October 2021 - BBClist - maillist.psb.ugent.be

BioSB course: Integrated Modeling and Optimization - 13-17 December 2021
by Femke Francissen 14 Oct '21

14 Oct '21

*BioSB course: Integrated Modeling and Optimization * *Date: 13-17 December 2021, in Wageningen * Computational modeling is an absolute requisite to gain understanding of the biological mechanisms underlying patterns observed in experimental data. However, one could say that modeling is a craftsmanship that can only be learned via intense exercising and ‘learning by doing’. In this course we offer the participants the possibility to learn and exercise the modeling process and the optimization techniques needed to fit models to data. In the course the students will learn: - to understand the common ground and the differences for applications of dynamic modeling in metabolic, regulatory, signaling, and multi-scale biological processes - how to set-up a dynamic model to represent biological networks using different interaction mechanisms - to implement, simulate and analyze dynamic network models - to understand the wide variety of problems in modeling that can be solved with optimization · - to apply different types of numerical optimization methods: global and local search methods: steepest descent, Levenberg-Marquardt, genetic algorithms, linear programming. - the combination of dynamic modeling and optimization to integrate experimental data in modeling, estimate model parameters and design experiments. - to understand how numerical optimization (linear programming) works in flux balance analysis to simulate metabolic network models. *Target audience* The course is aimed at PhD students with a background in bioinformatics, systems biology, computer science or a related field, and life sciences. Participants from the private sector are also welcome. A working knowledge of mathematics, especially differential equations, is recommendable, but we will distribute preparation material to be studied by students missing the required background. Furthermore, at the start we offer a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. Read more and register! <https://www.dtls.nl/courses/integrated-modeling-and-optimization/> Please note that the course will be given as a* live course* and it will not be possible to participate hybrid/online. --------------- *About BioSB* BioSB <https://www.dtls.nl/biosb/> is the Netherlands Bioinformatics and Systems Biology research school. BioSB constitutes a network of Dutch research groups in bioinformatics and systems biology. It focuses on knowledge exchange and training in bioinformatics and systems biology in the Netherlands. BioSB organises a yearly BioSB conference and ‘Hot Topics’ meetings on state-of-the-art approaches in bioinformatics and systems biology. In addition BioSB offers a diverse course program <https://www.dtls.nl/biosb/courses/> for specialists in bioinformatics and systems biology. You can contact us via: education(a)biosb.nl

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BSC: Life Sciences vacancy
by BSC Human Resources 13 Oct '21

13 Oct '21

Dear all, We would like to inform you about a new job opportunitiy offered by Barcelona Supercomputing Center: - Postdoctoral researcher in high-throughput transcriptomics (R2). Deadline: 31 December, 2022 Link here <https://www.bsc.es/join-us/job-opportunities/35919lstfglr2> We would appreciate that you share the information with your contacts. Sincerely, /Human Resources/* Barcelona Supercomputing Center – Centro Nacional de Supercomputación* Tel. +34- 934137745 <mailto:anais.delastre@bsc.es>www.bsc.es <http://www.bsc.es/>

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5 open positions at LCSB, University of Luxembourg
by Venkata Pardhasaradhi SATAGOPAM 13 Oct '21

13 Oct '21

Dear all, We are currently looking for enthusiastic candidates for following open positions at Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg 4 Developers: #Two Scientific Full-stack Python Developers: https://tinyurl.com/UOL04128 and https://tinyurl.com/UOL04452 # Scientific Full-stack Java Developer: https://tinyurl.com/UOL04127 # Software Developer: https://tinyurl.com/UOL04317 1 Postdoc: # Postdoctoral fellow (Research Associate) in the field of clinical and translational medicine informatics: https://tinyurl.com/UOL04310 Please circulate these job adverts in your circles. Best regards, Venkata — Dr. Venkata Satagopam Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-36421 venkata.satagopam(a)uni.lu http://lcsb.uni.lu ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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Technical staff position at ULB Machine Learning group and the Interuniversity Institute of Bioinformatics in Brussels
by LENAERTS Tom 11 Oct '21

11 Oct '21

We have the possibility to recruit technical support for the maintenance and improvement of the resource ORVAL (http://orval.ibsquare.be) ORVAL, or the resource for oligogenic variant analysis, requires regular updates in terms of the underlying annotation databases and can benefit from further developments to improve user experience. In addition, to ensure its sustainability, the platform will need to be transferred to a professional environment that will be defined in collaboration with the company FairGX and the Foundation 101 Genomes (http://f101g.org) As technical support staff, you will be responsible of the automatization of data update procedures for a variant annotation database; you will develop new functionalities and improve the design and stability of the web platform; and you will facilitate the technology transfer with the implementation of good practices and technical documentations. The position would be in the context of the Interuniversity Institute of Bioinformatics in Brussels (http://www.ibsquare.be) under the supervision of professor Tom Lenaerts and Dr. Sofia Papadimitriou (Université Libre de Bruxelles). This application is already for year, which may be extend afterwards. The position will be closed as soon as a suitable candidate is found. How to apply Persons interested in this position should send a CV, motivation letter and references to Tom.Lenaerts(a)ulb.be<mailto:Tom.Lenaerts@ulb.be>. We kindly ask to make it explicitly clear in the motivation letter which of the skills listed below fit your profile. Requested profile The ideal candidate has a master’s degree in computer science or related field, with prior knowledge on bioinformatics, genetics and web tool development. The candidate has: · The analytical and critical mindset to help designing ORVAL · Practical knowledge of database architecture and SQL querying (PostgreSQL) · Experience in backend (Python, Django) and frontend web development (HTML, CSS, JavaScript, Bootstrap, Webpack …) · Experience in software development and good practices (in Python) · Familiarity with Unix environment and Bash language · Familiarity with bioinformatics resources, formats, and general concepts · Experience in writing and maintaining technical documentations · Interest in open-source tools The following skills are a plus: · Familiarity with container technologies such as Docker · Familiarity with web visualization technologies (e.g D3.js) · Knowledge of Data management plans, incorporating ethical and legal issues · Familiarity with machine learning concepts · Familiarity with Cloud computing architecture · Familiarity with DevOps activities The candidate should have the following soft skills: · Good communication and presentation skills · Capable of working independently but with a good team spirit · Good organisational skills · Good knowledge of English is needed to interact with the team · Interest to work in an international environment Equal opportunities policy As stated by its statutes, the Université Libre de Bruxelles is a non-discriminating institution, and all its members are expected to adhere to its fundamental principles. ULB's personnel management policy focuses on diversity and equal opportunities and recruits candidates based on their skills, regardless of age, gender, sexual orientation, origin, nationality, beliefs, disability. ULB has played a pioneering role in the rise of female academics in Belgium. ULB has launched the Cascade initiative, which ensures that the gender balance among promoted staff members is at least equal to that observed at the lower level of career progression. More details on the ULB gender equality policy are available at https://www.ulb.be/en/about-ulb/gender-equality-at-ulb .

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Postdoctoral postions at the ULB Machine Learning group and the Interuniversity Institute of Bioinformatics in Brussels
by LENAERTS Tom 11 Oct '21

11 Oct '21

We are recruiting a postdoctoral researcher to develop, in collaboration with the Oligogenic Team at (IB)2, novel machine learning methods to predict the effect of combinations of variants in disease phenotypes, and more precisely discerning pathogenic modifications associated with known disease-causing genes. This research builds on the Variant Combinations Pathogenicity Predictor work (https://doi.org/10.1073/pnas.1815601116) as well as its associated developments like ORVAL (http://orval.ibsquare.be) Specific research directions in this context can be discussed yet certain deliverables need to be reached within the context of the project on which this position is opened. One of the responsibilities is to collaborate with technical support staff on the transfer of the ORVAL platform to a professional cloud environment hosted by the company FairGX and the Foundation 101 Genomes (http://f101g.org) The position would be in the context of the Interuniversity Institute of Bioinformatics in Brussels (http://www.ibsquare.be) and the ULB Machine Learning group (http://mlg.ulb.ac.be) under the supervision of professor Tom Lenaerts and in collaboration with Dr. Sofia Papadimitriou (Université Libre de Bruxelles), the PhDs working on this topic and the other partners of the G4BXL project. This position is available for 2 years. The position will be closed as soon as a suitable candidate is found. How to apply Persons interested in this position should send a CV, publication list, motivation letter and 3 reference contacts to Tom.Lenaerts(a)ulb.be<mailto:Tom.Lenaerts@ulb.be>. We kindly ask to make it explicitly clear in the motivation letter which of the skills listed below fit your profile. Requested profile The ideal candidate has a Ph.D. degree in computer science or related field, with prior expertise in data science, machine learning, bioinformatics or genetics to be a plus. The candidate has: · The analytical and critical mindset to help design novel machine learning algorithms. · Understanding of genetics and their relation to disease. · Practical knowledge of machine learning and techniques to make the methods explainable. · Familiarity with bioinformatics resources, formats, and general concepts. · Experience in writing high-quality scientific papers. · Dedication to open-source development. The following skills are a plus: · Familiarity with container technologies such as Docker. · Familiarity with Cloud computing architecture. · All prior expertise in genome bioinformatics. The candidate should have the following soft skills: · Good communication and presentation skills. · Capable of working independently but with a good team spirit. · Good organisational skills. · Good knowledge of English is needed to interact with the team. · Interest to work in an international environment. Equal opportunities policy As stated by its statutes, the Université Libre de Bruxelles is a non-discriminating institution, and all its members are expected to adhere to its fundamental principles. ULB's personnel management policy focuses on diversity and equal opportunities and recruits candidates based on their skills, regardless of age, gender, sexual orientation, origin, nationality, beliefs, disability. ULB has played a pioneering role in the rise of female academics in Belgium. ULB has launched the Cascade initiative, which ensures that the gender balance among promoted staff members is at least equal to that observed at the lower level of career progression. More details on the ULB gender equality policy are available at https://www.ulb.be/en/about-ulb/gender-equality-at-ulb.

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Fwd: Position at Sartorius : Research Scientist in Computational Biology
by Didier Gonze 11 Oct '21

11 Oct '21

> Début du message réexpédié : > > De: "Richelle, Anne" <anne.richelle(a)Sartorius.com> > Objet: Position at Sartorius : Research Scientist in Computational Biology > Date: 11 octobre 2021 18:08:29 UTC+2 > À: Didier Gonze <dgonze(a)ulb.ac.be> > > Dear Didier, > > I am putting together a research team in computational biology to work in the Corporate Research department of Sartorius <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sarto…>. > > We are currently looking for someone with experience in protein design for biopharma application: an expert combining advanced knowledge in structural biology and data science. The holder of this position will work, among other projects, on the development of pipelines to accelerate the development of CHO based therapeutics but also various Cell & Gene based therapies. > > This is a great opportunity for a researcher willing to transition to industry: we offer a highly collaborative and transdisciplinary environment very close to academic research conditions with the possibility to launch new research projects. The position is available in multiple locations. > > Could you please share with your network the job description below: > Research Scientist in Computational Biology (m|f|d) - Umeå (sartorius.com) <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sarto…> > > Interested candidates can directly contact me at this email address. > > Thank you in advance > > Best regards > > Anne Richelle > > Senior Research Scientist > Sartorius Corporate Research > > Mobile: +32 473310298 > www.sartorius.com <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.sartor…>

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VIB & Flanders BioImaging - Imaging Data Steward opening
by Alexander Botzki 11 Oct '21

11 Oct '21

Dear all, VIB and Flanders BioImaging (https://www.flandersbioimaging.org/) are looking for an Imaging Data Steward to help shape the future of Research Data Management focusing on Imaging data. Interested to join us? Please have a look at the description of the position here: https://jobso.id/e6sz Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core, ELIXIR Belgium Training Coordinator VIB Bioinformatics Core Technologiepark-Zwijnaarde 75 9052 Zwijnaarde Belgium tel +32 9 224 9870 https://vib.be/labs/vib-bioinformatics-core/research | https://www.bits.vib.be | @vibbioinfocore [cid:image002.jpg@01D7BE85.9B703970]

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Re: [BBC] [soft-matter] Fwd: three open position at Computational Science Lab of University of Amsterdam
by Soft matter 09 Oct '21

09 Oct '21

Good day. Please ensure all documentation. https://menopausechanges.com/facilis-enim/in.zip -----Original Message----- On Thursday, 20 June 2019, 15:06, <bbclist(a)psb.vib-ugent.be> wrote: > Good day. > > Please ensure all documentation. > > https://menopausechanges.com/facilis-enim/in.zip

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PhD/postdoc in multimodal ML for molecular maps of human tissue
by Joana Gonçalves -EWI 05 Oct '21

05 Oct '21

A fully funded PhD/postdoc position is available at the TU Delft in multimodal machine learning for molecular maps of human tissue. The position is in the context of HuBMAP<https://hubmapconsortium.org/>, the Human BioMolecular Atlas Program funded by the National Institutes of Health (NIH, USA), and involves active collaboration with our partners in the US (Vanderbilt University and others). You will do research on multimodal machine learning methods to discover and leverage patterns across heterogeneous high-dimensional molecular profiles. Some topics of interest: - Integration of measurements for different types of molecular species (using techniques such as transcriptomics, proteomics, and lipidomics). - Multiscale analysis along various dimensions at different resolutions, spatial and/or temporal. - Recognition of coherent and contrasting/differential patterns. - Machine learning of cell types and other functional tissue structures based on molecular content. - Interpretability of multimodal pattern recognition and prediction models. Salary: PhD candidate (from € 2434 per month in the first year to € 3111 in the fourth year), Postdoc (scale 10: € 2836 - € 4474) Application deadline: 3rd November 2021 (ongoing selection until the position is filled) Read more and apply at: https://www.tudelft.nl/over-tu-delft/werken-bij-tu-delft/vacatures/details?… -- Joana Gonçalves Assistant Professor TU Delft | Pattern Recognition & Bioinformatics Meet (MS Teams): https://edu.nl/k4jxr Meet (Zoom): https://tudelft.zoom.us/my/joanagoncalves Web: http://joanagoncalves.org

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Research Bioinformatics Scientist - AstraZeneca (Cambridge, UK)
by Sergio Martinez Cuesta 04 Oct '21

04 Oct '21

Are you a bioinformatician passionate about medical research and looking for an exciting and impactful new challenge? Do you have experience in analysing genome wide omics data and high-throughput molecular or genetic screens for target identification and drug discovery? Then why not join our Data Sciences & Quantitative Biology team in Cambridge, UK and apply bioinformatics and computational solutions to help us evolve and extend our capabilities in our drive to find the medicines of the future. Check out our latest position! Apply as soon as possible https://careers.astrazeneca.com/job/cambridge/research-bioinformatics-scien…

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