- BBClist - maillist.psb.ugent.be

job vacancy Project Lead Artificial Intelligence
by BeNeLux bioinformaticians forum 09 Oct '23

09 Oct '23

Dear Sirs, Could you please share the vacancy below with the mailing list? *Project Lead Artificial Intelligence* *Job objective * Our organization keeps moving. This results in a fast-changing and, therefore, challenging environment. As a Project Lead Artificial Intelligence and Data Science you strengthen the R&D Trait Genetics group. With your solid background in bioinformatics you lead projects, work packages and activities on the design of algorithms and pipelines using high throughput phenotyping methods like imaging data. You translate these pipelines into solutions for our global breeding and research programs. In addition, you are responsible for setting up, developing and maintaining the IT solutions for our Trait Genetics team. Collaboration is key for this job position. You will work closely with breeders and scientists from different backgrounds (including bioinformatics, biology, genetics, phytopathology and trait discovery) to develop tailored solutions that meet their needs. You will report to the Technology Lead Trait Genetics in the Breeding Technology Centre in De Lier. *Your tasks and responsibilities* · Design, improve and maintain innovative software solutions for large data challenges within the global Dümmen Orange R&D portfolio. · Initiate and lead work packages and projects on developing pipelines for computer vision (preprocessing, segmentation, machine learning, deep learning, etc), which feed into genomic analyses and molecular breeding applications. · Deploy software tools and pipelines for routine breeding application through automation or for end-users through web-apps or Notebooks. · Perform scouting activities for novel tools and technologies. · Design, improve and maintain IT infrastructure and solutions for our Trait Genetics team. · Build and maintain an internal and external network of collaborations. · Provide functional and organizational leadership. *Your profile* · PhD in a relevant field in computer science or biology with a strong computational focus (for example bioinformatics, data science) and preferably >2 years experience in industry. · You have a thorough understanding of the Linux operating system and are proficient in coding in Python and R (other programming languages are nice to have). - Proven experience in advanced computer vision applications preferably using various deep learning approaches (for example for object detection and segmentation). - Proven experience in analyzing large datasets and data visualization. · Experience with DevOps (Kubernetes, Docker), databases (SQL), workflow management (Airflow) and cloud computing (Azure) is desirable. · Experience with front-end development (Dash, Pyscript, Rshiny) is desirable. - Prior knowledge of biology is not essential, but affinity with plant breeding and quantitative genetics is desirable. · Ability to work independently as well as in fast-paced multidisciplinary teams. · Inquisitive, innovative and critical mind-set and a creative and pro-active attitude. · Ability to communicate across disciplines and functions. · Excellent command of English and willingness to learn Dutch. Vancy can be found online on : https://emea.dummenorange.com/site/nl/vacatures/detail?job=project-lead-art… *Camillo Berenos*

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[bioinfo] CMSB 2022: call for participation
by BeNeLux bioinformaticians forum 09 Oct '23

09 Oct '23

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Vacancy: PhD position in computational single-cell cancer biology
by BeNeLux bioinformaticians forum 04 Oct '23

04 Oct '23

Dear all, For an exciting project using state-of-the-art single cell measurements to elucidate the interplay between cell state and drug response in cancer we are looking for an enthusiastic PhD candidate with a strong quantitative background. The position is shared between the groups of Lodewyk Wessels (NKI) and Evert Bosdriesz (VU). Deadline for application is October 22. More information in the link. https://werkenbij.vu.nl/ad/phd-kwf-cell-state-dependent-drug-response/mq7m4j Kind regards, Evert Bosdriesz ---- Assistant Professor Bioinformatics - VU Amsterdam www.evertbosdriesz.org<http://www.evertbosdriesz.org> | e.bosdriesz(a)vu.nl<mailto:e.bosdriesz@vu.nl>

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BioSB news - courses and events
by BeNeLux bioinformaticians forum 27 Sep '23

27 Sep '23

Dear all, The BioSB research school is happy to invite you to the HotTopic Symposium: Computational Methods for (single cell) Spatial Data Analysis<https://www.dtls.nl/events/biosb-hottopics-symposium-computational-methods-…> – LUMC Leiden, 17 November 2023 (Free entrance after registration) BioSB and ‘single cell network Netherlands’ (scNL) are co-organising this symposium. The goal of this informal meeting is to bring together people who are interested in this topic in order to learn about the latest development, and to build a community. For more information click here. <https://www.dtls.nl/events/biosb-hottopics-symposium-computational-methods-…> BioSB also announces that registration is open for BioSB course: Integrated Modeling and Optimization<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…> - Wageningen, 11 - 15 December 2023 (early bird fee till October 16) In validating models one always meet with the need to fit models to data. So, the parameters that are present in any realistic model have to be chosen based on comparison of model predictions with data. In this matching process optimization techniques are indispensable. That’s why a considerable part of this course is spent on getting you acquainted with the optimization techniques that are nowadays available and widely used. Numerical optimization also is the basis for so-called flux balance analysis (FBA), commonly used to study large metabolic networks. This type of models and their analysis and simulation is also introduced in the course. For more information click here<https://www.dtls.nl/courses/integrated-modeling-and-optimization-fundamenta…>. Last but not least: please mark your calendars and SAFE THE DATE for The BioSB 2024 conference: 18 - 19 June 2024, Egmond aan Zee, NL. More information will follow soon! We hope to see many of you at one of the BioSB events and courses. Be welcome! Best regards, Petra Aarnoutse BioSB community manager [cid:part1.pLKCtXnZ.4aYrC2St@health-RI.nl]

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Open Positions - BioMed X, Germany
by BeNeLux bioinformaticians forum 25 Sep '23

25 Sep '23

Hello, My name is Bianca, and I am the Recruiting & Communications Manager at the BioMed X Institute<https://bio.mx/>, in Heidelberg, Germany. We have two open positions in one of our research teams - Team VPE<https://bio.mx/research-teams/artificial-intelligence/team-vpe/>, Virtual Patient Engine - to be filled out by researchers with expertise in machine learning/AI and bioinformatics. Would it be possible for you to advertise these two positions? We would be very grateful for your help. Here are the links, let me know if you require more information (or if the information needs to be in a different format): 1) Bioinformatician Position at BioMed X<https://atpscan.global.hornetsecurity.com/index.php?atp_str=kpHUHng3sjeHbfj…> 2) Algorithm Researcher Position at BioMed X<https://atpscan.global.hornetsecurity.com/index.php?atp_str=EspSwRYAmgFUwDv…> Thank you very much! Best wishes, Bianca --------------------------------------------------- Flavia-Bianca Cristian PhD Recruiting & Communications Manager [cid:image001.jpg@01D9EFBF.4A084BF0] BioMed X GmbH Im Neuenheimer Feld 515 69120 Heidelberg, Germany Tel.: +49 6221 426 11 706 Mobile: +49 172 7540707 E-Mail: fbc(a)bio.mx<mailto:fbc@bio.mx> ----------------------------------------------------------------------------------------- Principal Office: Heidelberg Commercial Register: Mannheim, HRB 716390 Managing Director: Dr. Christian Tidona Chairman of the Supervisory Board: Dr. Gerhard Ries -----------------------------------------------------------------------------------------

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PhD application: Integration of multi-omics data for the analysis of microbial community dynamics in plant health
by BeNeLux bioinformaticians forum 23 Sep '23

23 Sep '23

Hi, Please find hereafter an annoncement for a PhD position at INRAe and Inria in modelling and applied mathematics, for the integration of multi-omic data in microbial community models in plant health. https://doctorat.campusfrance.org/en/CF202333407 Sincerely, Valentina Baldazzi & Simon Labarthe

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Vacancy: PhD position in computational single-cell cancer biology
by BeNeLux bioinformaticians forum 21 Sep '23

21 Sep '23

Dear all, For an exciting project using state-of-the-art single cell measurements to elucidate the interplay between cell state and drug response in cancer we are looking for an enthusiastic PhD candidate with a strong quantitative background. The position is shared between the groups of Lodewyk Wessels (NKI) and Evert Bosdriesz (VU). More information in the link. https://werkenbij.vu.nl/ad/phd-kwf-cell-state-dependent-drug-response/mq7m4j Kind regards, Evert Bosdriesz ---- Assistant Professor Bioinformatics - VU Amsterdam www.evertbosdriesz.org | e.bosdriesz(a)vu.nl

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Conference ELIXIR Belgium: Your data, Our services, European success - Registration open
by BeNeLux bioinformaticians forum 21 Sep '23

21 Sep '23

Dear, We are pleased to invite you to the ELIXIR Belgium conference: Your data, Our services, European success which will take place on 23 & 24 October 2023 in Ghent. At this year's national meeting, we will showcase the variety of services in our portfolio with scientists illustrating how the services facilitate their research. The connection with existing European initiatives will also be demonstrated. For the first time, our national event will run for two days - starting on Monday 23 October in the afternoon. Also new are the poster sessions covering more services and providing space for engaging discussions and networking. <https://www.elixir-belgium.org/events/elixir-belgium-your-data-our-services…>Link to the programme and registration <https://www.elixir-belgium.org/events/elixir-belgium-your-data-our-services…>. The registration deadline is 10 October 2023. Please feel free to advertise this further in your network. On behalf of the organising committee, Kim De Ruyck Kim De Ruyck, PhD VIB Data Core ELIXIR Belgium Node Coordinator Technologiepark-Zwijnaarde 71 9052 Zwijnaarde, Belgium

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Amazing opportunities to learn Git and GitHub!
by BeNeLux bioinformaticians forum 23 Aug '23

23 Aug '23

[cid:image001.png@01D91546.6FFD3720] [signature_2008044598] Git and GitHub at VIB/ELIXIR-BE, check NOW! Dear colleagues, Join us for some amazing training sessions! Don’t forget to subscribe! Introduction to Git & GitHub ____________________________________________________________________________________ 11th and 12th Sep 2023 – Leuven Face to Face training This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers The course will happen in the Park inn by Radisson in Leuven, next to the trains station (only 3 min walk). Easy to find! 2 days you can use Git on your own projects and for collaborations! Come join us! If you want to know of more about VIB<https://training.vib.be/all-trainings?date=Upcoming%20trainings> and ELIXR-BE<https://www.elixir-belgium.org/training> trainings, check our website. VIB Technology Training & ELIXIR Belgium Training teams Technologiepark-Zwijnaarde 75 9052 Zwijnaarde, Belgium [signature_2008044598] [cid:image001.png@01D91546.6FFD3720] [cid:image003.png@01D966EB.C9291200]

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Autumn courses at VIB/ELIXIR-BE, check NOW!
by BeNeLux bioinformaticians forum 18 Aug '23

18 Aug '23

[cid:image001.png@01D91546.6FFD3720] [signature_2008044598] [Pumpkin with solid fill] Autumn courses at VIB/ELIXIR-BE, check NOW! Dear colleagues, Join us for some amazing training sessions! Don’t forget to subscribe! Introduction to Git & GitHub ____________________________________________________________________________________ 11th and 12th Sep 2023 – Leuven Face to Face training This workshop will take you through the basic use of Git and GitHub. Git is a free and open source distributed version-control system designed to maintain code, track changes, recover old versions and collaborate with other developers Registration and info: Link for Git & GitHub<https://training.vib.be/all-trainings/introduction-git-github-7> Docker and Singularity for reproducible and automated data analysis ____________________________________________________________________________________ 12th and 13st Oct 2023 – Brussels Face to Face training The course will give an introduction to containers (Docker & Singularity) which are great components to achieve portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, Singularity will be highlighted as well. Registration and info: Docker and Singularity <https://training.vib.be/all-trainings/docker-and-singularity-apptainer-repr…> Nextflow for reproducible and automated data analysis ____________________________________________________________________________________ 16th and 17st Nov 2023 – Ghent Face to Face training You will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language. Registration and info: NextFlow<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…> Research Data Management: your ally on the way to your publication ____________________________________________________________________________________ 13th and 14st Nov 2023 – Leuven Face to Face training It is better to start with the publication in mind! In this course you will learn how to use Research Data Management (RDM) in order to improve the writing of your publications and potentially increase its impact. Starting from basic concepts together with hands-on activities and discussions, during two days you will learn how to standardize, document and submit your data in a repository and how all of this will help you to underpin your publication! Registration and info: RDM is your ally<https://training.vib.be/all-trainings/research-data-management-your-ally-wa…> If you want to know of more about VIB<https://training.vib.be/all-trainings?date=Upcoming%20trainings> and ELIXR-BE<https://www.elixir-belgium.org/training> trainings, check our website. VIB Technology Training & ELIXIR Belgium Training teams Technologiepark-Zwijnaarde 75 9052 Zwijnaarde, Belgium [signature_2008044598] [cid:image001.png@01D91546.6FFD3720] [cid:image003.png@01D966EB.C9291200]

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