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2019

  • 2 min read

Weekly news 15.04.2019

The ELIXIR Data Platform published a paper to present the collective usage and impact of ELIXIR Core Data Resources

Applications are open for the second year of the PgCert in Biocuration at Cambridge University. The deadline is on 17 May, with the course starting in October 2019.

Applications are open for two SIB courses:

Registrations are open for the Summer School - Bioinformatics for Biologists: An introduction to Data Exploration, Statistics and Reproducibility, on 1-5 July 2019, Cambridge, UK. 

Registration is open for the Summer School Integrative X-omics analyses empowering personalized healthcare on 1-5 July 2019 in Nijmegen, the Netherlands.

Registration open for the course FAIR Data Stewardship -  Digital data scholarship for wetlab scientists, 27-29 May, Niel, Belgium. This course is part of the Interreg-funded  Helis Academy and organised by DTL/ELIXIR Netherlands.

Registrations are open for the Workshop on High-Content Imaging and Data Science for Virtual Screening and Drug Discovery, taking place in Bled, Slovenia, on 13-17 May 2019. The deadline for regular registration is April 30. Registration will still be open afterwards but with higher fees.

Applications open for ELIXIR Sweden (NBIS) courses:

 

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Weekly news 08.04.2019

Registrations are open for the course, Summer School - Bioinformatics for Biologists: An introduction to Data Exploration, Statistics and Reproducibility, 1-5 July 2019, Cambridge, UK. The course will focus on solutions around handling biological data and will cover introductory lessons in data manipulation and visualisation in R, statistical analyses, and reproducibility. No prior R experience or previous knowledge of programming/coding is required. Register here.

ELIXIR France and GREEK COST Action organise a 3-days training session / hackathon in Marseille on 23-24 April 2019. It will focus on interoperable workflows invoking remote bioinformatics resources (knowledge bases, databases, analysis tools) to gather information about regulatory networks and enable an integrative analysis of gene regulation processes.

Registrations are still open for the Docker and Reproducibility Course, organised by ELIXIR Italy in Turin, on 13-14 June 2019. During the workshop, the participants will learn the core concepts of Docker and how to easily embed bioinformatic pipelines/workflows into a docker container.

Registration is now open for the ELIXIR EXCELERATE WP10 course Single RNA-seq data analysis with R which takes place at CSC in Espoo (Helsinki), Finland on 27-29 May 2019. The application deadline is 16 April 2019, the course is free of charge.

FAIRsharing as a community approach to standards, repositories and policies, read the new paper presenting FAIRsharing in Nature Biotechnology.

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Train the Trainer course May 30-31 in Italy

ELIXIR-EXCELERATE, in collaboration with ELIXIR-IIB, is pleased to announce a Train the Trainer (TtT) event.

 

IMPORTANT DATES

Course date: 30-31 May, 2019

 

VENUE

University of Padua, Campus of Biology and Biomedicine “Fiore di Botta”, Italy

 

We will accept a maximum of 20 participants. Priority will be given to candidates from Elixir Italy institutes and other ELIXIR Nodes. Notifications of acceptance will be sent shortly after the application, which will remain open until we reach 20 participants.

 

 

Full details and the application form at: https://elixir-iib-training.github.io/website/2019/05/30/train-the-trainer-padua.html

 

 

COURSE DESCRIPTION:

The course is organized around four sessions, covering:

* Learning principles and how they apply to training and teaching

* Teaching techniques that can be used to enhance learner engagement and participation

* Lesson, course, and materials design

* Assessment and feedback in training and teaching

 

Examples and discussions will also focus on the challenges presented by academic teaching.

 

Who may be interested in this course?

Whoever wants to become a teacher or a better one. If you have questions like the following ones, this course may be very helpful to you.

 

* How learning works?

* How can I use learning principles to improve my teaching?

* How can I make my teaching more engaging and effective?

* How should I adjust my teaching to different types of learners?

* How can I help slow learners?

* How can I assess whether my students are actually understanding my

 lessons? Are they actually learning?

* What is the best balance between theory and practice?

* How can I best assess whether learning is occurring and/or has occurred?

* What works in a classroom and what doesn’t?

* Etc.

 

Should you have any question about organizational issues, do not hesitate to contact us at elixir.ita.training@gmail.com.

If you have questions regarding the course goals and content, you may contact Allegra Via (allegra.via@gmail.com).

 

Thank you for your interest,

Loredana Le Pera

(ELIXIR-IIB Deputy TRaining Coordinator)

Train the Trainer course May 8-10 at the University of Basel, Switzerland.

ELIXIR-CH and ELIXIR-SE are pleased to announce an ELIXIR Train the Trainer course, which will take place on 8-10 May at the University of Basel, Switzerland. 

Train-the-Trainer courses are for scientists:
- with some to little or no teaching experience,
- who want to become a teacher or a better one, and
- who believe teaching is - or may become - a relevant aspect of their professional development.
 

This course will cover 4 main topics:
- learning principles and how they apply to education and training;
- teaching techniques that can be used to enhance learner engagement and participation;
- design of lessons, course and materials;
- assessment and feedback in training and teaching.

Examples and discussions will also focus on the challenges presented by academic teaching.

Full details and the application form can be found here. 

Should you have any question about organizational issues, do not hesitate to contact me, the local organizer.

If you have questions regarding the course goals and content, you may contact the trainers: Jessica Lindvall (jessica.lindvall@nbis.se) and myself.

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Weekly news 02.04.2019

Please note that registration is now open for the  ELIXIR EXCELERATE course "Single cell RNA-seq data analysis with R" which takes place 27.-29.5.2019 at CSC in Espoo (Helsinki), Finland. This hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is organized by ELIXIR Finland in collaboration with ELIXIR Sweden, Norway, Germany, Netherlands and France, and it is free of charge.

The application deadline for the course is 16.4.2019. Participants are selected based on their motivation description, and we will also do our best to ensure that every country / research group gets at least one representative in the course. For registration and more information, please see the course website at https://www.csc.fi/web/training/-/scrnaseq.

The BioHackathon2019 call for hacking projects will close on 7 April. Submission of proposals will be coordinated through Easychair bh2019; if you have any questions contact Jen Harrow (jen.Harrow@elixir-europe.org).

BioContainers presents two new features: (1) users can trace the usage of every container on the registry page. (2) a similarity component  between all containers taking into account the metadata. At the end for each container, there is a set of suggestions for similar containers. See blast

 

Registration is open for the BioExcel Summer School on Biomolecular Simulations, taking place in Pula, Italy on 30 June - 5 July 2019. The summer school includes lectures and hands-on sessions on Molecular Dynamics simulations, Biomolecular Docking, QM/MM, Free energy calculations and advanced sampling methods (Metadynamics).
Registration to the PRACE/BioExcel Seasonal School HPC for Life Sciences is now open. The programme will allow participants to get a comprehensive understanding of the usage of the different codes; their scalability and performance, as well as ways to avoid potential issues; and learn the best practices about using them on HPC systems.

The next CORBEL webinar titled “A Basic Introduction to Bioimage Analysis” featuring Christian Tischer from the EMBL Centre for Bioimage Analysis (CBA), will take place on 11 April 2019 at 15:30 CEST.

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Advanced R Programming for Bioinformatics Summer School in Visby (10-20.06.2019)

Dear Colleagues, 

 

Between 10-20 June 2019, Elixir-SE (National Bioinformatics Infrastructure Sweden) is organising RaukR, Advanced R Programming for Bioinformatics Summer School in Visby (Gotland, Sweden). 

We will cover a broad range of topics including writing R packages, reproducible research with R, using tidyverse packages, creating publication-quality plots with ggplot2 and working with GitHub, maps, machine learning and advanced statistics. W

Our guests, Jenny Bryan (RStudio, UBC), and Yhui Xie (RStudio) will share their knowledge and expertise with us!

You are welcome to register (no later than 01.04.2019) on: https://nbisweden.github.io/workshop-RaukR-1906/registration/

More info on: https://nbisweden.github.io/workshop-RaukR-1906

Please, spread the word! 

 

On behalf of the Organising Committee,

Marcin Kierczak, Sebastian DiLorenzo

————————————————————————
Marcin Kierczak, PhD
Bioinformatics data scientist

Bioinformatics Long-term Support (WABI)
National Bioinformatics Infrastructure Sweden at SciLifeLab 

www.nbis.se, www.scilifelab.se/platforms/bioinformatics


BMC E10:3206, entrance C11
Husargatan 3, SE-752 37 Uppsala

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Weekly news 25.03.2019

Open-access online tutorial How to install and deploy Beacon has been launched on the ELIXIR Slovenia eLearning Platform. The tutorial is also registered as TeSS material. The tutorial contains learning materials provided by Beacon developers from ELIXIR Finland and ELIXIR Spain. They contain instructions for Beacon installation and deployment, available as text and video.

Registrations are open for the Advanced Bioinformatics Workshop held together with the CODATA-RDA Research Data Science Summer School at the ICTP in Trieste, Italy, from 19 - 23 August 2019. The workshop will provide an introduction to Machine Learning in omic data analysis, as well as automation approaches using CWL and Docker. The workshop is supported by ELIXIR and being organized by Fotis Psomopoulos (ELIXIR Greece)

The Galaxy Community is pleased to announce that registration and abstract submission for the 2019 Galaxy Community Conference (GCC2019) are now open.

Registrations are open for two HPC workshops in Utrecht Netherlands, organised by ELIXIR Netherlands and SURFsara: Cluster Computing for Life Sciences on 23-24 April 2019 and Deep Learning for Life Sciences on 9 May 2019.

Join full-day Train-the-Trainer Bootcamp organized by FOSTER, CESSDA, ELIXIR and DANS: Open Science and Research Data Management Train-the-Trainer Bootcamp, Wednesday 17th April 09:00-17:00, The Hague, The Netherlands.

 

 

 

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Weekly news 18.03.2019

The first ELIXIR Bioinformatics Supplier Forum will take place in London on 7 May 2019. The programme and registration are available through the ELIXIR webiste.

The ELIXIR Innovation and SME Forum took place on 5 March in Stockholm, Sweden. The topic was Genomics and Associated Data in National Healthcare Initiatives, the presentations of Illumina, Genomics England, AstraZeneca and others. The photos and slides are now available online.

The BioHackathon2019 call for hacking projects is now open and will close on 7 April. Submission of proposals will be coordinated through Easychair bh2019 and if you have any questions please contact Jen Harrow (jen.Harrow@elixir-europe.org). 

If your role involves the management, storage, transformation and annotation of data in order to answer biological questions, take part in an online survey to map the landscape of biocuration, the resources and tools used and the training that is available and required.

Registrations are open for the Bioinformatics Education Summitaimed at bioinformatics trainers and educators. The event will take place in Cape Town, South Africa, 14-17 May 2019 and is being organised by H3ABioNet in collaboration with ELIXIR, GOBLET and the ISCB Education Committee. The meeting will focus on developing guidelines and materials for bioinformatics trainers.

Registrations are open for four SIB courses:

Registrations are open for the ELIXIR Software Carpentry in Ljubljana on 16-17 May 2019. The workshop is organised by ELIXIR Slovenia in cooperation with Data & Software Carpentry and will focus on the basics of the R programming language. There is no registration fee. The limit of participants is 20.

University of Ljubljana and the Ministry of Education, Science and Sport in Slovenia is organizing a Symposium Systems Medicine in Clinical Practice under the ERA-NET initiative ERACoSysMed. Ljubljana, Slovenia, 10-11 June 2019. Registration is open!

Registrations are open for the course PDA19 - Proteomics Data Analysis on 1-5 April 2019 with Lennart Martens, Harald Barsnes and Lieven Clement. The deadline for applications is on 25 March.

Registrations are open for the ELIXIR Greece Carpentries workshop, June 3-4, at the National Hellenic Research Foundation in Athens Greece. The course will address core concepts on Unix, Git and Data Analysis and Visualization in R.

Registrations are open for the course, Summer School - Bioinformatics for Biologists: An introduction to Data Exploration, Statistics and Reproducibility, 1-5 July 2019, Cambridge, UK.  The course will focus on solutions around handling biological data and will cover introductory lessons in data manipulation and visualisation in R, statistical analyses, and reproducibility.  The Registration is now open!

Registrations are open for the ELIXIR-UK course Transcriptome Analysis for Non-Model Organisms, April 15-17, Cambridge, UK. This course provides an overview of modern applications of transcriptome sequencing and popular tools, and algorithms, for exploring transcript reconstruction and expression analysis in a genome-free manner.

Registrations are open for the Genome assembly and annotation course 5, to take place in Milan, Italy, on 1-5 July 2019. The course is organized by ELIXIR Italy in cooperation with ELIXIR France, Sweden and Slovenia.

Registrations are now open for the ELIXIR Finland course Variant analysis with GATK on 14-17 May 2019 in Espoo, Finland.

ELIXIR Luxembourg is running its annual R tidyverse course in Luxembourg, May 14-17, 2019. In this four day course, D1 and D2 are devoted to introduction to the basic tidyverse packages, D3 are advanced topics and changes, D4 is BYOD/project work. Registration is open!

Registrations are open for the ELIXIR Belgium workshop on Computing skills for reproducible research: Software Carpentry on 16-17 April 2019 in Brussels, Belgium.

Registrations are open for two HPC workshops in Utrecht Netherlands, organised by ELIXIR Netherlands and SURFsara: Cluster Computing for Life Sciences on 23-24 April 2019 and Deep Learning for Life Sciences on 9 May 2019.

 

 

 

 

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Biocuration survey

On behalf of our ELIXIR colleagues, please find time to contribute to a biocuration survey.

 

Dear colleagues,

we would need your help to disseminate a survey among all scientists you may know. Please forward it as much as possible.

This survey is part of an ELIXIR Implementation Study designed to map the landscape of biocuration, the resources and tools used, and the training that is available and required.

It is addressed to scientists who may have a role in the management, storage, transformation and annotation of data and that in order to help answer biological questions. Your answers would help us understand who does this work, which tools and resources are used, or what are the training needs.

You can launch the survey by following this link: https://www.surveymonkey.co.uk/r/Biocuration-ELIXIR 

We greatly value your contribution and look forward to sharing the outcomes with you.

Best wishes,

Sarah, Alex, Melissa (ELIXIR-EMBL-EBI),  Pete (FAIRsharing/ELIXIR-UK), and Patricia (SIB/ELIXIR-CH).

On behalf of the Elixir Implementation Study - Mapping the landscape of Biocuration in ELIXIR: Practice, capability and training requirements 

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CodeRefinery workshop April 2-4

On April 2-4, 2019, Elixir Estonia together with the Nordic e-Infrastructure Collaboration (NeIC) is hosting a CodeRefinery workshop for graduate students and researchers. The workshop will take place in Tartu.

 

The main focus is on professional tools for efficiently developing and maintaining research software.

Who the course is for?

Are you doing any of these things below:

  • You write scripts to process data.

  • You change scripts written by your colleagues.

  • You write code that is used in research by you or others.

If yes, then this course is for you. Most participants are not "professional code developers" or computer scientists.

Venue: University of Tartu Library, W. Struve 1, 51003, Seminar room Kodavere.

 

Space is limited and it will likely fill quickly. The workshop is free for everyone.

 

More information, agenda and registration here: https://coderefinery.org/workshops/2019-04-02-tartu/

 

We hope to see you at the workshop!