From oliver.billker at umu.se Tue Jul 3 11:26:16 2018 From: oliver.billker at umu.se (Oliver Billker) Date: Tue, 3 Jul 2018 09:26:16 +0000 Subject: [SocBiN] Computational Biologists to study molecular and single cell genomics of malaria transmission Message-ID: <1530609976689.27671@umu.se> Hi all The Billker lab has a top job for an experienced Computational Biologist to study the genomics of malaria transmission. We are building a new interdisciplinary team at Umeå University with funding from the ERC and Wallenberg foundation, which is aimed at gaining a molecular understanding of malaria transmission by mosquitoes. We tend to tackle big questions through big experiments in a collaborative manner, and we therefore need strong team players. For the senior role you will be able to take the lead on the analysis of large datasets from genetic screens, bulk and single cell transcriptomics. You will have key roles in communicating our data through publications, conference contributions and a public phenotype database. The challenges will be diverse, and your work will be tightly integrated at every stage with that of experimental molecular biologists working in our labs. We are moving from the Wellcome Sanger Institute, and there will be opportunities to spend time training and working with our Cambridge colleagues and collaborators. Postdoctoral fellowships and potentially PhD positions with strong computational elements are additionally available. Please vist our lab pages or get in touch to learn more. For more, see our lab homepage: billkerlab.org To see the full advert and how to apply: UmU advert The deadline for application is 2018-07-30 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dag.ahren at biol.lu.se Thu Jul 5 17:04:33 2018 From: dag.ahren at biol.lu.se (Dag Ahren) Date: Thu, 5 Jul 2018 17:04:33 +0200 Subject: [SocBiN] Two bioinformatics positions at NBIS Message-ID: <48a3840e-ac5f-90c6-1e94-a389bef16f59@biol.lu.se> Dear colleagues, NBIS is looking for two new members to support Swedish researchers in advanced bioinformatics projects. The two positions are full time and placed at Medicon Village, Lund University. One position will be affiliated with the Department of Laboratory Medicine at the Medical Faculty and one with the Department of Immunotechnology at the Technical Faculty. The successful applicant will be integrated in a vibrant bioinformatics team, with many opportunities to further improve current skills as well as develop new skills to keep up with novel sequencing technologies and other bioinformatics challenges as they emerge. Deadline Sepember 7. https://lu.mynetworkglobal.com/en/what:job/jobID:216986/ For more information, please contact Fredrik Levander fredrik.levander at nbis.se or Dag Ahrén dag.ahren at nbis.se From laurent.guyon at cea.fr Thu Jul 12 15:11:56 2018 From: laurent.guyon at cea.fr (GUYON Laurent 217719) Date: Thu, 12 Jul 2018 13:11:56 +0000 Subject: [SocBiN] Understanding microRNA cooperative modes of action - postdoctoral offer Message-ID: <6323DD9DAB1A284AB09792977FE2377337706956@EXDAG0-B0.intra.cea.fr> Dear all, We are looking for a motivated postdoctoral candidate to work on a better understanding of cooperative modes of actions of microRNAs through data mining and integration. The work will be located in Grenoble, France. More details https://www.biostars.org/p/326482/ or by direct contact. PhD students who are about to defend (at last autumn 2018) are also encouraged to apply. Best, Laurent Guyon ____________________________ Laurent GUYON, PhD - Bioinformatics CEA BIG (Biosciences and Biotechnology Institute of Grenoble) BCI (Biology of Cancer and Infection laboratory) UMR_S 1036 CEA/Inserm/Université Grenoble Alpes CEA Grenoble - Bât C3 - Bureau 224 17 rue des Martyrs 38054 GRENOBLE Cedex 9 Tél : (+33)4.38.78.04.53 Fax : (+33)4 38 78 50 58 Email : laurent.guyon at cea.fr http://laurent.guyon.phd.free.fr/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From paolo.romano at hsanmartino.it Mon Jul 16 10:04:10 2018 From: paolo.romano at hsanmartino.it (Romano Paolo) Date: Mon, 16 Jul 2018 08:04:10 +0000 Subject: [SocBiN] NETTAB 2018 Tutorials defined Message-ID: NETTAB 2018 Workshop Building a FAIR Bioinformatics environment October 22-24, 2018, Genoa, Italy. http://www.igst.it/nettab/2018/ Dear all, please find here below the list of tutorials that will be given at the NETTAB 2018 Workshop on “Building a FAIR Bioinformatics environment”. You will also find some more information on-line and further below. List of tutorials Tutorial 1, Monday October 22, 2018, morning (09:00 – 12:30) Bioschemas, a lightway approach to enable FAIRer data resources Speakers: Leyla Jael Garcia Castro, Ricardo Arcila, Rafael Jimenez, Victoria Dominguez del Angel Registration fee: 10.00 € Tutorial organized in collaboration with ELIXIR. Tutorial 2, Wednesday October 24, afternoon (14:30 – 19:00) The ELIXIR Data Stewardship Wizard – how to guide life science researchers towards FAIR data management Speakers: Rob Hooft, Vojtěch Knaisl, Jan Slifka Registration fee: 10.00 € Workshop/hackhathon organized by ELIXIR-NL and ELIXIR-CZ. Registration for one or both tutorials can be done through the workshop registration form that will be available on-line soon. I take this occasion to remind you of the following deadlines: Submission of abstracts for posters: September 16, 2018 Early registration: September 28, 2018 I hope to meet many of you at next NETTAB 2018 Workshop in Genoa. All the best. Paolo Romano (===) Tutorial 1, Monday October 22, 2018, morning (9:00 – 12:30) Bioschemas, a lightway approach to enable FAIRer data resources Bioschemas is an open community project aiming to contribute with Life Science specifications to schema.org. Schema.org provides an easy way to add structured markup to web pages thus corresponding resources become more findable and interoperable. Building on schema.org, Bioschemas specifications include new types and properties, but also type customization and usage guidelines, a.k.a. profiles. Bioschemas approach relies on simplicity, with just enough guidelines in schemas such as ‘DataSet’, ‘BioChemEntity’ and ‘LabProtocol’ to enable FAIRer data resources. During this half-day tutorial, people will learn about Bioschemas, its approach and its principles. Talks will be combined with hands-on activities so attendees can use Bioschemas profiles to better understand them, discuss on new specifications, and explore how extracted data can be used. People bringing their own data can either use existing profiles to markup their data, or contribute to tasks under development or to new profiles. Tutorial speakers Leyla Garcia, EMBL-EBI, UK; Ricardo Arcila, ELIXIR Hub, UK; Rafael Jimenez, ELIXIR Hub, UK; Victoria Dominguez del Angel, ELIXIR-FR/IFB. Leyla Garcia is a Senior Software Engineer at the Protein Function Development team working mainly on web development, but also on training activities. She is involved in other projects related to semantic web, linked data, ontologies and machine learning. Before joining EMBL-EBI, eight years ago, she used to work as a lecturer and web developer in Colombia. She obtained her MSc in Software Engineering in Colombia and her PhD in Computer Science (artificial intelligence) in Spain. Ricardo Arcila is a Software Engineer at ELIXIR, with theoretical and practical experience in the creation of innovative technology processes. He has experience in areas such as data science, semantic web, software and infrastructure design, front-end and back-end development. For the past six months, he has been actively involved on Bioschemas.org project, semantic web and data science. He joined ELIXIR team after five years of experience as a Software Engineer on several successful projects in the software industry. Rafael Jimenez is the Chief Data Architect at ELIXIR. He has an active role in the technical design, coordination and implementation of the ELIXIR data infrastructure. He joined ELIXIR after four years at EMBL-EBI as a software engineer and technical lead in the Proteomics Services team. He is specialised in the coordination and management of bioinformatics services, and is interested in topics relating to data infrastructure, data integration, data federation, data visualisation and software development best practices. Rafael has experience coordinating technical projects, developing technical strategies, leading software development and managing community groups. He obtained his MSc in Molecular Biology in Spain and his MSc in Computer Science in South Africa. Victoria Dominguez del Angel is the French ELIXIR Training coordinator. She comes to ELIXIR-FR (IFB) with over 15 years of experience in bioinformatic project management. Before joining ELIXIR-FR, Victoria worked as research scientist in UNAM Mexico, Pasteur Institute and INRA. More recently as CEO in a start-up bioinformatics company. Victoria has a PhD in Genome Analysis and Structural Genomics from University of Paris VII (Denis-Diderot) and is recently also rolling in a MBA in Management Research Infrastructures (Ritran) at the University of Milano-Bicocca (2017-2019). Victoria is also responsible of Sustainability Model of the software, databases, infrastructure and training produced by ELIXIR-FR. === Tutorial 2, Wednesday October 24, afternoon (14:30 – 19:00) The ELIXIR Data Stewardship Wizard – how to guide life science researchers towards FAIR data management Target audience This workshop is for Data Stewards and Bioinformaticians who are assisting life science researchers with the data management and data management planning in their projects. Organisers Rob Hooft (DTL, ELIXIR NL), Robert Pergl (ELIXIR CZ), Vojtěch Knaisl (ELIXIR CZ), Jan Slifka (ELIXIR CZ), Celia van Gelder (DTL, ELIXIR NL). The ELIXIR Data Stewardship Wizard (DSW, https://dsw.fairdata.solutions/) is a solution for “Smart Data Management Plans for FAIR Open Science”: incorporating expert knowledge on “FAIR” data management and data stewardship into daily practice, directly benefiting data-intensive research projects. In this workshop participants will be shown how the ELIXIR Data Stewardship Wizard can guide researchers towards FAIR data stewardship, how it can help data stewards to stay organized, and how it can help data experts of all kinds to advertise their expertise. We will walk together through: 1.how the wizard works for researchers, 2.what kind of knowledge is captured there, 3.how the wizard can be customized. We also briefly touch how to run your own copy of the Wizard. During the workshop, participants will have the opportunity to work with the authors of the wizard to contribute their own expertise to the knowledge model. There will also be time to discuss what kinds of questions the workshop attendees are asked by researchers and how the wizard, in current or future form, will be able to contribute to answering such questions. For the workshop organisers, this workshop will be a valuable occasion to get feedback on the current tool, and they will collect a list of suggestions for developments and improvements. Tutorial speakers Rob Hooft, DTLS, NL; Vojtěch Knaisl, ELIXIR CZ, CZ; Jan Slifka, ELIXIR CZ, CZ. Rob Hooft was educated as a structural chemist at Utrecht University. He did his PhD studies modeling sweet tasting compounds. He spent 4 years at the EMBL in Heidelberg where he developed tools to verify the quality of protein structures in the group of Gert Vriend and Chris Sander. Rob then worked in industry for 12 years, first as application software developer and later as manager of the R&D department. In 2009 he moved back to the academic world and joined the Netherlands Center for Bioinformatics, NBIC. Via a two year excursion to the Netherlands eScience Center from where he ran the data program of the Dutch Techcenter for Life Sciences (DTL), he is now working for DTL itself managing the Dutch tasks in the European ELIXIR infrastructure for life science data. As part of these roles, Rob has been building up a body of knowledge on FAIR research data stewardship since early 2014. Vojtěch Knaisl is a Ph.D. student at Faculty of Information Technology at Czech Technical University in Prague, where he also got a master degree in Software Engineering. His fields of study are evolvable software systems and functional programming languages. Further, he is a member of ELIXIR CZ Interoperability platform and one of the main developer of Data Stewardship Wizard in ELIXIR CZ. He has experiences from an industry while he worked as senior developer for telecommunication and big financial companies. Jan Slifka got his Master’s degree in Software Engineering at the Czech Technical University in Prague. He is now Ph.D. student there, focusing on evolvable systems and functional programming. He acquired hands-on experience from the industry while working as a senior developer for several startups with wide range of technologies. He is also a member of ELIXIR-CZ Interoperability Platform where he works as a chief User Interface developer on the Data Stewardship Wizard. Paolo Romano Ospedale Policlinico San Martino Genova, Italy Skype: p.romano Email: paolo.romano at hsanmartino.it - paolo.dm.romano at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From christof.winter at tum.de Mon Jul 16 10:24:59 2018 From: christof.winter at tum.de (Christof Winter) Date: Mon, 16 Jul 2018 10:24:59 +0200 Subject: [SocBiN] PhD position (Munich, Germany) in Bioinformatics for blood-based cancer diagnostics Message-ID: Dear all, we have an open position for a PhD student in Bioinformatics for blood-based cancer diagnostics (liquid biopsy) at the Technical University of Munich (university hospital) -- see attached job ad. Best wishes, Christof Winter -- Christof Winter, MD, PhD Clinical Bioinformatics and Liquid Profiling Institute of Clinical Chemistry and Pathobiochemistry Klinikum rechts der Isar Technische Universität München Ismaninger Str. 22 81675 München, Germany Tel. +49 89 4140 4765 -------------- next part -------------- A non-text attachment was scrubbed... Name: PhD position in Bioinformatics for blood-based cancer diagnostics TUM 2018 07.pdf Type: application/pdf Size: 204023 bytes Desc: not available URL: From esko.ukkonen at helsinki.fi Mon Jul 16 18:28:38 2018 From: esko.ukkonen at helsinki.fi (esko.ukkonen at helsinki.fi) Date: Mon, 16 Jul 2018 19:28:38 +0300 Subject: [SocBiN] WABI 2018: call for participation & call for posters Message-ID: WABI 2018 - 18th Workshop on Algorithms in Bioinformatics Helsinki, 20-22 August 2018* WABI 2018: call for participation* http://algo2018.hiit.fi/registration/ http://algo2018.hiit.fi/wabi/ WABI 2018: call for posters http://algo2018.hiit.fi/wabi/posters/ *Scope* All research in algorithmic work in bioinformatics, computational biology and systems biology. The emphasis is mainly on discrete algorithms and machine-learning methods that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that have been implemented and tested in simulations and on real datasets. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research. Poster Submission We invite researchers to submit their latest results that fall into the general area of algorithms in bioinformatics in the form of a poster. Therefore they are requested to submit an abstract that will be included in the conference package handed out at the workshop. A poster abstract must be in plain text and no longer than 500 words, not including bibliographic references. Submission form: https://elomake.helsinki.fi/lomakkeet/90457/lomake.html The poster session will be in the afternoon of Monday, August 20. The format will be A0 vertical (84cm=33.1" wide, 118cm=46.8" high). At least one author of each accepted poster is required to register for and attend the workshop. Important Dates * Poster submission deadline: August 3, 2018. * Notification of poster acceptance: August 8, 2018. * Workshop: August 20-22, 2018. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne at bioinfo.se Tue Jul 24 14:29:12 2018 From: arne at bioinfo.se (Arne Elofsson) Date: Tue, 24 Jul 2018 15:29:12 +0300 Subject: [SocBiN] Fwd: Permanent post in Structural Bioinformatics In-Reply-To: References: Message-ID: ---------- Forwarded message --------- From: Charlotte Deane Date: Tue, 24 Jul 2018, 15:01 Subject: Permanent post in Structural Bioinformatics To: arne.elofsson at scilifelab.se Dear Arne, I am emailing to ask if you would advertise a position in Structural Bioinformatics that I am currently advertising. This is a permanent post that offers an unrivalled and privileged opportunity to interact directly between the Oxford Protein Informatics group http://opig.stats.ox.ac.uk/ (OPIG) and many pharmaceutical companies. The project is pioneering an academic business model for how to achieve simultaneously the ideal of fully open software while sustaining a long-term funding. OPIG has developed a large number of world leading computational tools which have proved to be of high interest to several pharmaceutical companies. These tools are open source and freely available to all users, academic and commercial. This open strategy has meant that the user base for the tools is broad both within academia and industry. Several of these tools have been taken in-house by pharmaceutical companies. This role supports these companies with deployment, maintenance, future developments and integration with their own in-house systems and requirements. The post holder will also carry out research and develop novel methodologies in at least one of the areas of research in OPIG. More details can be found here https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form?p_company=10&p_internal_external=E&p_display_in_irish=N&p_process_type=&p_applicant_no=&p_form_profile_detail=&p_display_apply_ind=Y&p_refresh_search=Y&p_recruitment_id=135897 Please share with anyone who may be interested. The closing date for applications is the 29th of August. Should you have any questions please do not hesitate to contact me. Best wishes Charlotte Professor Charlotte Deane ------------------------------------------------------------------------------------------------------------------------------ Professor of Structural Bioinformatics & Head of Department, Department of Statistics University of Oxford, 24-29 St Giles', Oxford, OX1 3LB Head of the Oxford Protein Informatics group Website: *http://opig.stats.ox.ac.uk/ * PA: *hodpa at stats.ox.ac.uk * | 01865 281252 ------------------------------------------------------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From besenbacher at clin.au.dk Fri Jul 27 10:05:05 2018 From: besenbacher at clin.au.dk (=?utf-8?B?U8O4cmVuIEJlc2VuYmFjaGVy?=) Date: Fri, 27 Jul 2018 08:05:05 +0000 Subject: [SocBiN] Postdoc position at Aarhus University Message-ID: A two-year postdoc position focused on analysis of de novo mutations is now available at Aarhus University. For details and application see https://tinyurl.com/y8nfsvvb. Application deadline August 15. Søren Besenbacher Associate professor at Department of molecular medicine, Aarhus University -------------- next part -------------- An HTML attachment was scrubbed... URL: