Agenda

The ELIXIR Director will welcome everyone to the 8th ELIXIR All Hands meeting, after which the head of the Dutch ELIXIR Node will provide an introduction. 

We will introduce ELIXIR-wide new intitatives starting in 2022.

Artificial intelligence (machine learning and deep learning) has widely been adapted across many sub-fields of Bioinformatics for robustly performing predictive and exploratory tasks such as drug-response and protein structure prediction, imputing missing data in single-cell gene expression patterns and many more. Driven by the power and usefulness of AI’s algorithms, it becomes imperative to know and understand the mechanism of its algorithms and their usage with real datasets. With this workshop, therefore, we aim to provide practical insights into the working of such algorithms. Moreover, we will showcase the usage of these algorithms available in Galaxy Europe using easy-to-understand Galaxy’s training materials and AI-enabled Jupyter notebook.

In this hands-on workshop, we will implement various classification, regression, clustering and deep learning models using Galaxy’s ML toolkit. The toolkit provides you with Scikit-learn, a popular Python ML library, Keras, a deep learning library based on Google’s Tensorflow, and various other tools for preprocessing and visualization. After completing this workshop, you should be able to upload and preprocess your dataset, build various ML models, train and evaluate your models, and visualize the results. Furthermore, you will learn how to use the DOME recommendations to annotate datasets so others can better understand and assess the performance and limitations of your approach. Using Galaxy’s workflows, you can capture all of the steps and dependencies in your analysis, along with the versions of the exact tools, so that your analysis is reproducible, or it can be run for a different dataset.

Agenda can be found here

This workshop will facilitate the coordination of the two currently ongoing IS Increasing and Bioschemas. Furthermore, it will allow outreach beyond those two original consortia. It will bring together the different streams of work to facilitate and ensure the alignment of the Implementation Studies with the activities and expectations of the community and the ELIXIR Platforms. It will provide an opportunity to disseminate existing results, gather additional requirements and discuss important matters, e.g. the proposed European Plant Data Portal, the ELIXIR Plant search service FAIDARE, the GenRes database EURISCO, and their connection with ELIXIR Core Data Resources.

Agenda can be found here

Are you an expert helping others, and you want to lower the barrier to your expertise? Data Stewardship Wizard (DSW) is an expert system suitable for planning and generally encoding expertise even beyond the field of data management. We will present to you various use cases where DSW helps researchers and communities from expertise encoded in a DSW knowledge model. You might want to use one of these implementations based on DSW or to integrate DSW according to your specific needs.

Agenda can be found here

This workshop has two objectives, to provide participants with:

1- Demos and insights on Beacon implementations. For this objective we will invite early Beacon v2 implementers who provided valuable feedback to the specification and will share their use-cases and experiences: Michael Baudis (Progenetix), Tim Beck (Café Variome), and Carles Hernandez (CNAG-CRG).

2- A training session on how to deploy a Beacon using the reference implementation. For this objective we will invite members of the European Genome-phenome Archive (Manuel Rueda) who support Beacon deployment in hospitals and clinical institutions and will provide a hands-on session.

Agenda can be found here

The workshop will increase the awareness of issues surrounding the sharing of phenotype definitions, and invite contributions from the participants. Specifically, we shall look at the “Author-Refine-Validate-Implement-Publish” phenotype creation pipeline, and discuss FAIR principles applicable at each stage.

Agenda can be found here

In this hands-on workshop, you will be able to bring your own containerized workflow, register it with the WorkflowHub (https://workflowhub.eu/) and use a web portal (https://github.com/athenarc/schema) to conveniently run it on your own data either via the ELIXIR::GA4GH Cloud infrastructure or the Galaxy::Pulsar network, all of which make use of at least some GA4GH Cloud standards. If you don’t have your own workflow and/or data, but you are still interested to try it out, we will of course supply some test data and workflows for you to toy with. Along the way, you will learn about the GA4GH Cloud API standards, current limitations, ongoing and future work and our vision towards an ELIXIR-wide, workflow language- and compute backend-agnostic, secure federated cloud infrastructure that is able to bring your data analysis needs to where the data resides, at scale.

Agenda can be found here

The workshop will be about multi-omics data analysis using both open-source software PathVisio, Cytoscape via programming interface R platform. We will analyze genome-wide gene transcriptomics) and metabolomics data using pathway and network analysis approaches on a publicly available dataset [1]. The dataset consists of integrated longitudinal molecular profiles of 132 participants with Crohn's disease, ulcerative colitis disease and healthy people. Differential expression analysis using R package DESeq2 [2] will be performed first to get altered genes during disease. Then pathway analysis will be conducted using PathVisio [3] with the curated pathway collection WikiPathways [4]. PathVisio provides overrepresentation analysis to detect enriched pathways in which both changed genes and/or metabolites are present. For network analysis, we will use the Cytoscape [5] program by which visualization of pathways can be performed and biological processes can be integrated. With these tools, participants learn how to use pathway and network analysis and they will learn how to visualize multi-omics data on biological processes and extend a network with the additional information.

The automated workflow is relevant for the Food and Nutrition Community since nutritional compounds and diets are known to influence the microbiome. Studies often combine host-transcriptomics and metabolomics data. For the Metabolomics community, it is of interest since we will show how metabolomics data can be analyzed and visualized in biological processes. The automated workflow includes commonly used systems biology approaches and is therefore relevant for the Systems Biology focus group. The duration of the workshop will be 1.5 hours.

Agenda can be found here

This workshop is composed of the following elements:

Brief update on the state-of-the-art of FEGA and Q&A session. Possible topics include: policy/governance, standards/technologies, and production operations.

Practical application of the FEGA Maturity Model and Q&A session. (including a pre-workshop survey/exercise for nodes to do some MM mapping and present their results)

FEGA Node Legal Agreement and Q&A session. (Attendees will be requested to come prepared having read the legal agreement and come with questions)

Practical FEGA node demonstrations from at least 2 FEGA nodes. Possible topics include: submission to a FEGA node, data download for approved researchers from a FEGA node, DPA/DAA related processes, CEGA<->FEGA node connection. Includes a Q&A session.

Agenda can be found here

The main goal of this practical workshop is to engage with ELIXIR Communities, both established and emerging, in order to establish a roadmap of the interaction between a Community and the Training Platform, which will be used as an exemplary moving forward. During the workshop, members / leads of the various activities of the ELIXIR Training Platform will work with the representatives of the selected Communities in order to demonstrate the use of the various TrP services. Additionally, the appropriate interaction and collaboration mechanism will be investigated, in order to facilitate any adaptation of the services to better fit the communities needs, and to collect domain-specific best training practices from the communities when available.

Agenda can be found here

The focus of this workshop will be on Biodiversity at scale. Members of the ELIXIR Galaxy Community, Tools Platform and the Biodiversity Focus Group will introduce the Vertebrate Genomes Project (VGP) and European Reference Genome Atlas (ERGA) initiatives, which will sequence and assemble the genomes of thousands of species over the next few years, and the plans that have been outlined in a submitted Horizon Europe call. We will also discuss how Galaxy is being integrated with RDM solutions (like COPO, InvenioRDM and RO-Crate) and with genome annotation tools (e.g. InterProScan, Apollo and Maker). Moreover, we will present the new microGalaxy communities, and how all these initiatives align with the other ELIXIR Communities and Focus Groups (e.g. Biodiversity, Federated Human Data, Human Copy Number Variation, Microbiome,...). This will also include the latest updates about our SARS-CoV-2 efforts and how the experience gained can be transferred to other outbreaks and diseases.

Agenda can be found here

In this session, each ELIXIR Platform will give an update on the outcomes and plans for the Platform. The order of the talks is:

Training Platform - Jessica Lindvall
Compute Platform - Juha Törnroos
Data Platform - Silvio Tosatto
Tools Platform - Salvador Capella
Interoperability Platform - Susanna-Assunta Sansone
Followed by a panel discussion

The social networking event will take place in the NEMO Science Museum on Tuesday the 7th June at 19:00 - 21:00. The museum is located not far from the Eye Film Museum. The distance from the hotels area is about 15 minutes by foot and from the venue 20 min including ferry. Please bring your conference badge.