Weekly news 25.11.2019
| The ELIXIR TeSS portal has a variety of interesting events and courses organised by the ELIXIR Nodes. ELIXIR events Webinar: Nextflow: Introduction and practical demonstration |
News
gProfiler is now running on Galaxy at https://usegalaxy.eu and https://galaxy.hpc.ut.ee/.
gProfiler (https://biit.cs.ut.ee/gprofiler) is a toolset for functional enrichment analysis and conversions of gene lists that is now available also at Galaxy platform. Galaxy is meant for supporting data intensive research in a convenient manner through building and using custom workflows.
Biological data analysis often deals with lists of genes arising from various studies. The gProfiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to their orthologs. The mission of gProfiler is to provide a reliable service based on up-to-date high quality data in a convenient manner across many evidence types, identifier spaces and organisms.
gProfiler relies on data retrieved from Ensembl database and fungi, plants or metazoa specific versions of Ensembl Genomes, and parasite specific data from WormBase ParaSite. In addition to Gene Ontology, supported data sources include KEGG, Reactome, WikiPathways, TRANSFAC, miRTarBase, Human Protein Atlas, CORUM and HP.
gProfiler supports close to 500 organisms and accepts hundreds of identifier types.
gProfiler has been supporting developers by offering a standardized access through public APIs. The usage of APIs was simplified by wrapping them into Python and R packages. The latter, `gprofiler2` (which was published as a Conda Forge package named `r-gprofiler2`), was wrapped to be used as a set of Galaxy tools:
- gProfiler GOSt performs functional enrichment analysis, also known as over-representation analysis (ORA) or gene set enrichment analysis, on input gene list; in addition to the detailed tabular results, it can also create a Plotly graph with the Manhattan plot very similar to the one shown by the web tool.
- gProfiler Convert enables to convert between various gene, protein, microarray probe and numerous other types of namespaces
- gProfiler Orth translates gene identifiers between organisms
- gProfiler SNPense maps SNP rs-codes to gene names, chromosomal coordinates and variant effects
- gProfiler Random fetches a (not actually random) list of gene identifiers; useful for testing purposes.
gProfiler Galaxy toolset was admitted to the Galaxy Tools IUC. It is distributed via the ToolShed and can be installed as a bundle with the gProfiler tool suite repository.
gProfiler is part of the ELIXIR infrastructure. It belongs to the portfolio of ELIXIR Recommended Interoperability Resources.
gProfiler is developed and maintained in Estonia, at the University of Tartu, Institute of Computer Science, BIIT research group. It is an ELIXIR Estonia service.
Our latest publication of the g:Profiler tool - Uku Raudvere, Liis Kolberg, Ivan Kuzmin, Tambet Arak, Priit Adler, Hedi Peterson, Jaak Vilo: g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) Nucleic Acids Research 2019; doi:10.1093/nar/gkz369
Weekly news 21.10.2019
The slides and recording of the presentation on the ELIXIR Beacon & Beacon Network as a service are now available on the ELIXIR website.
ELIXIR Innovation and SME forum highlights from 'Distributed data analysis - the (health) data train' in Utrecht are available in the industry news release.
DNAstack have launched Clinical Evidence Beacons, extending from the GA4GH approved Beacon standard, as detailed in their latest news release.
We're pleased to announce the publication of the Intrinsically Disordered Protein (IDP) community's white paper in the ELIXIR F1000 channel.
FAIDARE, the Plant Data Lookup service, is now fully operational both with Phenotyping and Genotyping data! Five data repositories from EBI, INRA, VIB, CIRAD and iBET are connected to this service, and others from Europe and beyond will be available soon.
BrAPI, the plant Breeding API, has a new publication out in Bioinformatics: BrAPI-an application programming interface for plant breeding applications.
We are delighted to announce a Memorandum of Understanding between FAIRsharing and DataCite to identify a set of criteria for the recommendation of research data repositories for the benefit of the broader research community. This project will be used to improve the recommendations that FAIRsharing provides to journal publisher and funder policy makers.
Are you attending ICSB in Japan this year? De.NBI are hosting a full day satellite workshop on 31 October - "COMBINE & de.NBI Tutorial: Modelling and simulation tools in systems biology" with an impressive speaker lineup and agenda that still has a few spots remaining for free registration.
EMBL-EBI have launched a new sister resource to the GWAS catalog for Polygenic scores - the PGS Catalog. As a new resource, they are seeking input into how to develop the resource to meet user needs. Please fill in and share their survey. You can find out more from this twitter thread.
ELIXIR Innovation and SME Forum: Data management in the life sciences - a driver for innovation
27 - 28 November 2019 | Milan, Italy
EMBO practical course: Integrative modelling of biomolecular interactions
10 - 15 May 2020 | Izmir, Turkey
Weekly news 14.10.2019
Take a look at our news release, ELIXIR as a global actor in bioinformatics training, to find out about how the ELIXIR Training Platform is supporting training across the world.
Can you can help drive the open source software community and make a positive contribution by taking part in Hacktoberfest 2019? Anyone and everyone is welcome to participate!
The final report of the project Towards a community-endorsed data steward profession for life science research, funded by ZonMw, DTL/ELIXIR-NL, UMC Groningen, Radboud University and UMC Utrecht is out now. Full details on the project can be found on the Zenodo website.
ELIXIR Finland have published a new case study on using AI for health risk assessments, with a specific focus on cardiovascular disease, presenting work by Andrea Ganna at FIMM.
EJP-RD Workshop and Hackathon: Molecular pathways for rare diseases - (FAIR) data analysis
26 - 29 November 2019 | Maastricht, Netherlands
ELIXIR Innovation and SME Forum: Data management in the life sciences - a driver for innovation
27 - 28 November 2019 | Milan, Italy
Gentle hands-on introduction to Python programming
9 - 10 January 2019 | Leuven, Belgium
Helis Academy - FAIR Data Stewardship course by DTL in Utrecht Nov 2019
From 4-6th November, 2019, we will give another round of the Helis Academy - FAIR Data Stewardship course:
FAIR Data Stewardship – digital data scholarship for life scientists
The target audience is life 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 is also relevant for Data Stewards who are supporting the life science researchers.
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 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.
We will pass the stages of the data life cycle in more detail in the training modules of this 3 day course.
- Day 1: Why use a data management plan and what for? On day one trainees will investigate data management plans, which types are there and how they should be used.
- Day 2: Mastering the data chaos during the research phase. 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.
- Day 3: Boost your visibility and get cited for your data! 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. The training is organised by DTLand delivered as a joint effort by DTL partners.
You can find all the information, including the full programme and registration possibilities here: https://www.aanmelder.nl/data-stewardship-course/part_program. 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.
Weekly news 23.09.2019
The Partnership for Advanced Computing in Europe (PRACE) have launched their 20th call for Proposals for Project Access. The call enables people to apply for access to high powered computer (Tier-0) systems. This year the applications are also open to Industry. Deadline 29 October 2019.
The Data Platform have released a new paper in our F1000 channel "Understanding life sciences data curation practices via user research".
ELIXIR Innovation and SME Forum: Distributed data analysis - the {health} data train 10 - 11 October 2019 | Utrecht, Netherlands
Weekly news 16.09.2019
ELIXIR Estonia together with Estonian Scientific Computing Infrastructure (ETAIS) has the first GDPR seminar today (16th of September). Futher information is available at https://elixir.ut.ee/node/262
We are pleased to announce three new ELIXIR Communities:
- 3D-BioInfo
- Intrinsically Disordered Proteins
- Microbial Biotechnology
Please read our latest news release to find out more about the aims of these Communities and who is involved.
The Pistoia Alliance FAIR/Ontologies Mapping (OM) project 'Communities of Interest' opens the first of its monthly webinar series with “Progress towards commercial FAIR data product and services” by Ted Slater this coming Thursday 19th September 2019 15:00 - 16:00 BST, join the meeting here.
Abstract: Elsevier is a global information analytics business that helps institutions and professionals advance healthcare and open science to improve performance for the benefit of humanity. In this webinar, we will discuss how Elsevier is increasingly leveraging the FAIR Guiding Principles to improve its products and services to better serve the scientific community. Ted is one of the authors on the seminal 2016 FAIR guiding principles paper. He has worked extensively within pharma R & D and more recently for providers of data analytics.
Fotis Psomopoulos (ELIXIR-GR) has been selected to be an Research Data Alliance (RDA) Europe Ambassador for Bioinformatics. Part of his activities in this role will be to act as the formal RDA liaison for the ELIXIR Training Platform, with an additional focus on early career researchers at the intersection of Life Sciences and RDA.
ELIXIR Finland have recently published a new user case study on Targeted treatment for venous diseases with vascular system modelling, which details a collaboration with academics in Belgium as well as a Finnish start up microfluidics company, FinnAdvance.
The National University of Ireland (NUI) Galway have been awarded €13 million for a new centre for Graduate Research Training in Genomics data science. The funding was awarded from the Science Foundation Ireland to train 115 PhD students over the next seven years. The centre is led by Prof. Cathal Seoighe, who is ELIXIR’s Training Coordinator for Ireland.
Gallantries RNA-seq workshop for beginners: from sequences to visualization using Galaxy and R, October 2019
Gallantries team is organising a workshop in three citys across Europe simultaneously about RNA-seq analysis for beginners.
Main document for the event is available at https://galaxy-carpentries.github.io/gallantries/event/2019-08-27-second-gallantries-workshop/. NB - participants form Tartu need to register through our local registration site at https://forms.gle/MhPNFQVz1yTupLUx6.
Below is most relevant information for workshop participants in Tartu.
The Gallantries team is offering its second RNA-seq workshop for beginners on October 7-9th.
This workshop will cover:
- Galaxy introduction
- Introduction to High-Throughput Sequencing and Quality Control
- Reference-based RNA-seq data analysis
- Basics of R programming
- Post-processing of RNA-seq data using R and Rstudio
Important notes
The workshop is free of charge and covers:
- 3 days of training
- Coffee and tea over the days
- Lunch
No stipends for travel or accommodation are available.
Desktop computers will be available. You can also bring your own notebook if you prefer . Eduroam is available, ask your institute how to connect.
A social dinner will be organised at each site on Tuesday October 8th. This dinner will be at your own cost, but we would love to have a chat with you after the workshop!
Workshop Format
This will be a hybrid training. This means the instructors will teach in front of a camera, and this video feed is live-streamed to multiple locations around the world. Each location will have several other instructors and helpers on site to answer questions and who can take over teaching in case this is needed.
We will use this collaborative document for asking and answering questions during the workshop. This document also contains links to all other materials you will need during the course.
Preparation
The workshop will use the European Galaxy server to perform all data analysis. Please register there ahead of time to streamline the training.
You must go through two Galaxy interactive tours before beginning the training. These interactive tours guide you stepwise through the Galaxy user interface and the history. They will help you to follow the Galaxy introduction, and ensure everyone has a basic understanding of how Galaxy works.
Weekly news 02.09.2019
The ELIXIR-CONVERGE application has been funded! We expect the project will start in early 2020, subject to negotiations with the EC.
The ELIXIR Hub and ELIXIR UK will also be a minor partner in another project called EnhanceEOSC, with the role of helping to integrate ELIXIR registries into the European Open Science Cloud (EOSC) eco-system.
The ELIXIR-EXCELERATE project was finalised on 31 August 2019. A big thanks to the Work Package leads and everyone involved in the projects. Read our news release highlighting the achievements of the project.
The next ELIXIR webinar will take place this Wed, 4 September at 14:00 (BST) / 15:00 (CEST) and will present the ELIXIR Implementation Study "FAIRness of the current ELIXIR Core Data Resources".
A paper authored by members and leads of the ELIXIR Human Data community and BBMRI-ERIC was published in Nature Reviews Genetics last week. The paper ‘Leveraging European infrastructures to access 1 million human genomes by 2022' explores how European research infrastructures can be leveraged to facilitate transnational access to at least one million human genomes.
SIB announces the BC2 Basel Computational Biology Conference will take place from 9-11 September in Basel.
Genomics for Biodiversity symposium
*Registration deadline 5 September*
12 - 13 September 2019 | Barcelona, Spain
ELIXIR Innovation and SME Forum: Distributed data analysis - the {health} data train
10 - 11 October 2019 | Utrecht, Netherlands
Weekly news 19.08.2019
Supporting innovation in bioinformatics. How ELIXIR connects public bioinformatics infrastructure with industry report is available at https://f1000research.com/documents/8-1136
The EC has opened a call for expression of interest in joining an eHealth stakeholder group to provide high-level advice and expertise. It may be of interest to those groups in ELIXIR working at the interface of human research data and eHealth.
A new "The bio.tools registry of software tools and data resources for the life sciences" on the bio.tools registry was released last week in Genome Biology. Read on to find out about the successes of the project, and about their future plans. ELIXIR Estonia members Ahto Salumets and Hedi Peterson are among the authors.
Upcoming ELIXIR events
Statistical tests and statistical learning for omics data
11 - 12 September 2019 | University of Luxembourg, Luxembourg
Current advances in text mining
25 - 26 September 2019 | University of Luxembourg, Luxembourg
ELIXIR Innovation and SME Forum: Distributed data analysis - the {health} data train
10 - 11 October 2019 | Utrecht, Netherlands
Algorithms for Genomics
14 - 18 October 2019 | Delft, Netherlands
Final OpenRiskNet Workshop: Creating powerful workflows combining data and software services demonstrated on risk assessment case studies [Industry workshop]
23 - 24 October 2019 | Amsterdam, Netherlands
Constraint based modelling
25 - 29 November 2019 | Leiden, Netherlands
Modelling and optimisation for bioinformatics and systems biology
9 - 13 December 2019 | Wageningen, Netherlands
EMBO Practical Course: Integrated multi-omic analysis of microbial communities
16 - 23 March 2020 | Luxembourg City, Luxembourg