September 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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Helis Academy Course: FAIR Data Stewardship - digital data scholarship for life scientists, 4-6 November 2019, Utrecht, the Netherlands
by Celia van Gelder 08 Oct '19

08 Oct '19

Dear colleague, >From 4-6th November, 2019, we will give another round of the Helis Academy - FAIR Data Stewardship course: FAIR Data Stewardship - digital data scholarship for life scientists The target audience is life scientists - from industry and academia - and graduate students in the Life Sciences who wish to improve their digital scholarship on data handling. Some basic experience with programming and scripting languages like python, perl, R, matlab, etc. are an advantage, but not needed. The course is also relevant for Data Stewards who are supporting the life science researchers. The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards. The course will introduce the trainees to important concepts of data stewardship <https://www.dtls.nl/fair-data/research-data-management/research-data-manage ment/> . We start with a general introduction covering the data life cycle, the FAIR principles <https://doi.org/10.1038%2Fsdata.2016.18> and a definition of data stewardship and data stewards. We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course. * Day 1: Why use a data management plan and what for? On day one trainees will investigate data management plans, which types are there and how they should be used. * Day 2: Mastering the data chaos during the research phase. On day two the course highlights how to work with data during the research phase, explaining how to create well formatted data which helps in the second module of day two to make data interoperable already during the active research phase. * Day 3: Boost your visibility and get cited for your data! On day three trainees will have an in-depth at persistent identifiers, different use cases and types of identifiers. Finally we are closing the data life cycle by making data fit for sharing, archiving and publishing. The training is organised by <http://www.dtls.nl/> DTL and delivered as a joint effort by DTL partners. You can find all the information, including the full programme and registration possibilities here: https://www.aanmelder.nl/helis-fair-data-stewardship-course This course is part of the Data Analysis and Stewardship theme of Helis Academy <https://www.helisacademy.com/en> and is organised by DTL and DTL collaborators. Info about other courses in the theme of Data Analysis and Stewardship can be found on the Helis Academy website <https://www.helisacademy.com/en/data-analysis-stewardship> and on the Helis Academy page on the DTL website <https://www.dtls.nl/training-and-education/helis-academy/> . Please spread this announcement in your organisation as you see fit. Best regards, Celia van Gelder Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <https://www.dtls.nl/> https://www.dtls.nl/, <https://www.elixir-europe.org/platforms/training> https://www.elixir-europe.org/platforms/training skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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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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Postdoc Position in Berlin on Human Evolution
by Katja Nowick 27 Sep '19

27 Sep '19

*Dear all,* *We are looking for a postdoc who is interested in Human Evolution. The position can be for a bioinformatician:* *Our group “Human Biology and primate Evolution“ investigates the molecular evolution of humans using state-of-the art experimental and computational methods. Our focus is on differences in gene regulation, evolution of transcription factors and non-coding RNAs and their influence on the evolution of the human brain, its development and functions. * *The postdoc position is fully funded. The applicant is expected to propose and develop a research project that fits to the general interests of the group. Requirements for the position are a Dr. rer. nat. or PhD in Biology or Bioinformatics or another relevant field. The ideal candidate would have a strong interest in human evolution and expertise within multiple of the following areas: conducting research with induced pluripotent stem cells, differentiation into neuronal cells, CRISPR/Cas9, functional investigation of transcription factors and non-coding RNAs, ChIP-Seq, ChIRP-Seq, RNA-Seq, gene regulatory networks, computational analysis of –omics data, R, Python, network analysis.* *She/he will participate in teaching “Human Biology” (in German) as well as in “Human Evolution” and/or “Bioinformatics for Biologists” (in English). The position allows for supervising Bachelor and Master students as well as for applying for own funding, and is thus a good opportunity for acquiring necessary experience for applying for faculty positions afterward. It is initially for three years but can be extended to up to six years. Scientific communication within the group is in English.* *If interested, please send a motivation letter including your project idea along with your CV and two reference letters to *katja.nowick(a)fu-berlin.de <mailto:katja.nowick@fu-berlin.de>*.* *Best wishes,* *Katja * -- Dr. Katja Nowick Professorin für Humanbiologie Freie Universität Berlin Institut für Zoologie Königin-Luise-Straße 1-3 14195 Berlin Phone: +49 30 83863761

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European Bioconductor meeting 2019, 9 - 10 December in Brussels, Belgium
by Laurent Gatto 27 Sep '19

27 Sep '19

The European Bioconductor meeting is aimed at biologists, bioinformaticians, statisticians, programmers and software engineers who use or contribute to the Bioconductor project, or are interested in using Bioconductor. The goals are to: - foster the exchange of technical expertise - keep contributors up to speed with the latest developments - coordinate any related efforts The main conference will be on Monday 9 and Tuesday 10 December 2019 at the Brussels campus of the UCLouvain. An optional developer/user day is scheduled on the 11 December. The conference will feature 10 invited speakers and contributed flashlight talks and poster sessions. For details and abstract submissions, see http://eurobioc2019.bioconductor.org/index

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IBIP19 Integrative Biological Interpretation using Proteomics - Course announcement / reminder
by Pedro L Fernandes 27 Sep '19

27 Sep '19

> Course Announcement / Reminder > > IBIP19 > Integrative Biological Interpretation using Proteomics > with Veit Schwämmle, Marc Vaudel and David Bouyssié > > IMPORTANT DATES for this Course > Deadline for applications: October 30th 2019 > Course date: November 04th - November 07th 2019 > > Course description > Quantitative proteomics by mass spectrometry has become an essential tool for multi-omics studies aiming at answering important biological questions in a system-wide perspective. Proteomics data contain rich and deep information that can become challenging to extract, interpret, and interface with other experimental outcomes. > This training course is aimed at researchers who are not expert in proteomics and want to integrate quantitative proteomics results into wider biomedical experiments. We will focus on quality control from an end-user perspective, link to the underlying genomic context, multivariate analysis, protein complexes investigation, and compare different platforms for biological interpretation. > After the training, participants will be able to critically interpret results, troubleshoot analyses, and will be ready to successfully attend more specialized training e.g. in proteogenomics or biological network analysis. > > For more information, including details about meeting the pre-requisites and how to apply, please visit: > > http://gtpb.igc.gulbenkian.pt/bicourses/2019/IBIP19/ > > Hoping that this course meets your interests, > > Pedro Fernandes > GTPB Coordinator > Biionformatics Training Coordinator, Bioidata.pt (Elixir-Portugal) > -- > The Gulbenkian Training Programme in Bioinformatics > Pedro L. Fernandes, Organiser > Instituto Gulbenkian de Ciência > Rua da Quinta Grande, 6 > 2780-156 OEIRAS > Portugal

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Workshop on biological data visualisation
by Jan Aerts 26 Sep '19

26 Sep '19

Dear all, We are again organising the workshop on biological data visualisation at the EBI in March 2020. Participants of this workshop will get acquainted with the fundamentals of data visualisation, be introduced to visual design, and practise coding these visualisations (depending on their background: in vega or D3). For more information and registration, see here: https://www.ebi.ac.uk/training/events/2020/data-visualisation-biology-pract… Jan Aerts

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Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
by Laurent Gatto 26 Sep '19

26 Sep '19

A position for a PhD student or post-doctoral research is open in the group of Prof Laurent Gatto at the UCLouvain (Brussels, Belgium) in collaboration with Prof Vince Carey at Harvard University (Boston, MA, USA) to develop the necessary infrastructure and statistical software to integrate genomic, mass spectrometry-based quantitative proteomics and transcriptomics expression data. The promise of omics integrative approaches is that the whole will become more than the sum of its parts and will thus reveal new insights into the comprehension of the underlying biology. Natural candidates for such integration are proteomics and transcriptomics. Both approaches aim, among other things, at measuring differences in expression of genes, albeit measuring different biological entities. Different studies have recorded diverging observations about the correlation of the measurements. The goal of this project is to develop and expand the Bioconductor infrastructure into an integrative proteogenomics framework to ensuring explicit and robust integration of quantitative proteomics, transcriptomics and genomics data. The successful candidate will be able to demonstrate experience in the following areas: - You have a master's degree or a PhD in computational biology/bioinformatics, computer science, data science, statistics, computer/electrical engineering, physics, or other related fields. - You have hands-on experience in analysing and interpreting omics data. - You have created/maintained/used software to address research problems in high throughput biology. - You are committed to open research best practices and know how to adapt these to biomedical research contexts. The ideal candidate will be able to demonstrate at least some of the following skills: - Experience with the processing and analysis of omics data (important). - Good knowledge of the R programming language and the Bioconductor infrastructure (important). - Experience in open and reproducible research, open source software and open data (important). - Experience in high performance computing (desirable). - Experience in C/C++ (desirable). - Experience with code versioning and collaborative tools such as, for example, git, and GitHub/GitLab (desirable). - Experience with other languages commonly used in computational biology and bioinformatics like Python or Julia (optional). - Knowledge of French and English is desirable. The contract is full time for a duration of 3 years (for the post-doctoral position) or 4 years (for the PhD position) and is available immediately. Candidates must be in a situation of “international mobility”, i.e. they should not have resided or carried out their main activity (work, studies, etc.) in Belgium for more than 12 months in the 3-year period before submission of their application. We value equality, diversity and an open, collaborative and welcoming work environment. To apply, please send your application by email to Laurent Gatto referencing this position, including a CV with publications and software outputs, a 1-page statement of research interests and names and email addresses of three references. Do not hesitate to contact Laurent Gatto (laurent.gatto(a)uclouvain.be) for additional information.

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