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  • 1 min read

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

  • 1 min read

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.

 

 

 

  • 3 min read

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.

 

 

 

 

  • 1 min read

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 

  • 1 min read

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!

  • 1 min read

Weekly news 25.02.2019


Radbound University (part of ELIXIR Netherlands) is organising a Summer School Integrative X-omics analyses empowering personalized healthcare on 1-5 July 2019 in Nijmegen.

Registrations are open for the SIB course on “NGS - Genome variant analysis”, in Bern on 29-30 April 2019.

The registrations are open for the ELIXIR Finland course Variant analysis with GATK in Helsinki, Finland, on 14.-17 May 2019.

5-6 March 2019 | Stockholm, Sweden ELIXIR Innovation and SME event: Genomics and Associated Data in National Healthcare Initiatives

 

  • 2 min read

Weekly news 14.01.2019

Application are open for CORBEL Data Visualisation for Biology: a practical workshop on design, techniques and tools in Hinxton, UK, on 11-15 March 2019. The registration deadline is on 25 January 2019.

The ELIXIR Plant Community is pleased to announce that MIAPPE version 1.1, an updated specification of the Minimal Information About a Plant Phenotyping Experiment, has been officially released. Work is now commencing on the next version of MIAPPE, v2.0 and further improvements can be suggested via miappe-feedback@ebi.ac.uk

DTL & ELIXIR Netherlands in collaboration with the French, UK, and German Nodes, is organising an event Boost Your Visibility – Improving “F” of FAIR for Dutch Training and Data Resources through Bioschemas in Utrecht, the Netherlands. The pre-registration is now open.

EMBL-EBI is organising a training course Metagenomics Bioinformatics on 10-13 June 2019 in Hinxton, UK. The registration is now open.

Applications are open for the ELIXIR Italy course Single Cell RNA Sequencing and Data Analysis, on 7-10 May 2019 at the Telethon Institute of Genetics and Medicine (TIGEM), Italy.

Applications are open for the ELIXIR Switzerland (SIB) courses NGS - Quality control, Alignment, Visualisation, Bern, 27 February - 1 March 2019 and Python for Life Scientists, Bern, 4-6 March 2019

ELIXIR Luxembourg is hiring Research Associate in the field of clinical and translational medicine informatics (postdoctoral position) to support the ELIXIR coordinated IMI project FAIRPlus.

IRB Barcelona (part of ELIXIR Spain) is currently looking to hire a talented and highly motivated Postdoctoral Researcher to join the Structural Bioinformatics and Network Biology group.

The Barcelona Supercomputing Center (part of ELIXI Spain) is looking for a highly motivated Research Engineer to join the Computational Genomics group.

The Vrije Universiteit Amsterdam (part of ELIXIR Netherlands) has an open tenure track position in Bioinformatics or Statistical Machine Learning. Applications need to be received by 19 December 2018.

 

 

Boost your Bioinformatics Backchat

Boost your Bioinformatics Backchat

Facilitating communication between individuals from different academic backgrounds in the bioinformatics space

 

 

 

 

Date: 17 December 2018

Time: 9:30-14:45 

Venue: University of Tartu, Estonia, Paabel (Ülikooli 17) 115/116

Trainer: Kim Gurwitz, University of Cambridge

ELIXIR ESFRI 5y Celebration Week

 

Audience: Biologists and Computer Scientists (and others) working in the field of Bioinformatics - maximum 14 participants. Registration is available here. 

 

This workshop aims to:

- enable workshop participants to develop an understanding of what the other bioinformatics subgroups actually do

- act as a springboard to improve communication between Bioinformatics subgroups (i.e. Biologists and Computer Scientists)

- facilitate the development of a culture of knowledge-sharing between Bioinformatics subgroups




 

Programme*

Time (EET)

Session

9:30 - 10:00

Welcome

10:00 – 10:10

Introduction

10:10 – 10:30

What do Biologists and Computer Scientists do?  No seriously, what do they really do?

10:30 – 10:45

How did you get into Bioinformatics, anyway?

10:45 – 11:15

tea/coffee break

11:15 – 11:45

What is a cluster? What is DNA?

11:45 – 12:00

Bioinformatics users vs. scientists vs. engineers

12:00 – 12:15

Opening up dialogue

12:15 – 13:15

Lunch

13:15 – 13:30

Continuing dialogue

13:30 – 14:00

Action plan write up and commitments

14:00 – 14:15

Action plan feedback

14:15 – 14:30

Workshop reflections

14:45

End

*subject to slight changes

Mini workshop about data management 13th December 2018

Most researchers know that data management is an important part of their work and is essential for getting the most out of your data. But what exactly is data management and what can you do to ensure that you’re managing your data well?

In this mini workshop you will learn what to consider when managing life science data and gain hints and tips for submitting your data to a public resource.

Dr. Melissa Burke and Dr. Sarah Morgan from EMBL-EBI training team (see more about them) will share best practicies, trips and tricks about managing your scientific data.

Registration and participation is free of charge. Up to 20 participants can take part. Please register here.

The workshop will take place at Ülikooli 17 (Paabel) on 13th of December at 9:30–12:30.

 

 

Software carpentry 17.-18.01.2019

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Seminar room Kodavere, University of Tartu Library (W. Struve 1), Tartu. 

When: Jan 17-18, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • Reference...

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...

Contact: Please email laura.altin@ut.ee for more information.

See https://elixirestonia.github.io/2019-01-17-tartu-NeIC for more information.

Register here https://goo.gl/forms/84EdtRsalQ6zayHu1