)iscbsc.org before JULY 7TH, 2018 Your application will be judged based on the scientific quality of your work and your motivation. In addition, your country of origin will be take into consideration; in the case of applications of equal quality preference will be given to applicants from lower income countries. Do not hesitate to spread this mail through your colleagues, Best regards The ESCS2018 executive team -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Chair of ESCS 2018 Kasteelpark Arenberg 10 - box 01.34 3001 Leuven, Belgium Tel: +32488794394

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[Gtpb] DMOS18 - Course announcement / Reminder
by GTPB Administration 23 May '18

23 May '18

Course Announcement / Reminder DMOS18 Data Management and Open Science with Rutger A. Vos, Pedro L. Fernandes and Elves H. Duarte Key terms: Data Management, Fair Data, Open Science, Open Access, Open Data IMPORTANT DATES for this Course Deadline for applications: June 7th 2018 Course date: June 12th - June 15th 2018 The GTPB is proud to announce that the above referenced hands-on training course is open for applications Admission: Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description: In an age of increasingly complex and data-intensive, collaborative scientific practices, scandals of irreproducibility, and a growing societal ethos of transparency and accountability, a new paradigm has arisen: Open Science. In this three day course, we will introduce to you the three organizing principles and practices that undergird this paradigm: Open Access scholarly publishing Open Source software development Open Data integration and sharing For this, we will be introducing a set of technologies and ways of using them. The reasonable expectation is that the participants will feel empowered and start using them for the above purposes in a highly productive way. The use-cases that we will be working on are going to be based on bioinformatics, but the principles are very broadly applicable to other fields. You do not need to have any particular programming or otherwise computational experience beyond what is normally required from a scientist in graduate school and beyond, i.e., you should not be afraid of interacting with a computer and editing simple text files. We will then steer the participants into good practices in data management and work on practical examples taken from published papers and data, showing how these practices influence replicability and reproducibility. At the end we will discuss publication bias and its consequences in current research quality. More information at the GTPB website, http://gtpb.igc.gulbenkian.pt/bicourses/2018/DMOS18/ Hoping that this course meets your interests, Pedro Fernandes -- The Gulbenkian Training Programme in Bioinformatics General Office Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Aalto-Janssen postdoctoral position in machine learning
by Herman, Dorota [RNDBE] 23 May '18

23 May '18

Dear All, Aalto University is looking for a postdoctoral researcher with expertise in machine learning to work on an exciting collaboration project between Prof. S. Kaski's team in Finnish Center for Artificial Intelligence FCAI at Aalto University and Janssen Pharmaceutica. The exciting research problem is to learn to infer toxicity of chemicals based on the chemical structure, and the great opportunity is that we have unique data for the learning. This is an outstanding opportunity to both develop new probabilistic machine learning methods and to gain necessary skills to place yourself for success both in the pharmaceutical industry as well as in academia. Janssen Pharmaceutica and FCAI support and expect publication of the outcome of this work in top peer-reviewed journals and scientific conferences. The successful candidate will be employed by Aalto University and work in Otaniemi campus (Helsinki, Finland) for the 1st year of 2-year contract. During the 2nd year, the will be performed at Janssen Pharmaceutica premises in Beerse, Belgium. Full details: http://www.aalto.fi/en/about/careers/jobs/view/1854/. Best regards, Dorota Herman, PhD Scientist - Computational Sciences - Discovery Sciences Janssen Pharmaceutica NV Pharmaceutical Companies of Johnson & Johnson Turnhoutseweg 30 B-2340 Beerse Turnhout Phone +32 1460 5636 dherma20(a)its.jnj.com<mailto:dherma20@its.jnj.com>

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Vacancy: Team Leader Bioinformatics - Rijk Zwaan
by Sara Movahedi 23 May '18

23 May '18

Dear all, We’re looking for a new Team Leader for our Bioinformatics department in Fijnaart . Your contribution... We are seeking a driven, resolute and results-oriented team manager. You take initiatives, are not afraid of making decisions and you are a good coach with excellent communication skills. You have thorough and up-to-date knowledge of bioinformatics. Thanks to your outstanding people skills, you are able to manage your team effectively. You have a long-term focus, you get excited by future possibilities and you enjoy working on the development, testing, usage and implementation of new techniques together with our own research departments and external research partners. Innovation is in your DNA. In addition, your CV ticks the following boxes: At least a PhD and postdoctoral research experience related to bioinformatics Minimum of 5 years’ experience in a managerial role Affinity with plant breeding is an advantage Interest in the complexity of biological processes See the link below for the full details: https://www.rijkzwaancareers.com/careers/team-leader-bioinformatics Met vriendelijke groeten / Kind regards, Sara Movahedi (PhD)| Researcher Bioinformatics | Bioinformatics Direct +31 168 46 86 78 | s.movahedi(a)rijkzwaan.nl Rijk Zwaan Breeding B.V. Burgemeester Crezéelaan 40 | PO Box 40 | 2678 ZG De Lier | The Netherlands T +31 (0)168 468 600 | F +31 (0)168 465 087 info(a)rijkzwaan.com | www.rijkzwaan.com Chamber of commerce Haaglanden 24126474 0000 <i><font size="3" color="grey"> You can find the disclaimer that applies to emails of Rijk Zwaan at: http://www.rijkzwaan.com/edisclaimer The registration number of Rijk Zwaan companies can be found at: http://www.rijkzwaan.com/registrationnumbers </font>

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postdoctoral position in Bioinformatics/Systems Biology (France)
by Marco Antonio MENDOZA PARRA 18 May '18

18 May '18

A postdoctoral fellowship in bioinformatics is available in the newly launched team SysFate<https://marcomendozabpn.wixsite.com/sysfate> driven by Dr. Marco Antonio Mendoza (UMR-8030, French National Sequencing Center, Genoscope<http://jacob.cea.fr/drf/ifrancoisjacob/english/Pages/Departments/Genoscope.…>). This position is open to candidates educated in France, currently performing a postdoctoral training abroad. Interested applicants should directly contact Marco Antonio Mendoza (marco(a)igbmc.fr) Deadline, 15 June 2018. ? Marco A. Mendoza; PhD CRCN - CNRS Institut de Génétique et de Biologie Moléculaire et Cellulaire 1 rue Laurent Fries 67404 Illkirch France Tel: +33 3 88 65 34 19 www.ngs-qc.org

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