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Weekly news 13.05.2019

Registration is open for the Helis Academy Course: Omics data analysis through data integration - using biological pathways, networks, and linear models, taking place from 11-14 June in Niel, Belgium. This course is part of the Interreg-funded Helis Academy and organised by VIB/ELIXIR-BE and University of Maastricht.

Free seats are still available for the the ELIXIR-DE epigenetics workshop “DNA Methylation: Design to Discovery” in Saarbrucken.

We invite you to join COMBINE 2019, the 10th Computational Modeling in Biology Network Forum event, taking place 15 - 19 July 2019 in Heidelberg, Germany. The event is hosted by the Heidelberg Institute for Theoretical Studies (HITS).
Registration and abstract submission are now open.

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-NL.

Registration is open for Data Steward Knowledge and Skills Workshops – A working meeting with and for the Data Steward Community, June 11 & June 12 in Utrecht, the Netherlands.

Registration open for the ELIXIR-ES Software Carpentry workshop "R for Reproducible Scientific Analysis", taking place from 6-7 June in Madrid, Spain. The workshop is hosted by the Spanish National Cancer Research Centre (CNIO).

Registrations are open for the SIB course on “NGS - Quality control, Alignment, Visualisation”, from 12-14 June in Bern, Switzerlan


 

FAIR Data Stewardship – digital data scholarship for wetlab scientists - course in the Netherlands

From 27-29 May, 2019, we will organize the first course in  Data Analysis and Stewardship theme of the Helis Academy:  

FAIR Data Stewardship – digital data scholarship for wetlab scientists

The target audience is wet-lab scientists – from industry and academia – and graduate students in the Life Sciences who wish to improve their digital scholarship on data handling. Some basic experience with programming and scripting languages like python, perl, R, matlab, etc. are an advantage, but not needed.

The course will introduce the trainees to important concepts of data stewardship. We start with a general introduction covering the data life cycle, the FAIR principles and a definition of data stewardship and data stewards. The course is also relevant for Data Stewards who are supporting the life science researchers.

 

We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course.

  • On day one trainees will investigate data management plans, which types are there and how they should be used.
  • On day two the course highlights how to work with data during the research phase, explaining how to create well formatted data which helps in the second module of day two to make data interoperable already during the active research phase.
  • On day three trainees will have an in-depth at persistent identifiers, different use cases and types of identifiers. Finally we are closing the data life cycle by making data fit for sharing, archiving and publishing. 

This course is part of the Data Analysis and Stewardship theme of Helis Academy and is organised by DTL and DTL collaborators. Info about other courses in the theme of Data Analysis and Stewardship can be found on the Helis Academy website and on the Helis Academy page on the DTL website.

You can find all the information, including the full programme and registration possibilities here: https://www.aanmelder.nl/helis-fair-data-stewardship-course

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Weekly news 22.04.2019

The Galaxy Training Network (GTN) is organizing online CoFests (Collaboration / Contribution Fests) every 3 months for a day of collaborative work on training content. The next one will be on 16 May. Anyone who would like to contribute is welcome to join. It will be coordinated via Hangout (drop-in channel to be kept open the whole day) and the GTN Gitter channel. More details are on the Galaxy website  and the dedicated GitHub issue.

Registration is now open for a brand new course on Managing single cell transcriptomics data, held at EMBL-EBI, Hinxton on 3-5 July 2019. The workshop aims to focus on how to generate high quality data and metadata, which follow the FAIR principles. The deadline for registration is 31 May 2019.

Registrations are still open for the Docker and Reproducibility Course, organised by ELIXIR Italy at the University of Turin, on 13-14 June 2019.

Registrations are open for two ELIXIR training courses taking place in May in Ghent, Belgium. The trainers are Mateusz Kuzak, Toby Hodges.

Registration open for BioSB course: Algorithms for Genomics, on 1-5 July 2019 in Delft, Netherlands.

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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.

  • 2 min read

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.

  • 2 min read

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.