July 2019 - BBClist - maillist.psb.ugent.be

NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Open PostDoc Position in Computational Biology - Marseille, France
by BAUDOT Anaïs 16 Nov '19

16 Nov '19

Dear colleagues, We have an opening position for a postdoctoral fellow in the network and systems biology group, in the Marseille Medical Genetics Unit. The project is dedicated to network modeling for rare genetic diseases. Please see attachement for more details, and feel free to forward this message to potential candidates. Best regards, Anaïs --------------------------------------------------------- Anaïs BAUDOT MMG, Marseille Medical Genetics U 1251, Faculté de Médecine de La Timone, 27 Bd Jean Moulin 13385 Marseille Cedex 5 0491324948 France anais.baudot(a)univ-amu.fr

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EuBIC 2020 Developer’s Meeting – Save the date & call for project proposals
by eubic 2020 14 Oct '19

14 Oct '19

Dear colleagues, We are pleased to announce that the upcoming EuBIC 2020 developer's meeting will be held in Nyborg, Denmark, on JANUARY 13TH TO 17TH 2020. The EuBIC 2020 developer's meeting will bring together scientists active in the field of bioinformatics and computational proteomics. It provides a highly interactive platform to develop projects that are relevant to the proteomics community. _Date_: January 13-17, 2020 _Venue_: Sinatur Hotel Storebælt, Østerøvej 121, 5800 Nyborg, Denmark _Website_: https://www.proteomics-academy.org/eubic-dev-meeting-2020 KEY DATES _September 18_, 2019: Project proposal submission deadline _October 1_, 2019: Announcement of selected projects _October 1_, 2019: Conference registration opens _January 13-17_, 2020: EuBIC 2020 developer's meeting in Nyborg CALL FOR PROJECT PROPOSALS _Do you want other researchers working on your project and set up future collaborations? _ The call for topics for the hackathon sessions during the EuBIC 2020 developer's meeting is now open! During the EuBIC 2020 developer's meeting the participants will engage in hackathon sessions where they will develop bioinformatics tools and resources. The participants will break up into small groups to work together on these topics in an open, constructive, and productive atmosphere. You can now submit project proposals for inclusion into the EuBIC 2020 developer's meeting program. Submit your project proposal before 18 September through the following website: https://github.com/eubic/EuBIC2020 5-8 hackathon projects will be selected by a community vote arranged by the EuBIC program committee and announced on the conference webpage. TOPICS Hackathon projects can cover all topics in computational mass spectrometry and proteomics bioinformatics, including, but not limited to: - Tools - Extension of existing bioinformatics tools under the guidance of their original authors - Development of novel bioinformatics tools to solve open problems - Benchmarking - Compilation of gold-truth datasets - Collection of reference algorithmic implementations - Specification of benchmarking criteria - Workflows - Definition of formal protocols - Development of tutorials for bioinformatics software usage - Data analysis - (Re)analysis of publicly available proteomics datasets - Functional data analysis and integration MORE INFORMATION - Website: https://github.com/eubic/EuBIC2020 - Social media hashtag: #EuBIC20 - Conference email: eubic2020(a)rub.de SPONSORSHIP inquiries are welcome at eubic2020(a)rub.de We are grateful to the European Proteomics Association (EuPA) for supporting EuBIC and to the Novo Nordisk Foundation for their generous support of the conference! We look forward to welcoming you in Nyborg! The organizing committee. Veit Schwämmle Marie Locard-Paulet Wout Bittremieux David Bouyssié Viktoria Dorfer Dominik Kopczynski Alessio Soggiu Julian Uszkoreit Bart Van Puyvelde Sander Willems

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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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Call for 15 PhD positions in the framework of the Marie Curie European Training Network (ETN)
by Hanneke Van Camp 31 Jul '19

31 Jul '19

Dear All, We are recruiting 15 PhD students (ESRs, Early Stage Researchers) in the framework of the Marie Curie European Training Network (ETN). All candidates with a strong commitment to Life Sciences; bioinformatics, biology, medicine, statistics, ethics in health sciences,... are invited to apply. The project is titled Translational SYStemics (TranSYS), Personalized Medicine at the Interface of Translational Research and Systems Medicine, and is coordinated by prof. Kristel Van Steen (KU Leuven). More info<https://gbiomed.kuleuven.be/english/research/50000622/translational-systemi…> on the project. Link to the recruitment tool: https://h2020transys.eu/recruitment/ Many thanks for spreading the word! Best wishes, Hanneke Hanneke Van Camp | Science Communication | Department of Human Genetics - KU Leuven Tel +32 16 194 328 | O&N4 Herestraat 49 box 602 | B-3000 Leuven (Belgium) http://www.kuleuven.be/cme Follow us on Facebook<https://www.facebook.com/CentrumMenselijkeErfelijkheid> and LinkedIn<https://www.linkedin.com/groups/13541759>

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Computational biology postdoc in Genomics of Myeloma at Memorial Sloan Kettering Cancer Center.
by Nicos Angelopoulos 30 Jul '19

30 Jul '19

Genomics Program of Myeloma Service: Postdoctoral Researcher Memorial Sloan Kettering Cancer Center (MSK) is one of the world’s premier cancer centers, committed to exceptional patient care, leading-edge research, and superb educational programs. The blending of research with patient care is at the heart of everything we do. The institution is a comprehensive cancer center whose purposes are the treatment and control of cancer, the advancement of biomedical knowledge through laboratory and clinical research, and the training of scientists, physicians, and other health care workers. The Myeloma Service in the Division of Hematologic Malignancies, Department of Medicine, is seeking outstanding postdoctoral candidates with a background in computational biology, experience in next generation sequencing analysis and an interest in cancer genomics. The applicant will work within the Genomics Program of Myeloma Service at Memorial Sloan Kettering Cancer Center (MSK). This position includes analyses of high-quality whole genome, targeted and RNA sequencing data from patients with multiple myeloma, to inform diagnostic and therapeutic strategies. The research will focus on cancer patients affected by multiple myeloma at the diagnosis, at relapse after novel therapies within clinical trials and patients with myeloma precursor entities (i.e. MGUS and smoldering myeloma) to identify the one that will progress and the one that will have a stable clinical course. The postdoctoral researcher will work within a team of researcher, including translational, clinical, and computational investigators working in cancer genomics and in its application into clinical practice. The Myeloma Service at MSK is a world-leader in early drug development and has a large clinical program which ensures access to samples and clinical data derived from the use of cutting-edge therapies. The main genomic aspects that we are currently investigating are the impact of mutational signatures, structural variants and rare drivers on myeloma pathogenesis and clinical outcome. Mentoring will be provided with strong focus on computational approaches, study design, and translational implications. Responsibilities Ensure generation and integration of high-quality genome and transcriptomic data from large cohort of patients Develop ideas and drive own independent research. Present findings in meetings and submit research for peer review and publication. Work independently and as a team member contributing towards collaborative research initiatives in the laboratory. Application Requirements Required Qualifications PhD in cancer biology Demonstrated experience in use of NGS datasets and related technologies. Proficient in either R (preferred) or Python. Good written and oral English communication skills. Please do not hesitate to contact us should you have any questions about our laboratory, and to address any informal questions or inquiries to Francesco Maura (mauraf(a)mskcc.org) or Ola Landgren (landgrec(a)mskcc.org)

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Bioinformatician vacancy at Radboudumc Human Genetics
by Marc.Pauper＠radboudumc.nl 30 Jul '19

30 Jul '19

Dear all, A new vacancy is open in the Genome Diagnostics bioinformatics team of the Human Genetics department at Radboudumc. Please see the link for details: https://www.radboudumc.nl/en/vacancies/70241-bioinformatician-human-genetics Kind regards, on behalf of Genome Diagnostics Marc Pauper, MSc Bioinformatician marc.pauper(a)radboudumc.nl<mailto:Marieke.klein@radboudumc.nl> T +31 (0)24 366 85 27 Radboud university medical centre Genome Diagnostics Department of Human Genetics P.O. Box 9101, 6500 HB Nijmegen, Netherlands (route 848) www.radboudumc.nl De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kopiëren en verspreiden van deze e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaande schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The content of this message is intended solely for the addressee. No rights can be derived from this message or its attachments. If you are not the intended recipient, we kindly request you to delete the message and inform the sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, without a written consent from the sender. Radboud university medical center is registered with the Dutch Chamber of Commerce trade register with number 41055629.

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EMBL-EBI Workshop - Finding Evidence in Research Publication
by Dayane Araujo 29 Jul '19

29 Jul '19

Dear all, Workshop: Finding Evidence in Research Publications Venue: EMBL-EBI, Hinxton, Cambridge, UK Dates: 10th - 11th September 2019 You will learn how to search and locate publicly-available open-access datasets from the scientific literature by using advanced search tools and programmatic access via APIs, which are freely available in Europe PMC <https://europepmc.org/>. Who is the workshop aimed at? The workshop is aimed at life science scientists interested to learn how to: I. Extract data and evidence from the research literature. II. Identify cited datasets for reuse, further analysis and background research. III. Apply literature analysis / text-mining in their own research. For more information and how to register: http://bit.ly/FindingEvidenceWorkshop <http://bit.ly/FindingEvidenceWorkshop> Application deadline: Friday 23 August 2019 We look forward to welcoming you! Best Regards, Dayane Araújo Dayane Araújo Technical Outreach Officer, Europe PMC email: dayane(a)ebi.ac.uk

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Upcoming BioSB courses, September-December 2019
by Femke Francissen 29 Jul '19

29 Jul '19

Dear researcher, BioSB <https://www.biosb.nl> is the Bioinformatics and Systems Biology community in the Netherlands. We are committed to train the next generation of computational life scientists. Our challenging and inspiring education programme covers essential topics in bioinformatics and systems biology, taught by teams of experts. *Upcoming BioSB courses* Registration is open for the following BioSB courses: - Machine Learning for bioinformatics and systems biology - 7-11 October 2019, Delft/Amsterdam, the Netherlands (fully booked) - Algorithms for Genomics <https://www.biosb.nl/archive-courses/course-algorithms-for-genomics/> - 14-18 October 2019, Delft, the Netherlands - Constraint based modelling <https://www.biosb.nl/archive-courses/constraint-based-modelling-introductio…> - 25-29 November 2019, Leiden, the Netherlands - Modelling and optimization for bioinformatics and systems biology <https://www.biosb.nl/archive-courses/modeling-and-optimization-2019/> - 9-13 December 2019, Wageningen, the Netherlands More information about the courses can be found below. A flyer with more information about the BioSB education programme can be found here <https://www.biosb.nl/wp-content/uploads/2019/07/BioSB-education-flyer-2019.…> . ________________________________ *Machine Learning for bioinformatics and systems biology <https://www.biosb.nl/archive-courses/machine-learning-for-bioinformatics-sy…>7-11 October 2019, Delft/Amsterdam, the Netherlands* The course is fully booked. If you want to be placed on a spare list, please send an email to education(a)biosb.nl. You can pre-register for next year's edition via the pre-registration form <https://www.biosb.nl/education/enrollment/pre-registration-courses/>. *Algorithms for Genomics <https://www.biosb.nl/archive-courses/course-algorithms-for-genomics/>14-18 October 2019, Delft, the Netherlands* Comparative genomics aims to compare large sets of genomes in order to understand and explain differences in traits of an organism. Contemporary methods are powered by fundamental algorithms and data structures, which are efficient and scale to large data sets. A thorough understanding of these algorithms and data structures is necessary for advanced users and developers in this area. In addition, understanding how comparative genomics is developing is important to shape your own research. In this 5-day course, we will cover genome analysis, variant analysis, and pangenomics. Core concepts, applications, and future trends will be discussed, with a focus on the algorithms and data structures underlying state-of-the-art methods. The course offers an engaging mix of lectures, paper discussions, hands-on tutorials, and a do-it-yourself project. *Constraint Based Modelling: Introduction & advanced topics <https://www.biosb.nl/archive-courses/constraint-based-modelling-introductio…>25-29 November 2019, Leiden, the Netherlands* Constraint-based modelling is a powerful modeling methodology that is being used to model a diverse range of biological phenomena. These include both fundamental and applied questions relevant to biotechnology, microbiology and medicine. Central to constraint-based modelling is the use of genome-scale reconstructions that represent particular cellular functions as a biochemical reaction network. In this 5-day course, you will be introduced to: - the principles of constraint-based reconstruction and analysis (COBRA) - the underlying mathematical foundations of constraint-based modeling - methods for integration of omics data with constraint-based models - basic and advanced methods for interrogating models and interpreting results - open source COBRA software, including the COBRA Toolbox - standards for reconstruction and model sharing - example applications to biomedicine and biotechnology The course is structured into both lectures and practical sessions so that theory can be illustrated with biologically motivated computational examples. *Modelling and Optimization for bioinformatics and systems biology <https://www.biosb.nl/archive-courses/modeling-and-optimization-2019/>9-13 December 2019, Wageningen, the Netherlands* In this course the participants learn how to describe the dynamic behavior of biological systems, and how to use optimization techniques to solve a variety of problems in bioinformatics and systems biology. Concepts of modelling in terms of differential equations are introduced via a great variety of case studies taken from diverse practices. This course also provides you with the main ideas underlying optimization, and to get you acquainted with the optimization techniques that are nowadays available and widely used. Examples of optimization problems in life sciences will be presented and discussed. 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 offers a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. The course is completed with assignments in the form of practical exercises as homework afterwards. *Courses planned for 2020 (preliminary)* - Algorithms for Biological Networks - Machine Learning - Managing and Integrating Information in the Life Sciences - Metagenomics - Modeling and Optimization - Statistics for Omics Data Analysis - Systems Medicine Find more information on our course portfolio page <https://www.biosb.nl/education/course-portfolio/>. If you want to stay up to date, please register for our newsletter <https://www.biosb.nl/newsletter/>! Best regards, Femke Francissen Community manager BioSB Research School

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PhD position in high-dimensional data analysis
by Brandt, B.W. 25 Jul '19

25 Jul '19

Dear all, We have a PhD position available. If you are interested, you can find more information via the link below. You can apply via the application button on that web page until 19 August 2019. PhD position in high-dimensional data analysis in relation to Oral Health https://workingat.vu.nl/ad/phd-position-in-high-dimensional-data-analysis-i… Kind regards, Bernd Brandt Academic Centre for Dentistry Amsterdam | Department of Preventive Dentistry | Gustav Mahlerlaan 3004 | 1081 LA Amsterdam | The Netherlands | www.acta.nl<http://www.acta.nl> ACTA is the collaborative Faculty of Dentistry of the University of Amsterdam and the VU Amsterdam

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