- BBClist - maillist.psb.ugent.be

Proteomics Service Facility Leader
by Andreas Beyer 24 Jun '19

24 Jun '19

Dear all, We are looking for a Proteomics Service Group Leader on a permanent position in our CECAD Excellence Cluster: https://www.nature.com/naturecareers/job/proteomics-service-group-leader-un… Please, forward this to potentially suitable candidates. Best, Andreas Beyer -- Prof. Dr. Andreas Beyer http://cellnet.cecad.uni-koeln.de/ Phone: +49 221-478 84429

1 0

CFP OLA'2019 Int. Conf. on Optimization and Learning @Spain
by El-ghazali Talbi 24 Jun '19

24 Jun '19

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2020 International Conference on Optimization and Learning: Challenges and Applications 17-19 Feb 2020 Cadiz, Spain http://ola2020.sciencesconf.org/ **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and learning methods and their applications. The conference OLA'2020 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2020 welcomes presentations that cover any aspects of optimization and learning research such as optimization for learning, learning for optimization, optimization and learning under uncertainty, new high-impact applications, parameter tuning, 4th industrial revolution, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept two different types of submissions: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 10 pages Important dates: =============== Submission deadline Sept 20, 2019 Notification of acceptance Nov 9, 2019 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings that will be available at the conference. In addition, a post-conference SCOPUS indexed Springer book and a special issue in a Journal are planned to be published. Participants will be invited to submit extended versions of their work for consideration. -- *********************************************************************** OLA'2020 Int. Conference on Optimization and Learning 17-19 Feb 2020, Cadiz, Spain http://ola2020.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

1 0

Fwd: three open position at Computational Science Lab of University of Amsterdam
by Sanne Abeln 20 Jun '19

20 Jun '19

---------- Forwarded message --------- From: Hoekstra, Alfons <A.G.Hoekstra(a)uva.nl> Date: Thu, 20 Jun 2019 at 17:02 Subject: three open position at Computational Science Lab of University of Amsterdam To: Cc: Hoekstra, Alfons <A.G.Hoekstra(a)uva.nl> Dear colleagues, We currently have three open positions in our lab, see below. If you happen to know suitable candidates, please forward these. Thanks a lot, best regards, Alfons Hoekstra == postdoc In silico Stroke Trials https://www.uva.nl/en/content/vacancies/2019/06/19-418-postdoctoral-researc… PhD position on High performance multiscale modeling of blood flows https://www.uva.nl/en/content/vacancies/2019/06/19-404-phd-position-on-high… Scientific Programmer Computational Biomedicine https://www.uva.nl/en/content/vacancies/2019/06/19-405-scientific-programme… -- Computational Science <http://uva.computationalscience.nl> Lab <http://uva.computationalscience.nl> Master Programme Computational Science <http://www.uva.nl/en/shared-content/subsites/graduate-school-of-sciences/en…> -- Sanne Abeln Associate Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

1 0

A conference to promote women's research in computational biology #AdvCompBio
by Alba Jene 18 Jun '19

18 Jun '19

Dear colleagues, The first <https://www.iscb.org/advcompbio2019> Advances in Computational Biology conference will bring together researchers working on systems biology, omics technologies, artificial intelligence and high-performance computing with applications to biology. The conference is open to everyone to attend, but all the speakers will be women, providing an excellent opportunity to share ideas and build research networks. You are invited to register to attend ( <https://www.iscb.org/advcompbio2019-registration> https://www.iscb.org/advcompbio2019-registration) and to submit an abstract for consideration for oral or poster presentations, please see more details here: <https://www.iscb.org/advcompbio2019-call-submissions> https://www.iscb.org/advcompbio2019-call-submissions. Topics included: 1. Learning from Biological Sequences: population genomics, evolutionary genomics, systems biology, transcriptomics, sequence analysis 2. When Computational Biology meets Medicine: biomedical applications, mutational landscapes, clinical genomics 3. Machines Speeding up Research: high performance computing, machine learning in the life sciences, imaging data analysis, dynamic simulations and algorithm development The keynote speakers of the conference are: <https://www.ucl.ac.uk/orengo-group/people/prof-christine-orengo> Christine Orengo, group leader of Orengo Group at University College London, <https://www.bsc.es/przulj-natasa> Natasa Przulj, group leader of the Life Sciences - Integrative Computational Network Biology at the Barcelona Supercomputing Center and <https://www.linkedin.com/in/marie-christine-sawley-70b5534/?originalSubdoma in=ch> Marie-Christine Sawley, director of the Exascale Lab at Intel. Furthermore the participants will have the opportunity to interact personally in round-table informal meetings with women leaders in the fields of IT, academia research and politics that support the conference. Confirmed discussion leads: <https://www.iscb.org/advcompbio2019-other-activities> https://www.iscb.org/advcompbio2019-other-activities. Important dates: Abstract submission opens May 6th, 2019 Abstract submission deadline July 1st, 2019 Poster and oral communication notification September 1st, 2019 Early bird registration deadline September 15th, 2019 The conference is organised by the Barcelona Supercomputing Center <https://www.iscb.org/advcompbio2019> (BSC-CNS), the joint <https://www.imim.es/> IMIM- <https://www.upf.edu/> UPF Research Programme on Biomedical Informatics ( <http://grib.imim.es/> GRIB) and the Universitat Politècnica de Catalunya ( <https://www.upc.edu/en?set_language=en> UPC). It is an affiliate conference of the International Society for Computational Biology ( <https://www.iscb.org/> ISCB). We look forward to meeting you at the #AdvCompBio Conference in Barcelona this November! Best regards, The Organizing Committee Mar Albà (UPF/IMIM) Eva Alloza (BSC-CNS) Rosa Maria Badia (BSC-CNS) Nataly Buslón (BSC-CNS) Osnat Hakimi (UPC) Alba Jené (BSC-CNS) Eva Navarrete (BSC-CNS) María José Rementería (BSC-CNS) <https://www.iscb.org/advcompbio2019> -- Alba Jené Sanz, PhD Bioinformatics Unit Coordinator Barcelona Supercomputing Center (BSC) <https://maps.google.com/?q=C/+Jordi+Girona+29,+08034-Barcelona,+Spain&entry =gmail&source=g> C/ Jordi Girona 29, 08034-Barcelona, Spain Tel: +34 93 413 7572 http://bsc.es/disclaimer

1 0

PhD or Postdoc position: The role of gut microbiota in immune senescence and cardiovascular diseases
by Patrick Deelen 18 Jun '19

18 Jun '19

*PhD or Postdoc position: The role of gut microbiota in immune senescence and cardiovascular diseases* The Departments of Genetics and Pediatrics, at the University Medical Center Groningen, the Netherlands, are looking for a potential PhD student or junior postdoc in the field of bioinformatics to assess the contributions of microbiome-derived signals in the etiology of age- and obesity-related cardio-metabolic diseases through (immune) senescence. The candidate will investigate the role of gut microbiota composition in immune senescence, predisposition to cardiovascular diseases, and its relation to host genome, environment and lifestyle. This project is a part of “Inflammatory Reprogramming by Ageing and Microbiome - Targets for Treatment of Cardiovascular Disease”, a large, national project funded by CVON (CardioVascular Onderzoek Nederland). This project involves multi-omics integration in multiple human cohorts and assesses the impact of the gut microbiota, immunological parameters related to ageing and risk to CVD. What do we need - M.Sc. (or PhD) degree in bioinformatics, computational biology, systems biology or a comparable discipline. The candidate with experiences in microbiome, metabolism and immunity is preferable. - Experience with advanced statistics, biology or biochemistry - Excellent oral and written communication skills - Fluency in English https://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/…

1 0

computational biologist position at NeuroDiderot
by Anne-Louise Leutenegger 14 Jun '19

14 Jun '19

Please spread the offer, Twitter <https://twitter.com/andree_delahaye/status/1133758315484372992> : https://twitter.com/andree_delahaye/status/1133758315484372992 LinkedIn <https://www.linkedin.com/feed/update/urn:li:activity:6539522340626157568> : https://www.linkedin.com/feed/update/urn:li:activity:6539522340626157568 https://itneuro.aviesan.fr/index.php?pagendx=751&p=1558 [image: image.png]

1 0

Researcher in Artificial Intelligence applied to life sciences (RRE) / Reference: 173_LS_AI_RRE
by BSC RRHH 13 Jun '19

13 Jun '19

Researcher in Artificial Intelligence applied to life sciences (RRE) Primary tabs *Context And Mission* The Life Sciences Department at the BSC integrates the independent research of senior scientists that work on various aspects of computational biology, ranging from bioinformatics for genomics to computational biochemistry and text mining. The Computational Biology group is involved in multiple projects in collaboration with experimental groups generating state-of-the-art genomics and epigenomics datasets, actively participating in the International Human Epigenome Consortium and with the general aim of enabling new approaches in personalized medicine. Current efforts involve integration of different types of omics data, with a particular emphasis on epigenomics. We are establishing methods to study genome architecture exploiting interdisciplinary tools such as machine learning and network theory. The mission of the Computer Science Department at the BSC is to influence the way machines are built, programmed and used: computer and system architecture, programming models and performance tools, resource management, Big Data and artificial intelligence. The HPAI (High Performance Artificial Intelligence) research group is part of the Computer Science department, and it performs research in Artificial Intelligence, focused on the solutions, problems and infrastructure provided by High Performance Computing. The group actively collaborates with researchers from other fields, with the goal of applying machine learning to challenging problems in a wide variety of domains. HPAI has active collaborations with several large tech companies, pursuing lines of research of common interest. The group is also involved in multiple research projects, both European and national. Although the HPAI is open to all aspects of AI, currently its main lines of research are deep neural networks and graph analytics. The post holder will collaborate with the Life Sciences department and the HPAI research group in the Computer Science department, with the goal of finding AI solutions to life sciences challenges. This will include working closely with researchers from both areas, programming, testing and dissemination of the research. The candidate will be able to develop an independent research programme within the broad topics mentioned above. The Researcher will work in a highly sophisticated HPC environment, will have access to state-of-the-art systems and computational infrastructures, and will establish collaborations with experts in different areas both at the local and international levels. *Key Duties* * Development of AI solutions, with special emphasis on machine learning methods, for the analysis and interpretation of biological data * Use predictive computational methods based on statistical and inference approaches to model complex biological processes * Integration of heterogeneous data sources using advanced data mining techniques *Requirements* * Education o PhD in computer science or bioinformatics with a strong AI component. o OR Alternatively, an MSc on AI or Bioinformatics, with a strong computer science background, or background on applied mathematics/physics with demonstrated experience in AI methods. * Essential Knowledge and Professional Experience o Experience in AI methodologies o Interest in the life sciences area * Additional Knowledge and Professional Experience o Knowledge and experience in life sciences research o Knowledge and experience in AI methodologies: - Data pre/post-processing (feature selection, feature reduction, plotting and visualization) - Supervised and unsupervised learning (classification, clustering, regression) - Knowledge representation - Complex networks (graph-based representation, graph analytics) - Deep learning (TensorFlow, PyTorch, Caffe, word embeddings) o Programming: Python (scikit-learn, numpy, matplotlib), Matlab, R, Java, C, C++, Git * Competences o Fluency in spoken and written English, while fluency in other European languages will be also valued o Capacity to explore new research lines o Good communication and presentation skills o Ability to work both independently and within a team *Apply here:* https://www.bsc.es/join-us/job-opportunities/173lsairre http://bsc.es/disclaimer

1 0

Post-doc Researchers in Computer Science and Bioinformatics (R2) / Reference: 270_LS_ICB_R2
by BSC RRHH 13 Jun '19

13 Jun '19

Post-doc Researchers in Computer Science and Bioinformatics (R2) *Context And Mission* Professor Nataša Pržulj is looking for several post-docs to work in machine learning and network science. They will be developing new algorithms for computationally hard problems and applying them to analyzing large-scale molecular and patient data to aid drug discovery and personalizing treatment. The successful candidates will work on the prestigious ERC Consolidator grant of Prof. Pržulj. The successful candidates will address developing and applying sophisticated machine learning and network science models and algorithms. The algorithms will be carefully tuned to extract relevant biological and medical knowledge from systems-level real-world molecular and medical data. The aim is to utilize them to understand the structure of the data that would enable mining the data for new biological and medical insight that would further lead to improving diagnostics, discovering new biomarkers, improving patient stratification and treatment, personalizing treatment and facilitate rational drug development. The successful candidates will join a dynamic research group of Prof. Przulj within BSC. The students will work in a highly sophisticated HPC environment, will have access to systems and computational infrastructures, and will establish collaborations with experts in different areas. *Key Duties* * Conduct high-quality research * Publish in high impact journals and conferences * Present research at national and international conferences and meetings * Collaborate with various research groups across Europe and elsewhere * Help supervise PhD and MSc students * Participate in grant writing and organizational activities * Participate in educational and outreach activities *Requirements* * Education o PhD in Computer Science, Mathematics, Physics, Bioinformatics, or a related field * Essential Knowledge and Professional Experience o Good publication record for the career stage o Fluency in spoken and written English * Competences o Good technical skills including at least several of the following: algorithms, data analysis, graph, network and complexity theory, scientific computing, statistics, machine learning, programming in C, C++, a scripting language and Matlab, using a parallel computing environment, bioinformatics, network biology, network medicine, network analytics, medical informatics. *Apply here: *https://www.bsc.es/join-us/job-opportunities/270lsicbr2 http://bsc.es/disclaimer

1 0

BSC: (bio-)informatician back-end engineers (RE12) / Reference: 97_LS_INB_RE12
by BSC RRHH 13 Jun '19

13 Jun '19

(bio-)informatician back-end engineers (RE12) *Context And Mission* The Spanish National Bioinformatics Institute (INB) is the major bioinformatics platform in Spain, and the Spanish representative in the European bioinformatics infrastructure ELIXIR. INB is fully oriented to complete a solid integration with International Bioinformatics infrastructures including specifically the ELIXIR consortium. *Key Duties* * Design, implement and document communication channels for data sharing honoring data ownership, and security * Contribute to the development of a Virtual Research Environment (VRE) for various research projects at the Life Sciences Department * Manage and support users of the INB computational resources, including computational equipment, databases, and software infrastructure * Develop, document and maintain software for the integration and biological data, following the guidelines of ELIXIR * Contribute to the management of data within the current projects * Maintain communication with ELIXIR platforms, communities, and management, participate in their regular meetings and discussions * Contribute to supervise junior members at the INB/ELIXIR-ES units *Requirements* * Education o BSc or MSc. in bioinformatics, computational biology or computer sciences with significant bioinformatics experience * Essential Knowledge and Professional Experience o At least 2 years of professional experience with a similar role o Experience in cloud computing o Experience in data management APIs and most common bioinformatic data sources and formats o Experience in database design and management (SQL and noSQL): MySQL/MariaDB, PostgreSQL, SQLite or similar; MongoDB, Elasticsearch, Cassandra or similar o Experience with advanced software packaging procedures o At least 2.5 years of professional experience on programming languages ecosystems such as C++, Perl, Python, PHP and/or Java o Vast experience working with Unix/Linux systems * Additional Knowledge and Professional Experience o Experience in modern authentication/authorization protocols o Experience on the development, generation and use of software containers e.g. Docker, Singularity and/or rkt, as well as their orchestration using docker compose, kubernetes, ansible and/or similar technologies o Experience on workflow managers such as Galaxy, Nextflow or similar o Experience on developing project technical specifications * Competences o Ability of understand scientific literature, and software documentation o Ability to communicate scientific results o Ability to work independently o Ability to represent the team in international project meetings o Used to work under pressure under strict deadlines *Apply here: *https://www.bsc.es/join-us/job-opportunities/97lsinbre12 http://bsc.es/disclaimer

1 0

BSC: (bio-)informatician web front-end developer (RE12) / Reference: 96_LS_INB_RE12
by BSC RRHH 13 Jun '19

13 Jun '19

(bio-)informatician web front-end developer (RE12) *Context And Mission* The Spanish National Bioinformatics Institute (INB) is the major bioinformatics platform in Spain, and the Spanish representative in the European bioinformatics infrastructure ELIXIR. INB is fully oriented to complete a solid integration with International Bioinformatics infrastructures including specifically the ELIXIR consortium. *Key Duties* * Contribute to the development of front-end platforms and associated APIs for the current research projects in the Life Sciences department, in close collaboration with back-end engineers * Contribute to ensure appropriate user experience at the developed front-ends * Work together with other developers at INB/ELIXIR-ES and other ELIXIR nodes to ensure the appropriate implementation of previously agreed standards and methodologies * Contribute to supervise junior members at the INB/ELIXIR-ES units *Requirements* * Education o Software Engineer Degree or equivalent Bioinformatics related degrees * Essential Knowledge and Professional Experience o At least 2 year of professional experience in web frontend technologies such as NPM, yarn, Bower, Grunt, Gulp, webpack, or and HTML, CSS and JavaScript ecosystems o At least 2 year of professional experience with programming languages such as Ruby, Python and/or Java o Vast experience working with Unix/Linux systems * Additional Knowledge and Professional Experience o Experience in microservices software architecture o Experience with back-end frameworks, like Spring, Django or Laravel o Experience with front-end frameworks, like Angular, Vue and/or React will be highly appreciated o Familiar with software containers technologies such as Docker and/or Singularity o Familiar with design, implementation and deployment of relational databases (MySQL, PostgreSQL or similar) and/or non-relational databases (MongoDB, ElasticSearch, Cassandra) o Experience in designing, implementing and documenting data management APIs o Experience on developing project technical specifications * Competences o Fluency in English o Good writing and presentation skills o Strong personal soft-skills sets: Communicative, enthusiastic, highly collaborative, proactive, self-driven o Strong technical writing skills o Ability to work independently o Ability to represent the team in international project meetings o Used to work under pressure under strict deadlines *Apply here: *https://www.bsc.es/join-us/job-opportunities/96lsinbre12 http://bsc.es/disclaimer

1 0