January 2019 - BBClist - maillist.psb.ugent.be

Course Single cell RNA-seq data analysis with Chipster, Espoo, Finland, 14-15 March 2019
by Celia van Gelder 18 Jan '19

18 Jan '19

On behalf of Eija Korpelainen (CSC/ELIXR-FI) Applications are open until 25.1.2019 for the ELIXIR-FI course "Single cell RNA-seq data analysis with Chipster" which takes place in Espoo, Finland 14.-15.3.2019. <https://www.csc.fi/web/training/-/bioweek-single-cell-chipster-2019> https://www.csc.fi/web/training/-/bioweek-single-cell-chipster-2019 Best Celia Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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CarpentryConnect Manchester 2019 Call for Proposals
by Mateusz Kuzak 17 Jan '19

17 Jan '19

On behalf of Alexandra > Dear All, > > The first European CarpentryConnect event will be held in Manchester, UK, on 25-27 June 2019 under the theme "Training Communities: Challenges and Opportunities in Europe" with an aim to, once again, bring the Carpentry community together. > > We are delighted to open the call for topic suggestions and abstract submissions for breakout sessions (group discussions such as “Carpentry Methods in University Courses”, “Diversity and Inclusion”, “Sustainable Software Practices”), workshops (longer sessions or training on specific topics such as “Ally workshop”, “Contributing on GitHub”, “Project Leadership”, “Shell Tips and Tricks”), lightning talks and posters under the following general themes: > > • > Lesson/curricula development (e.g. working on existing curricula or establishing completely novel materials, new introductory or intermediate lessons) > • > Increasing the sustainability of scientific software and research through training > • > Good teaching practices in research computing (e.g. different approaches for different levels of lesson, different workshop formats) > • > Tools and resources for teaching computational methods to researchers > • > Other topics relating to The Carpentries community or delivering training in research software: > > • > Building a local carpentry group/community at research institutions > • > Running a Carpentry membership at an institution > • > Bringing the Carpentries curriculum to universities > • > Attracting funding or making a case with the senior management for workshops/membership at your institution > > > > We strongly encourage contributions from new members of the Carpentries community, with or without any experience of running a session at a conference. > > A draft programme for the conference is available online. > > You can submit an abstract or your suggestions using the submission form until 1 March 2019. The notification of the outcome of your application will be sent out by 1 April 2019. > > Looking forward to seeing you in Manchester in June! > > Best wishes for 2019, > The CarpentryConnect Manchester 2019 Programme Subcommittee > The Carpentries / discuss / see discussions + participants + delivery options Permalink

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Cytometry Part A special issue on Machine Learning for Single-Cell Analysis
by Yvan Saeys 14 Jan '19

14 Jan '19

Dear colleagues, Please findattached a call for papers for a special issue of Cytometry Part A on Machine learning for single-cell analysis that I am editing together with Greg Finak. If you know of any interested colleagues, please forward further. Best regards, Yvan -- =============================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine UGent Department of Applied Mathematics, Computer Science and Statistics Krijgslaan 281, S9, B-9000 Gent VIB-UGent Center for Inflammation Research Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto: yvan.saeys(a)ugent.be http://www.dambi.ugent.be ===============================================================================

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Save the date: Boost Your Visibility - Improving F of FAIR for Dutch Training and Data Resources through Bioschemas, Hackathon, 7-8 February 2019, Utrecht, the Netherlands
by Mateusz Kuzak 10 Jan '19

10 Jan '19

-- apologies for cross posting -- Dear colleague, Are you a training provider/organizer with a catalogue of training events and/or training materials or a data provider, curator or manager of Life Science resources such as Biobanks, Proteins, Samples, Beacons, Tools? Then this hackathon may be very relevant for you! DTL and ELIXIR-NL are organising a workshop/hackathon for content providers of Life Science resources such as Proteins, Samples, Beacons, Tools, and Training events and materials. Join this event to learn how to make your resources rank higher on (Google, Bing, Yahoo and other) search result pages or include your resource in relevant registries (like TeSS, the ELIXIR Training Portal) and receive more web traffic can raise the exposure of your work to be found by larger audiences. The event will start at lunch time on Thursday February 7 and will finish on Friday February 8 at 4pm. In the first half day of this 1.5 day event participants will learn about schema.org and bioschemas from experts working on Bioschemas definitions and implementations for ELIXIR resources and they will get some examples of successful Bioschemas implementations in Life Science resources, both from within and outside the Netherlands. The second day will have the form of a hackathon during which participants will work on adding Bioschemas metadata to their resources with the help of the experts. For training materials and events we will also add them to the ELIXIR’s Training Portal TeSS. Please find more information and the draft agenda here and mark the dates in your agenda if you are interested. The registration will open at the beginning of January. Looking forward to seeing you at the hackathon! On behalf of DTL/ELIXIR-NL, Celia van Gelder and Mateusz Kuzak — Mateusz Kuzak Scientific Community Manager | Dutch Techcentre for Life Sciences e-mail: mateusz.kuzak(a)dtls.nl | tel. +31 643707254 twitter: @matkuzak | github: mkuzak | skype: mkuzak Visting address: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw Jaarbeursplein 6 | 3521 AL Utrecht

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PhD position in Medical Genetics, VUB
by Matthieu Defrance 09 Jan '19

09 Jan '19

PhD Position: Integromics (genomics, transcriptomics, epigenomics) data analysis & applied bioinformatics in rare genetic diseases like cardiac arrhythmias and neurodevelopmental disorders Location: Centre for Medical Genetics Vrije Universiteit Brussel (Faculty of Medicine and Pharmacy) Contact: Sonia Van Dooren (Sonia.VanDooren(a)uzbrussel.be) Starting date: as soon as possible Context: Doctoral research concerning the added value of integrated versus single multi-omics (whole genomics, transcriptomics, epigenomics) data analysis in the context of the Innoviris BRIDGE project IGenCare ‘Integrated Medical Genomics Care Solution for Patients with Rare Genetic Diseases’ in a collaboration between VUB, ULB, BRIGHTcore (http://www.brightcore.be/) and (IB)2 (http://ibsquare.be/) Some background: In the era of high-throughput massive parallel sequencing, genome-wide analyses have become standard in medical health care. Although this (r)evolutionary technology has been increasingly important in the improvement of the genetic diagnostic yield in patients with rare genetic diseases, scientists and health care providers still phase many challenges. Indeed from the laboratory point of view, scientists had to limit most of the diagnostic genomic analyses to partial analysis of the human genome for cost-effectiveness reasons. This has on the one hand led to a higher number of genetic diagnoses, but on the other hand also to a higher number of unsolved cases, due to lack of identification of potentially causal variants and/or due to uncertainty in interpretation of the data. The project: With the implementation of low cost whole human genome sequencing, transcriptomics and epigenomics we enter a novel time frame of functional genomics and integromics health care, further expanding the possibilities in identifying the cause of rare genetic diseases. Part of the IGenCare project focuses at the laboratory level, where we plan to extend the diagnostic yield of rare genetic diseases by a multi-omics / functional genomics / integromics approach through simultaneous analysis of the patient’s whole genome, gene expression and epigenetic regulation profile in an integrative way. The tasks: - Support in the massive parallel sequencing & array multi-omics data generation through NovaSeq6000, HiSeq1500 & Iscan in collaboration with the BRIGHTcore team - Analysis of the multi-omics data and genotype-phenotype correlation at the single omics level - Evaluation and validation of the multi-omics data interpretation bioinformatics tool and GUI in collaboration with the (IB)2 multi-omics data integrator team - Support in the optimization of multi-omics integrator pipelines, algorithms and annotation tools - Implementation and application of the multi-omics integrator tool Continuous communication in a constant feedback loop between the multi-omics integrator tool and GUI developers on the one hand and the omics data interpretation experts on the other hand You are a bioengineer or a master in computational, biomedical or life sciences, with a strong affinity for applied bioinformatics and multi-omics data analysis. Requirements: You have knowledge of: - Multi-omics (full genome, transcriptome & epigenome) technology - Bioinformatics in a next generation sequencing and array workbench environment (data assembly, analysis and annotation) You are competent in: - Computational aspects of genomics, transcriptomics and / or epigenomics - Scripting and / or programming (eg R, Perl, Linux, Python, C, ...) - Relational databases (MySQL, PostgreSQL) You have capacities in: - Problem-solving (thinking & acting) - Fluent communication (oral & written) - Multi-tasking - Taking initiative, working autonomously - Positive attitude and team work - Eagerness to learn and you are driven to contribute to innovative research and diagnostics You are fluent in languages: - Excellent knowledge of the English language (oral & written) - Some knowledge of Dutch is desirable but not essential

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Fwd: [SocBiN] Reminder: Well funded assistant professor in Computational Biology at Stockholm University
by Gerard Schaafsma 09 Jan '19

09 Jan '19

---------- Forwarded message --------- From: Arne Elofsson <arne(a)bioinfo.se> Date: wo 9 jan. 2019 om 09:41 Subject: [SocBiN] Reminder: Well funded assistant professor in Computational Biology at Stockholm University To: <socbin(a)socbin.org> Assistant Professor in Computational biology Ref. No. SU FV-1696-18 Share Share Tweet <https://twitter.com/share> *at the Department of Mathematics <https://www.math.su.se/english/>. Closing date: 15 January 2019.* Stockholm University is a leading European university and one of the world’s top 100 institutes of higher education and research. Stockholm University has more than 60,000 students and 5,000 staff. The Science for Life Laboratory <https://www.scilifelab.se/> (SciLifeLab) is a national center for large-scale biosciences with a focus on health and environmental research and is a collaboration between Stockholm University, Karolinska Institutet, the Royal Institute of Technology, and Uppsala University. SciLifeLab-Stockholm is located in a new building on the Karolinska Institutet campus. The last century of research has led the Department of Mathematics at Stockholm University to acquire a prominent place in Scandinavian mathematics. The department consists of three divisions: Mathematics, Mathematical statistics, and the recently formed Computational mathematics. The research in the division of mathematics include algebra, geometry and combinatorics, analysis and logic. The research in mathematical statistics include probability theory and statistical inference theory, with applications in biostatistics, climatology, econometrics, finance and insurance. Computational mathematics is a new direction for the department, with activities in computational biology, stochastic modelling, scientific computing for climatology, and logic of programs. During the first six years, the main workplace for this position will be at the Science for Life Laboratory. The formal employment will be at the Department of Mathematics. https://www.su.se/english/about/working-at-su/jobs?rmpage=job&rmjob=6380&rm… Yours Arne ----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)70 695 1045 Stockholm University http://bioinfo.se/ Box 1031, Email: arne(a)bioinfo.se 17121 Solna, Sweden Twitter: https://twitter.com/arneelof Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 _______________________________________________ SocBiN mailing list SocBiN(a)lists.su.se https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se -- Gerard C.P. Schaafsma 224 74 Lund Sverige

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Wet Lab Scientist & Computational Biologist Single Cell Omics @Janssen Belgium
by Joke Reumers 08 Jan '19

08 Jan '19

Dear all, We have two job openings (permanent positions) for single cell omics at the Janssen campus in Beerse, Belgium: one wet lab scientist, and one computational biologist. While the focus of the job will lie heavily on single cell (seq) analysis, application is open for anyone with relevant experience in the context of ‘omics or related areas. Applications can be submitted via: https://jobs.jnj.com/jobs/1805706109W?lang=en-us (computational) https://jobs.jnj.com/jobs/1905707858W?lang=en-us (wet lab) Please feel free to share to other channels. For more information, please contact us at jreumers(a)its.jnj.com<mailto:jreumers@its.jnj.com> or JVanHou2(a)its.jnj.com<mailto:JVanHou2@its.jnj.com> Best regards, Joke Reumers, Jeroen Van Houdt

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Spring Data Science Fellowship Opportunity - ==
by Stephane Rombauts 08 Jan '19

08 Jan '19

For those that want to expand their data-science network > From: "Michael Li" <michael.li(a)mailg.thedataincubator.com> > To: "Stephane Rombauts" <strom(a)psb.vib-ugent.be> > Sent: Tuesday, January 8, 2019 4:45:28 PM > Subject: Spring Data Science Fellowship Opportunity - == > Hi Stephane Rombauts, > Our application is currently live. I would be extremely grateful if you could > forward this opportunity to master or PhD students, postdocs , or those already > with their graduate degrees in the workforce you may know. > Program: The Data Incubator is an intensive 8 week fellowship that prepares > masters students, PhDs, and postdocs in STEM and social science fields seeking > industry careers as data scientists. The program is free for Fellows and > supported by sponsorships from hundreds of employers across multiple > industries. In response to the overwhelming interest in our earlier sessions, > we will be holding another fellowship. > Who Should Apply: Anyone who has already obtained a masters or PhD degree or who > is within one year of graduating with a masters or PhD is welcome to apply. > Applications from international students are welcome. Everyone else is > encouraged to [ > http://email.mailg.thedataincubator.com/c/eJxtjMuKxCAURL9GdyPXR3wsXDQ0-Y-rb… > | sign-up for a future session ] . > Locations: In addition to the below in-person locations, we will have a remote > online session: > * New York City > * San Francisco Bay Area > * Boston > * Washington, DC. > Dates: All sections will be from 2019-04-01 to 2019-05-24. > Application Link: [ > http://email.mailg.thedataincubator.com/c/eJxtjMuKxCAURL9GdyPXR3wsXDQ0-Y-rb… > | https://www.thedataincubator.com/fellowship.html?ch=rec&ref=racc42073f60e ] > Early Deadline: 2019-01-14. > Regular Deadline: 2019-01-21. > We are assessing and interviewing candidates who apply for the Early Deadline > first and then based on remaining availability, will take candidates who > applied for the Regular Deadline on a first-come first-serve basis. > Data Science in 30 minutes: Learn how to build a data-science project in our > upcoming [ > http://email.mailg.thedataincubator.com/c/eJw9jbsOwyAMRb8mbEEGEwIDQ5f-BxArQ… > | free Data Science in 30-minutes webcast ] . Signup soon as space is limited. > Learn More: You can learn about our fellows at [ > http://email.mailg.thedataincubator.com/c/eJxtjj2OxCAUg0-TdA9BgJApUkwz94BAC… > | The New York Times ] , [ > http://email.mailg.thedataincubator.com/c/eJxtjj2OxCAUg08TuiAe_ykoppl7AGEBL… > | LinkedIn ] , [ > http://email.mailg.thedataincubator.com/c/eJxtTkuuwyAQO03YFc0A4bNg0U3vMRCao… > | Amazon ] , [ > http://email.mailg.thedataincubator.com/c/eJxtj0tuxCAQRE9j7xqBjW28YDGbuUfzi… > | Capital One ] , or [ > http://email.mailg.thedataincubator.com/c/eJxtj0mOxCAMRU-T7EAMCUUWLGpT9zCEJ… > | Palantir ] . To read about our latest fellow alumni, check out our [ > http://email.mailg.thedataincubator.com/c/eJx1jUsOgyAUAE8juxIeIDwWLNx4D35VU… > | blog ] . To learn more about The Data Incubator, check us out on [ > http://email.mailg.thedataincubator.com/c/eJwVTkGShCAMfM14gwqKCgcOc5l_AAald… > | Venture Beat ] , [ > http://email.mailg.thedataincubator.com/c/eJw9jstuhDAMRb9m2DlKAnmwYDGb-Y-8g… > | The Next Web ] , or [ > http://email.mailg.thedataincubator.com/c/eJwVjsuuwyAMRL8m7EC8QxYsuul_8CpBT… > | Harvard Business Review ] . > Sincerely, > Michael > Postdoc, Cornell > If you would like to stop receiving quarterly notices, please notify us [ > http://email.mailg.thedataincubator.com/c/eJxtjUlqxDAQRU8j7yJUGmxroUVD8DUaD… > | here ] .

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The Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg is looking for two data stewards ...
by Venkata Satagopam (TeC) 04 Jan '19

04 Jan '19

Dear all We are looking for two data stewards, please refer the below URL for more details: http://emea3.mrted.ly/21qif Best regards, Venkata — Dr. Venkata Satagopam Technical Coordinator ELIXIR-Luxembourg Node 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)elixir-luxembourg.org<mailto:venkata.satagopam@elixir-luxembourg.org> https://www.elixir-europe.org/about/elixir-luxembourg ----- 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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ELIXIR Luxembourg Node looking for a postdoc ...
by Venkata Satagopam (TeC) 04 Jan '19

04 Jan '19

Dear all, We are looking for a 'Research Associate (postdoc) in the field of clinical and translational medicine informatics’ at ELIXIR Luxembourg Node to work on newly funded IMI project - FAIRplus. Please refer the below URL for more details. http://emea3.mrted.ly/21uyv Best regards, Venkata — Dr. Venkata Satagopam Technical Coordinator ELIXIR-Luxembourg Node 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)elixir-luxembourg.org<mailto:venkata.satagopam@elixir-luxembourg.org> https://www.elixir-europe.org/about/elixir-luxembourg ----- 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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