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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

 

 

  • 2 min read

Boost your Bioinformatics Backchat - ELIXIR ESFRI 5y Celebration week 17.12.2018


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 (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

  • 2 min read

Introduction of presenters of ELIXIR ESFRI 5y Celebration Week

ELIXIR Estonia is happy to welcome guests from three ELIXIR nodes abroad who will add an international touch to the events

Sarah Morgan

Sarah Morgan

Sarah is the training coordinator of the EMBL-EBI node.
After years of tumor research she switched her focus to training researchers. Currently she is training programme manager at EMBL-EBI and her everyday tasks involve coordination of training events both locally and internationally.

 

Melissa Burke

Melissa Burke

Melissa is scientific training officer at the EMBL-EBI training team. She is specialised in e-learning and manages online training courses that EMBL-EBI offers on variety of topics.

 

Kim Gurwitz

Kim Gurwitz

Kim is the ELIXIR Training Impact Coordinator, based at the University of Cambridge (ELIXIR-UK node). She coordinates the assessment of training quality and impact across ELIXIR. She was previously Training and Outreach officer at H3ABioNet, the Pan African Bioinformatics Network.

 

Mateusz Kuzak

Mateusz Kuzak

Mateusz is a Scientific Community Manager at ELIXIR-Neatherlands. He works at DTL at the interface of training, technology and data platforms and the research community in the Netherlands. Before joining DTL, Mateusz was building research software at the Netherlands eScience Center in collaborative projects with domain scientists. Before becoming Research Software Engineer, he worked in the field of Biophysics spending lots of time with microscopes.

 

Ilkka Lappalainen

Ilkka Lappalainen

Ilkka is the deputy head of node at ELIXIR-Finland. At CSC Ilkka is the head of service development for health and life sciences. He is an expert in sensitive data management and has long standing career in developing infrastructure for genomic data. Before joining CSC Ilkka worked at EMBL-EBI managing genomic variation archive services: EGA and DGVa and acting as Human Data Coordinator at the ELIXIR-Hub.

 

  • 2 min read

ELIXIR Information Day 14.12.2018

ELIXIR Estonia celebrates 5 years of ELIXIR with a series of events.

The major event is ELIXIR Information Day that takes place on 14th of December 2018 at Hotel Lydia Conference Center in Tartu. The day starts with welcoming coffee at 9am and finishes with drinks session around 4pm.

The event is free of charge for all registered participants.

The info day will give researchers from academia and industry, funders, decision makers and wider public an overview what ELIXIR is how it serves the scientific community.

Presenters include: Dr. Mateusz Kuzak (DTL; ELIXIR-Neatherlands), Dr. Ilkka Lappalainen (CSC; ELIXIR-Finland), Dr. Sarah Morgan (EMBL-EBI), Dr. Ulvi Gerst-Talas (TÜ; ELIXIR-Estonia; ETAIS), Dr. Hedi Peterson (TÜ; ELIXIR-Estonia), Prof. Jaak Vilo (TÜ; ELIXIR-Estonia). Learn more about the presenters here.

The purpose of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society.

These resources include databases, software tools, training materials, cloud storage and supercomputers.

The goal of ELIXIR is to coordinate these resources so that they form a single high quality infrastructure. This coordinated infrastructure makes it easier for researchers to find and share data, analyse their experiments, exchange knowledge, and agree on best practices.

Estonian ELIXIR Node
The Estonian node focuses on developing and maintaining software tools and databases, linking of bioinformatics and biobanking, and last but not least, training researchers across borders.


ELIXIR Information Day is a day full of opportunities to learn how ELIXIR can be beneficial to researchers' every day task. 

Registration is open - https://goo.gl/forms/0ACHoTb5aSmA9iFZ2 Registration deadline December 9th, 11.59pm

Schedule for the Information Day

09.30 - 10.00 Welcoming coffee
10.00 - 10.30 Prof. Jaak Vilo, ELIXIR Estonia Head of Node - “How ELIXIR helps the life science community”
10.30 - 11.00 Dr. Ilkka Lappalainen, ELIXIR Finland  - “What it takes to handle sensitive human data - Finnish and European experience”
11.00 - 11.30 Coffee and discussions
11.30 - 12.00 Dr. Hedi Peterson, ELIXIR Estonia - “Small but important - Estonian contributions to life science infrastructure”
12.00 - 12.30 Dr. Sarah Morgan, ELIXIR EMBL-EBI - “Improving European life science by providing world class trainings in physical and virtual class rooms”
12.30 - 14.00 Lunch
14.00 - 14.30 Dr. Ulvi Talas, ETAIS and ELIXIR Estonia - “Interaction of infrastructures - making scientific computing easier for life scientists in Estonia”
14.30 - 15.00 Dr. Mateusz Kuzak, ELIXIR-Netherlands "Training life science researchers in foundational coding and data science skills in the Netherlands and ELIXIR.”
15.00 - Closing remarks followed by apéro

The accompanying events include:

 

  • 1 min read

Weekly news 19.11.2018

The Biohackathon took place this week in Paris. Around 150 participants worked on 29 projects that support the operations across ELIXIR technical Platforms. See photos by Bérénice Batut (ELIXIR Germany), read the Daily reports from the event. From ELIXIR-Estonia Ivan and Erik took part.

 

Registrations are open for the course on “High Performance Computing for genomic applications”, organized for the D-BIOL researchers by Scientific IT Services, in Zürich, Switzerland, on 26-27 November 2018.

de.NBI (ELIXIR Germany) organises the  4th FAIRDOM/de.NBI Systems Biology Developers Foundry on 6-7 December in Frankfurt.

de.NBI also hosts COMBINE (Computational Modellig in Biology Network) 2019 Conference on 15-19 July 2019 in Heidelberg.

  • 2 min read

ELIXIR ESFRI 5y Celebration Week

The Life Science Infrastructure ELIXIR is celebrating its 5 year anniversary this December. On December 18th 2013 Estonia was the 5th member country that signed the collaboration agreement, thus officially launching ELIXIR (see the old news items (eng),(est)). Therefore, to bring ELIXIR knowledge closer to our life science community in Estonia we are celebrating the 5th anniversary with a series of events in Tartu.

The main event will be ELIXIR Info Day on 14th of December where Estonian ELIXIR team gives an overview of the actions taking place in Estonia and international speakers add flavour with demonstrating what is done in different countries across Europe.

The main event is accompanied by several smaller events happening in Tartu.

On Wednesday 12th, we are organising a Train the Trainer refreshment event for the people who are actively training researchers. This event is brought to us by EMBL-EBI training team members Sarah Morgan and Melissa Burke.  

On Thursday 13th, we have Data Management - what to consider when you manage your data workshop that is targetted for the life scientists who need to handle the data they create or use. This event is also delivered to us by EMBL-EBI training team members Sarah Morgan and Melissa Burke. 

On Thursday 13th in the afternoon we have a working seminar with Ilkka Lappalainen from CSC (ELIXIR-Finland) to exchange his and Estonian experience in handling sensitive data. For participation please contact Ulvi Gerst-Talas.

On Monday the 17th, we have Kim Gurwitz from ELIXIR-UK running a workshop "Facilitating communication between individuals from different academic backgrounds in the bioinformatics space”.



Please contact Laura Altin for further information about the events (laura.altin@ut.ee).

  • 1 min read

Weekly news 22.10.2018

EMBL-EBI is organising training course Introduction to RNA-Seq and Functional Interpretation on 26-29 March 2019 in Hinxton, UK. Registration is now open!

Registrations are open of the SIB course on “Data Visualization with Cytoscape, in Lausanne, on 1 November 2018. This workshop will directly follow a 3-day course about “Introduction to Network Analysis” and we recommend to attend both. It will focus on understanding sources of biological data and how to approach visualizing the data.

 

There are still free places for the SIB course on “Ligand-protein docking, and computer-aided drug design, in Basel, Switzerland, on 27-28 November 2018.

Booking now open for the course Bioinformatics for Biologists: An introduction to programming, analysis, and reproducibilityin Cambridge, United Kingdom, on 3-7 December 2018. The course will cover introduction to R, version control, statistical analyses, data management and reproducibility.

Registrations are open for the RNA Seq Data Analysis by using the Galaxy platform in Debrecen, Hungary, on 17-18 November. The course is free!

Join us in Ghent, Belgium, for the workshop NGS introduction using Galaxy on 6 November 2018. The registration is free.

  • 1 min read

Weekly news 08.10.2018

ELIXIR Training is organising a satellite event at NETTAB in Genova, Italy on 22 October 2018 Adopting Open Source Software FAIR Practices.

The registration is now open for the EMBL-EBI course ‘Introduction to Metabolomics Analysis Course’ on 5-8 February 2019 in Hinxton, UK.

Members of ELIXIR Slovenia are co-organising  the largest Systems Medicine symposium in Europe, the 2nd Conference of the European Association of Systems Medicine on 7 – 9 November 2018 in Utrecht, the Netherlands. Registration is still open. Please consider joining the conference that represents a unique occasion for closer links between ELIXIR and the leaders in the field of Systems Medicine.

Registrations are open for the SIB course on “Single-cell RNA-Seq Analysis”, in Bern (Switzerland), on 28-30 November 2018. This course will close with a minisymposium consisting of short scientific talks from SIB researchers on single-cell.

There are still free seats available for the 1st de.NBI Cloud User Meeting. In a 3-day event on 29 - 31 October 2018 at Bielefeld University you can learn about life science projects hosted in the de.NBI Cloud. Talks and workshops will be given about current de.NBI Cloud projects and state of the art cloud computing technologies like Spark, Docker and Kubernetes.