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April 29 – May 10, 2024: May Institute on computation and statistics for mass spectrometry and proteomics
by BeNeLux bioinformaticians forum 29 Jan '24

29 Jan '24

Dear colleagues, See below for a highly recommended course on computational mass spectrometry and proteomic. For more information, please contact Olga Vitek (o.vitek(a)northeastern.edu) Best, Wout ________________________________ Dear friends and colleagues: The May Institute on Computation and Statistics for Mass Spectrometry and Proteomics, taking place on April 29 – May 10, 2024 on the campus of Northeastern University in Boston MA, is now accepting applications. The application deadline is February 15, 2024. Instructors are leading experts, who contributed numerous experimental and computational methods and software. The target audiences are both beginners and experienced scientists, with both experimental and computational expertise. Participants can select a subset of the following programs: * April 29 - May 1, Quantitative proteomics with Skyline. Lead instructors: Tina Ludwig, Brendan MacLean and Lindsay Pino * May 1 – May 3, Beginners R and beginners statistics. Lead instructor: Ryan Benz * May 1 – May 3, Intermediate R, data visualization and statistics. Lead instructor: Kylie Bemis * May 6 – May 8, Statistics for quantitative mass spectrometry: methods and case studies with MSstats. Lead instructors: Olga Vitek and Devon Kohler * May 6, Analysis of mass spectrometry images with Cardinal. Lead instructor: Kylie Bemis * May 7, Modern software development practice with Python. Lead instructor: Charles Tapley Hoyt * May 8, Scientific writing. Lead instructor: Alicia Williams * May 8 – May 10, Interpretation of proteomic experiments in the context of biomolecular networks with INDRA. Lead instructor: Ben Gyori * May 10, Barnett Institute 50th Anniversary and Karger Medal Celebration. Featured speakers: Jenny Van Eyk and Nikolai Slavov A limited number of registration fee wavers will be available for students and postdocs affiliated with academic or nonprofit institutions in the US. Please share this widely. More information is at https://computationalproteomics.khoury.northeastern.edu/

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Learning to Code with Dodona: A Webinar for Educators - 13 March 2024, 11h-12h CET
by BeNeLux bioinformaticians forum 24 Jan '24

24 Jan '24

[cid:image010.png@01DA4EB4.82646BB0] Learning to Code with Dodona: A Webinar for Educators Discover how Dodona (https://dodona.be/en) can enhance your programming, statistics and data science education in this special webinar for educators. In 1 hour, you will learn about: 1. Dodona’s user-friendly interface, and how its automated feedback system smoothly integrates into your curriculum and significantly elevates the learning experience; 2. Dodona's extensive library of coding exercises, suitable for various languages and skill levels; 3. how to create personalized exercises to meet specific teaching goals. The session will be hands-on, so you’re sure to leave with actionable insights to effectively implement Dodona into your courses. Furthermore, Prof. Lieven Clement will share how he successfully created a basic R skills course with Dodona. That course was an independent learning module in his university class, illustrating the practical application of Dodona in a real-world academic setting. Join us for an engaging overview of how Dodona can be a vital tool in your educational arsenal! REGISTER HERE<https://us06web.zoom.us/meeting/register/tZ0uf-2gqj8tHNW0HJJdRfkeirXPgA0MbI…> [Bart Mesuere (@BartMesuere) / X] Bart Mesuere Prof. Big Data Science University of Ghent [Peter Dawyndt | ELIXIR Belgium] Peter Dawyndt Prof. Computational Biology University of Ghent [Prof. dr. Lieven Clement | UGAIN - UGent academie voor ingenieurs] Lieven Clement Ass. Prof. Statistical Genomics University of Ghent

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'RNA-seq Data Analysis' - BioSB course - 8-12 April
by BeNeLux bioinformaticians forum 23 Jan '24

23 Jan '24

Dear all, Check this out! ________________________________ RNA-sequencing Data Analysis<https://www.dtls.nl/courses/rna-seq-data-analysis-2024/> <https://www.dtls.nl/courses/rna-seq-data-analysis-2024/>BioSB course, Breda, 8 - 12 April 2024 (9th edition!) ________________________________ (Be quick, early bird discount ends on 11 February!) What is this course about? This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. The course consists of a mixture of lectures and Galaxy, Linux and R practicals. Also the potential of long-read based RNA-seq and AI based analysis enrichments will be explored. Renowned teachers will be happy to teach you the latest insights and skills! More information and registration: click here<https://www.dtls.nl/courses/rna-seq-data-analysis-2024/> We look forward to welcoming you. Kind regards, Petra Aarnoutse Community manager BioSB [cid:part1.qY990pC0.sfRrox51@health-RI.nl]

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'RNA-seq Data Analysis' - BioSB course - 8-12 April
by BeNeLux bioinformaticians forum 23 Jan '24

23 Jan '24

Dear all, Check this out! ------------------------------------------------------------------------ *RNA-sequencing Data Analysis* <https://www.dtls.nl/courses/rna-seq-data-analysis-2024/> <https://www.dtls.nl/courses/rna-seq-data-analysis-2024/> *BioSB course, Breda, 8 - 12 April 2024 (9th edition!)*** ------------------------------------------------------------------------ *(Be quick, early bird discount ends on 11 February!) * * What is this course about?** *This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. The course consists of a mixture of lectures and Galaxy, Linux and R practicals. Also the potential of long-read based RNA-seq and AI based analysis enrichments will be explored. Renowned teachers will be happy to teach you the latest insights and skills! *More information and registration: **click here* <https://www.dtls.nl/courses/rna-seq-data-analysis-2024/>* *We look forward to welcoming you.* ** *Kind regards, Petra Aarnoutse Community manager BioSB*** ***

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Disease Maps Community Meeting 2024: Abstract submission deadline extended
by BeNeLux bioinformaticians forum 22 Jan '24

22 Jan '24

[Apologies for multiple postings] Call for abstracts for the 8th Disease Maps Community Meeting extended! https://disease-maps.org/DMCM2024 Submit your abstracts via the EasyChair link<https://easychair.org/cfp/dmcm2024> by 31 January 2024. Register via this registration form<https://disease-maps.org/DMCM2024#:~:text=Please%20register%20by%2025th%20F…> by 24 February 2024. DMCM’24 a joint event of the Disease Maps Community<https://disease-maps.org/> and the ELIXIR Systems Biology Community<https://elixir-europe.org/communities/systems-biology>. See the agenda<https://disease-maps.org/DMCM2024/programme/> for more details. Keynote speakers * James Glazier, Professor of Intelligent Systems Engineering, Professor & Director of Biocomplexity Institute Biophysics, Indiana University, Bloomington, USA * Liesbet Geris, Collen-Francqui Research Professor in Biomechanics and Computational Tissue Engineering, University of Liège and KU Leuven, Belgium * Henning Hermjakob, Head of Molecular Systems Services, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK * Reinhard Schneider, Head of Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg Featured workshop imSAVAR Symposium: Disease maps and irAOPs in the immune system effects of immunomodulatory therapies. Scope We will focus on systems medicine topics, including tools, standards, and applications of bioinformatics, computational and systems biology to research on human diseases. Join us to discuss challenges of building reliable models of disease mechanisms from prior knowledge and data, and applying their predictions. The topics include, but are not limited to: * Curation of diagrammatic models of diseases using systems biology standards * Visual analytics of systems biology diagrams * Modelling of disease mechanisms: network-based, Boolean or continuous * Interpreting multi-omics data using systems biology diagrams * Using omics data for model building and parameterisation Abstract Submission Deadline: 31 January 2024 (the EasyChair link<https://easychair.org/cfp/dmcm2024>) Registration Deadline: 24 February 2024 (registration form<https://disease-maps.org/DMCM2024#:~:text=Please%20register%20by%2025th%20F…>) When: 25th-27th of March 2024 Where: University of Luxembourg, Campus Belval, Maison du Savoir 2, avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg https://www.uni.lu/en/about/campuses/belval-campus For all details see https://disease-maps.org/DMCM2024<https://disease-maps.org/DMCM2024> With warm regards, on behalf of the organisers --- Marek Ostaszewski University of Luxembourg Luxembourg Centre for Systems Biomedicine (LCSB) Campus Belval | House of Biomedicine 6, avenue du Swing, L-4367 Belvaux, Luxembourg Tel: +352 46 66 44 5604<tel:+3524666445604> http://lcsb.uni.lu<http://lcsb.uni.lu/>

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ESSAI 2024 CALL FOR COURSE PROPOSALS
by BeNeLux bioinformaticians forum 17 Jan '24

17 Jan '24

ESSAI 2024 CALL FOR COURSE PROPOSALS (Apologies for multiple postings) The 2nd European Summer School in Artificial Intelligence - ESSAI 2024 July 15-26, 2024 Athens, Greece https://essai2024.di.uoa.gr/ IMPORTANT DATES 07 Feb 2024: Course Title submission deadline (mandatory) 14 Feb 2024: Final submission 06 Mar 2024: Notification ABOUT ESSAI 2024 is the second edition of the annual summer school on AI held under the auspices of the European Association for Artificial Intelligence (EurAI). ESSAI 2024 will provide an interdisciplinary setting in which courses are offered in all areas of Artificial Intelligence and also from wider scientific, historical, and philosophical perspectives. ESSAI is a central meeting place for students and young researchers in Artificial Intelligence to discuss current research and share knowledge. Courses will consist of five 90-minute sessions, offered daily (Monday-Friday) in a single week, to allow students to develop in-depth knowledge of a topic. The first edition of ESSAI was held in Ljubljana, Slovenia (https://essai.si/ ) between the 24th and 28th of July 2023 and was extremely successful, attracting over 500 participants. We look forward to a second edition of ESSAI that is at least as successful. TOPICS AND FORMAT ESSAI aims to cover all subdisciplines of AI and the interactions between them. Proposals for courses at ESSAI 2024 are invited in all areas of Artificial Intelligence, including but not limited to the following: * Autonomous Agents and Multi-agent Systems (MAS) * Causality and Causal Learning (CL) * Ethical, Legal and Social Aspects of AI (ELS) * Foundation Models (FM) * Knowledge Representation and Reasoning (KR) * Learning Theory (LT) * Natural Language Processing (NLP) * Neuro-Symbolic Learning and Reasoning (NSLR) * Planning and Strategic Reasoning (PLAN) * Reinforcement Learning (RL) * Robotics (ROB) * Safe, Explainable and Trustworthy AI (SET) * Search and Optimization (SO) * Supervised and Unsupervised Learning (ML) * Vision (VIS) Each course will consist of five 90-minute lectures, offered daily (Monday-Friday) in a single week. While introductory courses will typically focus on one subarea of AI, advanced courses are encouraged to present a broader perspective on AI and should be of interest beyond one specific area. CATEGORIES Each proposal should fall under one of the following categories. INTRODUCTORY COURSES Introductory courses are intended to introduce a research field to students, young researchers, and other non-specialists, and to foster a sound understanding of its basic methods and techniques. Such courses should enable researchers from related disciplines to develop some comfort and competence in the topic considered. Introductory courses in a cross-disciplinary area may presuppose general knowledge of the related disciplines. ADVANCED COURSES Advanced courses are targeted primarily to graduate students who wish to acquire a level of comfort and understanding in the current research of a field. PROPOSAL GUIDELINES To be considered, course proposals should closely adhere to the following guidelines: * Courses must be presented by lecturers who submitted the proposal. For courses with more than two lecturers, the role of each lecturer should be clearly explained and justified in the proposal. * Course proposals should explicitly state the intended course category. Proposals for introductory courses should indicate the intended level, for example, as it relates to standard textbooks and monographs in the area. Proposals for advanced courses should specify the prerequisites in detail. Proposals must be submitted in PDF format via: https://easychair.org/conferences/?conf=essai2024 and include all the following: 1. Personal information for each proposer: Name, affiliation, contact address, email, homepage (optional) 2. General proposal information: Title, category 3. Information about the course content: a. Abstract of up to 150 words b. Motivation and description (up to two pages) c. Tentative outline d. Expected level and prerequisites e. Appropriate references (e.g., textbooks, monographs, proceedings, surveys) f. Whether the course will appeal to students outside of the main discipline of the course 4. Information about the proposer(s): a. Short CVs of the proposer(s) b. Evidence that the proposer(s) are excellent lecturers with relevant teaching experience, in particular in delivering intensive courses in an interdisciplinary setting. To keep participation fees to a minimum, all the instructional and organizational work of ESSAI is performed on a completely voluntary basis. However, the registration fees of organizers and instructors will be waived. In addition, and where appropriate, ESSAI will seek to partially reimburse travel and accommodation expenses associated with delivering a course. If lecturers can cover their travel and accommodation expenses from other sources, this is greatly appreciated. SUBMISSION INFORMATION By February 7, 2024: Proposers must submit on EasyChair at least the name(s) of the lecturers(s), the ESSAI area and course level and a short abstract. By February 14, 2024: Submission must be completed by uploading a PDF with the actual proposal as detailed above. SUBMISSION PORTAL Please submit your proposals to https://easychair.org/conferences/?conf=essai2024 ORGANIZING COMMITTEE Chair: Brian Logan, Utrecht University Co-chair: Magdalena Ortiz, TU Wien Local Chair: Manolis Koubarakis, National and Kapodistrian University of Athens ESSAI Steering Committee Chair (EurAI Board representative): Giuseppe De Giacomo, Oxford University

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Postdoctoral position in bioinformatics of the human gut microbiome - VIB
by BeNeLux bioinformaticians forum 12 Jan '24

12 Jan '24

> Begin forwarded message: > > From: Jeroen Raes <jeroen.raes(a)kuleuven.be> > Subject: Postdoctoral position in bioinformatics of the human gut microbiome - VIB > Date: 11 January 2024 at 15:52:08 CET > > > Postdoctoral position in bioinformatics of the human gut microbiome > Leuven VIB-KU Leuven Center for Microbiology > > https://jobs.vib.be/j/69697/postdoctoral-position-in-bioinformatics-of-the-… > > > > — > Prof. Jeroen Raes, PhD > > Group leader, Bioinformatics and (eco-)systems biology lab > Department of Microbiology and Immunology, Rega institute, KU Leuven > > Vice-director, VIB Center for Microbiology > > KU Leuven - Campus Gasthuisberg > Herestraat 49 - box 1028 > 3000 Leuven > Belgium > > jeroen.raes(a)kuleuven.be <mailto:jeroen.raes@med.kuleuven.be> > Phone: +32 (0)16 330678 <tel:%2B32%20%280%2916%20330678> > http://www.raeslab.org <http://www.raeslab.org/> > > NOTE: All mail on my KU Leuven address is monitored by my PA, Elisa van der Zande (elisa.vanderzande(a)kuleuven.be <mailto:elisa.vanderzande@kuleuven.be>) - for personal matters, please contact me in person >

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Job Offer - Bioinformatics Scientist at BASF Nunhems Vegetable Seeds
by BeNeLux bioinformaticians forum 12 Jan '24

12 Jan '24

Dear all, We have a new vacancy for a bioinformatics scientist at BASF (Nunhems) Vegetable Seeds. At BASF | Nunhems it is our ambition to make healthy eating enjoyable and sustainable. Together and in collaboration with partners we are eager to improve our vegetable varieties and solutions for our customers, the vegetable value chain and consumers worldwide. To further develop and grow this ambition we are looking for a Scientist Bioinformatics. Your Job As Bioinformatics Scientist you build knowledge and insights from digital data. Together with bioinformatics colleagues at BASF Nunhems Vegetable Seeds, you are responsible for managing our genome-wide digital genetic resources, such as gold standard reference genomes, high quality gene annotation and population-wide re-sequencing. Together with our genomics and molecular biology colleagues, you create pipelines and tools for data acquisition and processing. You provide elegant and intuitive methods to create, explore and analyze large genetic resources, geared towards next-generation and long-read sequencing. Major Accountabilities • Create and maintain unsupervised data-analysis pipelines • Develop user-facing data applications • Data processing, ensure quality and delivery of routine analysis experiments • Design and execute bespoke analyses on multi-omics datasets • Provide specialized technical expertise and technical advice in relation to data management, workflow development and data analysis methods • Innovation; propose out-of-the-box solutions for the utilization, storage and management of data Key activities: Tool and Pipeline development • Use industry-standard methods to create and maintain data-analysis applications (e.g. git, test-driven, agile/scrum) • Develop client-server applications for data delivery and exploration using various interfaces (scripting clients, Web, API, etc) Routine and bespoke data processing • Align with molecular scientists on experimental design, project goals and applications. • Ensure analysis activities are focused and delivered on time Technology scouting and innovation • Identify computational methods and other opportunities to improve speed, quality and extract more value from our datasets. • Evaluate new technologies and create business cases for implementation. Together with Genomics and Molecular Genetic teams collaborate in developing databases, gold standard reference genomes, high quality gene annotation and functional genomics integrative tools that facilitate gene discovery. Your profile • Ph.D. in Bioinformatics, Systems Biology, Genomics, Molecular Biology, Plant Sciences, with a clear computational component, or computer sciences with a clear interest in plant biology • Proven expertise in creating and support digital solutions for biological challenges • Strong ability to create scalable and maintainable software in python • Above-average knowledge of at least one other programming language (R, SQL, Rust, C) • Proven competence in usage of software-development best practices (version control, TDD etc) • Knowledge of Linux HPC environments • Proficiency in data analysis and interpretation using relevant software and tools Do you recognize yourself in the following competencies and skills? • Strong communication and presentation skills to effectively collaborate with internal and external stakeholders • Self-motivated, innovative, and able to work both independently and collaboratively fast-paced research environment • Solution-driven, with attention to detail and quality • Curiosity and drive to understand the new genomic technologies • Strong entrepreneurial and innovative spirit are crucial Interested in this job? You will be successful in this position when you are able to create efficient applications for data processing and access, playing a crucial role in implementing the ‘big-data genomics’ side of the digitalization strategy. This position contributes to speed and novelty in variety development and trait and gene discovery by enabling genetic and genomic data to integrated breeding teams, also ensuring gene discovery securing IP for BASF. Ready to join this team and contribute to our ambition to make healthy eating enjoyable and sustainable for everyone worldwide? Send us your resume (CV) and motivation letter to contact Michiel Weijters, Senior Global Talent Acquisition Specialist via michiel.weijters(a)vegetableseeds.basf.com<mailto:michiel.weijters@vegetableseeds.basf.com> What’s in it for you? Adding value to our customers begins with adding value to you. At BASF we believe that people are the key to our long-term success and that talent is in everyone. That’s why we empower you with the tools, guidance and opportunities you need to advance and succeed in work and life. Giving you the support that you need to be your best and fulfill your personal ambitions is what helps us achieve our ambitions. After all, our success is linked to yours. Whatever path you envision, BASF is a great place to build a rewarding, successful career. For BASF, diversity is one of the essential keys to business success and the well-being of our employees. We promote an inclusive culture that accepts the diversity of people, experiences and capabilities. By embracing talents and abilities of all kinds, we aim to boost creativity and motivation, and enhance our teams’ performance. Personal Data When processing your personal data during the applicant’s procedure, Nunhems Netherlands BV adheres to the applicable law and regulations, amongst others the General Data Protection Regulation (“GDPR”). For more information about the processing of your data and your rights, we would like to refer you to our privacy notice for applicants on our website www.nunhems.com.

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Selected VIB Training Activities in February and March: register now
by BeNeLux bioinformaticians forum 10 Jan '24

10 Jan '24

Dear colleague, Happy New Year! As we step into 2024, we're excited about the opportunities that lie ahead. May this year bring you success, growth, and new horizons. Explore a selection of our upcoming courses and embark on a journey of learning and development. Introduction to Git & GitHub 5 & 6 February, Brussels<https://vib.lt.acemlnc.com/Prod/link-tracker?notrack=1&redirectUrl=aHR0cHMl…> Research Data Management: Your Ally on the Way to Your Publication 12 & 13 February, Ghent<https://vib.lt.acemlnc.com/Prod/link-tracker?notrack=1&redirectUrl=aHR0cHMl…> Apply Scop3PTM Web-interface to Understand PTMs of Proteins 6 March, Leuven<https://vib.lt.acemlnc.com/Prod/link-tracker?notrack=1&redirectUrl=aHR0cHMl…> Apply MutationExplorer to Study Mutation of Proteins and Visualize their Energetic Impact 6 March, Leuven<https://vib.lt.acemlnc.com/Prod/link-tracker?notrack=1&redirectUrl=aHR0cHMl…> Enjoy your training! Best regards, Alex

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Call for submissions: Disease Maps Community Meeting, 25th-27th of March 2024, Luxembourg
by BeNeLux bioinformaticians forum 09 Jan '24

09 Jan '24

Call for submissions for the 8th Disease Maps Community Meeting 2024 on 25th-27th of March 2024 in Luxembourg. https://disease-maps.org/DMCM2024 Submit your abstracts via the EasyChair link<https://easychair.org/cfp/dmcm2024> by 24 January 2024. Register via this registration form<https://disease-maps.org/DMCM2024#:~:text=Please%20register%20by%2025th%20F…> by 24 February 2024. DMCM’24 a joint event of the Disease Maps Community (https://disease-maps.org<https://disease-maps.org/>) and the ELIXIR Systems Biology Community (https://elixir-europe.org/communities/systems-biology) We plan intensive exchanges during panel discussions, poster sessions and focus group workshops. See the agenda<https://disease-maps.org/DMCM2024/programme/> for more details. Keynote speakers * James Glazier, Professor of Intelligent Systems Engineering, Professor & Director of Biocomplexity Institute Biophysics, Indiana University, Bloomington, USA * Liesbet Geris, Collen-Francqui Research Professor in Biomechanics and Computational Tissue Engineering, University of Liège and KU Leuven, Belgium * Henning Hermjakob, Head of Molecular Systems Services, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK * Reinhard Schneider, Head of Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg Featured workshop imSAVAR Symposium: Disease maps and irAOPs in the immune system effects of immunomodulatory therapies. Scope We will focus on systems medicine topics, including tools, standards, and applications of bioinformatics, computational and systems biology to research on human diseases. Join us to discuss challenges of building reliable models of disease mechanisms from prior knowledge and data, and applying their predictions. The topics include, but are not limited to: * Curation of diagrammatic models of diseases using systems biology standards * Visual analytics of systems biology diagrams * Modelling of disease mechanisms: network-based, Boolean or continuous * Interpreting multi-omics data using systems biology diagrams * Using omics data for model building and parameterisation Abstract Submission Deadline: 24 January 2024 (the EasyChair link<https://easychair.org/cfp/dmcm2024>) Registration Deadline: 24 February 2024 (registration form<https://disease-maps.org/DMCM2024#:~:text=Please%20register%20by%2025th%20F…>) When: 25th-27th of March 2024 Where: University of Luxembourg, Campus Belval, Maison du Savoir 2, avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg https://www.uni.lu/en/about/campuses/belval-campus For all details see https://disease-maps.org/DMCM2024<https://disease-maps.org/DMCM2024> With warm regards, on behalf of the organisers --- Marek Ostaszewski University of Luxembourg Luxembourg Centre for Systems Biomedicine (LCSB) Campus Belval | House of Biomedicine 6, avenue du Swing, L-4367 Belvaux, Luxembourg Tel: +352 46 66 44 5604 http://lcsb.uni.lu<http://lcsb.uni.lu/>

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