Strengthen data management in Galaxy

31 May 2021 - 30 May 2023

This project focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. Existing technologies and services in ELIXIR will be supported and ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data Portal, EOSC-Life, etc.) will be complemented while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

Building on PDBe-KB to chart and characterize the conformational landscape of native proteins

31 May 2021 - 30 May 2023

This implementation study will create infrastructure to chart the experimentally sampled conformational diversity of native proteins by exploiting data from the PDB, augmented with results of state-of-the-art computational tools. By integrating resources and tools, workflows will be developed to:

  • compare and cluster different conformations adopted by homologs of the same protein and
  • identify protein regions with different flexibility properties. 

Pipelines will be created to characterize conformational ensembles in terms of:

Increasing Plant data findability and reuse beyond ELIXIR

31 May 2021 - 30 May 2023

Though the Plant Sciences Community has already implemented some critical elements of its roadmap, the project plan for this community implementation study features three key objectives, with each objective addressed in a corresponding work package:

Making container services integratable, sustainable and widely used

31 May 2021 - 30 May 2023

The aim of this new strategic implementation study (SIS) is to build on the current progress made through the ongoing implementation study, enabling the adoption and deployment of protocols and services by the broader ELIXIR community at scale.

The first SIS Containers study (2019-2021) has successfully convened and established a growing ELIXIR wide consensus on high-level community-driven service needs and related standards including:

Functional Plant Bioinformatics (PLAZA)

This two-day workshop will introduce the basic concepts of comparative and functional -omics data analysis in plants through lectures and practical hands-on sessions. Plant biologists and geneticists with an interest in bioinformatics and data analysis are encouraged to attend this training.  After this workshop, you will have a good understanding of the organization of plant genomes, the evolution of plant gene families and the different systems used to describe gene functions.

Introduction to NGS analysis

This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', Hands-on introduction to NGS variant analysis', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.

 

Objectives

 

Introduction to NGS analysis

This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', Hands-on introduction to NGS variant analysis', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.

 

Objectives

 

Introduction to NGS analysis

This training is an introduction to 'Bulk RNA-Seq analysis for differential expression', Hands-on introduction to NGS variant analysis', and 'Hands on introduction to ChIP-Seq analysis'. If you want to follow one of these trainings and you have no experience with NGS data you should follow this introduction first.

 

Objectives

 

Gentle hands-on introduction to Python programming

This course gently introduces programming to new programmers. There are plenty of opportunities to apply and practice what you learn, and ask questions in a safe place. Furthermore, surprise yourself by building a substantial project over the 3 course weeks. We use the popular Python programming language to prepare you for real-world research application of what you learn.

 

Objectives

 

Analysis of 16S rRNA metagenomic experiments

This training will start with the presentation of a 16S pipeline in a linux environment, using a minimal amount of linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees. The second part of the training will give an overview of numerical ecology and takes part entirely in R.

 

Objectives

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