Bioinformatics Education Summit

Bioinformatics Education Summit

UK, 15–17 May 2023.

The Bioinformatics education summit provides a platform for discussion, development and dissemination of advances, guidance and best practice for training and education in bioinformatics as part of a global network.

Held as a working meeting (rather than a conference or workshop), its goal is to promote the advancement of training and education through the development of resources, best practices and guidance for delivery, all of which are made openly available to the global community through its partner networks.

The first summit was held in Cape Town in 2019 under the auspices of H3ABioNet, with subsequent summits held virtually, hosted by different organisations with a key interest in training and education (EMBL-EBI, CABANA and APBionet). Outputs from previous summits have included a training guidance and resources portal (hosted by GOBLET); the third evolution of the ISCB bioinformatics competency framework and guidance on its implementation; best practices and resources for the delivery of bioinformatics training in LMICs; guidance and recommendations for virtual and hybrid course delivery; and a globally available virtual Train-the-Trainer course.


This year’s meeting will offer both in-person and virtual attendance and will focus on three main themes:

  • Furthering the use and adoption of the ISCB competency framework through extending the framework itself to include health data science roles and developing further practical support for people to use it in developing training.
  • Exploring how we can make our training and teaching more green, including improving compute practices for environmental sustainability
  • Developing and sharing best practice for building and supporting communities of best practice in training.

There will also be opportunity to further review challenges and opportunities for developing and delivering training to participants in low resource settings, as well as participating in initiatives focused on ensuring that training materials are FAIR, train-the-trainer activities, and much more.

If you are involved in the design and delivery of bioinformatics training and education and would like to spend 3 days working with a global community of trainers and educators to develop guidance and practice with impact on a global scale, then please join us!

Travel bursaries are made possible through RItrainPlus, a co-organiser of the Education Summit. The RItrainPlus project received funding from European Union’s H2020 programme under grant agreement no.101008503, and LifeWatch ERIC is a partner.

More information is available here.

AZTI SUMMER SCHOOL 2023 ‘Innovative and practical tools for monitoring and assessing multiple human pressures affecting biodiversity in marine systems’

AZTI Summer School

San Sebastian, Spain, 5–7 June 2023.

In this edition of the AZTI Summer School, the topic proposed is “Innovative and practical tools for monitoring and assessing multiple human pressures affecting biodiversity in marine systems“. This year, the school is organised in the framework of several Horizon Europe projects:  GES4SEAS, OBAMA-NEXT, BiOcean5D, ACTNOW and MARBEFES). LifeWatch ERIC is a partner in the latter.

The main objective of the AZTI Summer School is to present the innovative tools that are already practically used in monitoring the ocean, and the tools used to assess the cumulative effects of multiple pressures, as well as the status of the ocean and the ecosystem services it provides.

WHEN: 5, 6 and 7 June 2023
WHERE: Aquarium of San Sebastian (Spain)
LANGUAGE: English
PROGRAMME: HERE
SPEAKERS INFO: HERE
REGISTER: HERE

Early registration fee: 90,00 € (VAT included). Deadline: 20 April
Standard registration fee: 115,00 € (VAT included). From 21 April to 2 June

BIOHACKATHON EUROPE

Biohackathon Europe

Barcelona, Spain, 30 October – 3 November 2023.

BioHackathon Europe is an annual event that brings together life scientists from around the world. It is organised by ELIXIR Europe, and offers an intense week of hacking, with over 160 participants working on diverse and exciting projects. The goal is to create code that addresses challenges in bioinformatics research. See the About page for more background.

ATTENDING THE BIOHACKATHON

This year we are holding the BioHackathon at Campus Belloch near Barcelona (see the Venue page), with remote access available for those that cannot attend the meeting in person. 

Spaces are limited for face-to-face participation and the registration is based on a first-come, first-served basis. Registration for the 2023 BioHackathon will open later in the year. Visit the BioHackathon website for updates.

SCOPE

BioHackathon activities are driven by practical sessions where people gather, discuss, and implement ideas and projects during intensive and productive coding sessions. The topics will be aligned to challenges proposed by ELIXIR Platforms, ELIXIR Communities, and/or Focus Groups, and a set of common challenges proposed by the sister BioHackathon organised in Japan.

GOALS

  • Advance the development of an open source infrastructure for data integration to accelerate scientific innovation. We will focus on technology implementations such as FAIR, identifiers, metadata standards, ontologies and metadata catalogues that support the operations across ELIXIR Platforms, Communities and Focus Groups.
  • Engage technical people in the bioinformatics community inside and outside ELIXIR to work together on topics of common interest aligned to ELIXIR activities
  • Strengthen the interactions with ELIXIR Platforms, Communities and Focus Groups to establish and reinforce collaborations through hands-on programming activities.

EXPENSES AND FUNDING

Registration for the BioHackathon is free, however you will have to pay your own travel, food and accommodation expenses. ELIXIR will pay expenses for a limited number of participants for accepted projects. More information will be published as it becomes available. 

Please be aware that those who register as face-to-face participants must stay at the venue for the duration of the event. This is to optimise the value of on-site interaction and collaboration.

For more information about accommodation prices see the Venue page. 

BENEFITS

NEW DEVELOPMENTS

  • Integrate prototypes, proof-of-concept proposals or drafts into production
  • Kickstart projects

EXISTING DEVELOPMENTS AND RESOURCES

  • Test new versions
  • Gather information for new features
  • Reach out to new users
  • Improve documentation and awareness
  • Receive input from experts in different fields

PERSONAL AND COMMUNITY BUILDING

  • Lead projects in one of the biggest BioHackathon events in Europe with international participation
  • Learn collaboratively with peers
  • Share interests to organise or grow communities
  • Meet and make new contacts
  • Publish pre-prints

OntoCommons Workshop

Hybrid, 4–6 April 2023.

The ambition to facilitate data sharing and interoperability within the Materials and Manufacturing domains is the core motivation for this event. Stemming from the OntoCommons H2020 project activities, this focused workshop provides a platform for academic researchers and industrial practitioners to meet and discuss about the Materials and Manufacturing Commons* key enablers, in particular, Digital Marketplaces, FAIR Principles and Ontologies. In this workshop, the Digital Marketplaces concept and its current status of implementation will be shown in order to continue the discussion about requirements and challenges using ontologies. Tools supporting data documentation and interoperability will be showcased, and concrete challenges, success stories, as well as experiences using ontologies will be shared. A session and panel discussion on the future developments of Materials and Manufacturing Commons with focus on materials and manufacturing data spaces will round up the first part of the workshop. In the second part, the FAIR principles will be introduced and existing tools and guidelines to leverage the FAIR principles in industrial context will be identified and discussed together with experts and participants. The third day of the workshop will be dedicated to participants’ input, feedback and questions, including an open pitch session for participants. Demos of the tools provided by the ontology commons ecosystem, a virtual tour of digital marketplaces and hands-on working sessions for enhancing the FAIRness score of participants’ own ontologies will provide a tangible take-away result from the workshop. To deepen and consolidate the communication and networking between OntoCommons, the digital marketplaces, FAIR initiatives and interested users of semantic tools, this workshop is open (no registration fee) and will take place on-site at the Fraunhofer Forum Berlin (Germany).

The FAIR-IMPACT project will be showcased in Session 3: FAIR Resources for Industry.

Registration and programme information can be found on the OntoCommons website.

Why Mappings Matter and how to make them FAIR – A FAIR-IMPACT Workshop

FAIR Impact Mapping Workshop

Online, 13 April 2023.

Semantic artefacts  – a broader term to include ontologies, terminologies, taxonomies, thesauri, vocabularies, metadata schemas and standards – are key to achieving data interoperability and are therefore essential to the implementation of the FAIR principles. With the growing number of semantic artefacts and their diversified uses, interconnecting these artefacts becomes critical but also more challenging. To achieve interoperability and integration, one solution is to identify/generate mappings/crosswalks between different artefacts of the same domain or used to represent the same type of information. This process, known in the semantic web domain as ontology matching or ontology alignment, should be applied to the whole spectrum of semantic artefacts.

As any other type of data, we need a strategy to deal with mappings and ensure mappings are made available following the FAIR principles in relevant mapping repositories where they can be curated, integrated and rendered for reuse. Recent initiatives like the SEMAF study or the SSSOM format or the activities within the FAIR-IMPACT and FAIRCORE4EOSC projects have highlighted the needs of communities to find, access and reuse mappings and crosswalks in a machine actionable format which is not currently addressed. 

FAIR-IMPACT is starting a series of workshops to discuss issues around mappings and crosswalks and how they can become shareable and reusable, i.e. FAIR, elevating them to “first class” citizens in the FAIR data world.

The first one will take place on Thursday 13 Apr at 14:00 – 18:00 CEST.

Registration and agenda information can be found on the FAIR-IMPACT website.

Goal of the event

The 1st FAIR-IMPACT workshop of the series, ‘Why Mappings Matter and how to make them FAIR?’, will introduce participants to the motivation behind doing mappings and how they could benefit even more by making mappings FAIR. Then a series of Show and Tell presentations will take place, where use cases and practices from a range of communities –spanning domains, research infrastructures, projects, task forces, and working groups– will be presented. During this workshop, FAIR-IMPACT will also introduce The Simple Standard for Sharing Ontological Mappings (SSSOM) as a candidate format for defining and sharing entity mappings, considering also its pivotal role in the FAIRCORE4EOSC technical specifications.

The presentations will be followed by a collaborative work on mapping aspects, including methodologies, formats, tools, requirements for FAIR mappings and examples.

The main objective of this workshop is to define, together with different communities, the initial requirements for developing a useful framework around FAIR mappings including the requirements to adhere to the FAIR principles. 

This workshop is organised by FAIR-IMPACT and the SSSOM developer community.

International Data Week 2023

International Data Week 2023

Salzburg, Austria, 23–26 October 2023.

The International Science Council’s Committee on Data (CODATA) and World Data System (WDS), and the Research Data Alliance (RDA) are delighted to announce International Data Week 2023: A Festival of Data.

IDW 2023 will be hosted by the University of Salzburg through its interdisciplinary Data Science group and the Geoinformatics department, supported by the Governor of Salzburg and with assistance from the Austrian Academy of Sciences – GIScience and the European Umbrella Organization for Geographic Information.

International Data Week brings together a global community of data scientists and data stewards; researchers from all domains; data, interoperability and informatics experts from all fields; industry leaders, entrepreneurs and policymakers.

This event will be an inclusive and celebratory Festival of Data, with in-person and virtual components, highlighting the opportunities for the positive transformation of our world in the light of the COVID-19 pandemic and other global challenges.

IDW 2023 will combine the RDA Plenary Meeting, the biannual meeting of this international member organization working to develop and support global infrastructure facilitating data sharing and reuse, and SciDataCon 2023, the scientific conference addressing the frontiers of data in research organized by CODATA and WDS.

Refer to these links to learn about SciDataCon 2023 themes and the call for sessions, presentations and posters.

Website: https://internationaldataweek.org

For more information on IDW 2023, contact:

  • Meredith Goins, WDS Executive Director
  • Hilary Hanahoe, RDA Secretary General
  • Simon Hodson, CODATA Executive Director

Workshop on Ontologies for FAIR and FAIR Ontologies (Onto4FAIR)

Onto4FAIR

Sherbrooke, Canada, 17–20 July 2023.

One the one hand, a key aspect is the ability of properly and semantically describing resources, in particular with the help of ontologies. On the other hand, ontologies themselves have to be compliant with the FAIR principles.

The Onto4FAIR workshop has the following goals:

  • to bring together leaders from academia, industry and user institutions to discuss the adoption of FAIR principles in research and real-world requirements
  • to serve to inform about existing research efforts that may meet their requirements.
  • to investigate how the FAIR principles are supported by the use of ontologies that ideally are themselves FAIR.
  • to discuss the challenges and perspectives in adopting FAIR principles.

Topics of Interest

The topics of interest include, but are not limited to, the following:

  • schemas, ontologies and vocabulaires for FAIR data and metadata;
  • domain and cross-domain ontologies for FAIR data;
  • approaches to make vocabularies and ontologies FAIR(er);
  • alignment of schemas, vocabulaires and ontologies for FAIR;
  • FAIR data management and stewardship;
  • best practices for implementing the FAIR principles;
  • FAIRification process and use cases;
  • metrics for FAIRness assessment;
  • provenance in FAIR environments;
  • FAIR principles and open science;
  • FAIR principles and Linked (Open) Data;
  • FAIR in industry, scientific communities (life science, digital humanities, health, smart cities, etc.).

Programme

TBA

Important dates

  • Workshop paper submission: May 24, 2023
  • Author notification: June 30, 2023
  • Camera-ready version: June 30, 2023 (strict)
  • Workshop: July 17-19, 2023

Submission guidelines

  • Regular papers: 10-14 pages (including references)
  • Short papers: 5-9 pages (including references)

Submissions must be in PDF, formatted in CEUR-ART, 1-column style conference proceedings. A Overleaf template is available. We strongly encourage authors to use Latex.

Please submit your contribution on EasyChair at the following link: https://easychair.org/conferences/?conf=fois2023. Papers have to be submitted to the track Workshop on FAIR Ontologies and Ontologies for FAIR. 

The proceedings will be made available through CEUR within the IAOA’s series.

More information on Onto4FAIR here.

DOORS Mobilisation and Mutual Learning Workshop

DOORS Workshop

Constanta, Romania, 6 April 2023.

The first round of the DOORS project’s Mobilisation and Mutual Learning (MML) workshops will kick off on April 6, 2023, in Constanta, Romania. The goal of the workshop is to bring together experts and users of marine products, to raise awareness and share knowledge and skills, using Responsible Research and Innovation (RRI) principles.

Objectives of the workshop

  • To engage Black Sea citizens and stakeholders in highly participatory training and co-creation activities to ensure suitability of existing and future Research Infrastructure services to the Black Sea region;
  • To train researchers and companies on how to use existing specific services, tools, data, EU data aggregation infrastructures and services (e.g. EMODnet) and protocols offered by the European Marine Research Infrastructures, to make the most of existing data and monitoring initiatives that can feed into the Blue Economy and political decision making for the region;
  • To set in motion inclusive mechanisms for international sharing of knowledge, building common understanding and cocreating solutions to marine societal challenges and base them on the RRI principles and socio-technical approach.

Session Topics

Sessions include plenary expert talks, round table discussions and hand-on practical exercises to explore existing pan-European marine data infrastructures including:

  • The European Marine Observation and Data Network (EMODnet) and how to navigate the marine products catalogue, identify relevant products for the specific users and how to use them.
  • The Marine Litter Watch (MLW), a citizen-based app that aims to help fill data gaps in beach litter monitoring.
  • DOORS Observation Mapping Tool which illustrates the main marine observing capacities and marine data infrastructures identified in the Black Sea.
  • The DOORS #BlackSeaLitterFree Campaign which raised awareness about marine litter, problems and solutions.
  • An introduction to the DOORS System of Systems (SoS), in a working beta version, demonstrating how to access marine data on the platform .

Introducing our System of Systems (SoS)

In DOORS, the foundation of our work will be our System of Systems (SoS) platform which will revolutionise how we handle, process and understand data from the entire region. One of our main goals is to harmonise scientific approaches for gathering data, integrating all existing data as well as new satellite data into a consolidated system that works for everyone.

Video: A short working demo of the System of Systems interface. © DOORS Black Sea

Register for the Event

This workshop is suitable for anyone responsible for collecting or managing marine environmental data in the public sector, industry for education or research. Please remember to share the event widely within your networks.

Webinar: Digital Earth Twins to build resilience to climate change

Digital Twins Climate Change

Online, 4 April 2023.

BioDT: a Digital Twin prototype to help protect and restore biodiversity

Understanding the forces shaping biodiversity is needed for rational management of natural resources and also to meet the EU Biodiversity Strategy for 2030 to restore biodiversity in Europe. In particular, researchers need to be able to better predict global biodiversity dynamics and how species interact with their environment and with each other. This can be an extremely difficult task because the processes underlying biodiversity dynamics are complex. Innovative ways to combine data, models and interaction processes are required to predict these dynamics and offer solutions that promote a sustainable management of Earth’s biodiversity and its ecosystems.

For this reason, the BioDT consortium aims to push the current boundaries of predictive understanding of biodiversity dynamics by developing a Biodiversity Digital Twin (BioDT) providing advanced modelling, simulation and prediction capabilities. 

BioDT, DestinE and Digital Earth Twins: a joint webinar to showcase opportunities, challenges and future trends in virtual twins

The webinar “Digital Earth Twins to build resilience to climate change” aims to showcase best practices, challenges and emerging patterns in developing digital twins. The involved speakers are experts and developers in the field and are going to highlight, during a one-hour event, the main aspects to be taken into account while developing highly-complex technology systems, such as BioDT, Destination Earth and ClimateDT.

The event includes also an interactive session where the participants can get in contact with the speakers and ask direct questions.

Registration for the webinar is mandatory, but free.

Register for the event

Draft Agenda (all times CEST)

  • 10:00 – Welcome & Introduction
  • 10:05 – Digital Earth Twins: a roadmap to build resilience to climate change – Christian Kirchsteiger, European Commission DG Connect
  • 10:10 – Introduction of the Biodiversity Digital Twin: objectives, scope, expected results – Jesse Harrison, CSC & BioDT project manager
  • 10:20 – Introduction of the digital earth twins and the DestinE work: objectives, scope, expected results – Thomas Geenen, EMCWF & DestinE
  • 10:25 – BioDT and DestinE: collaboration to strengthen the development of Digital Earth Twins – Jeroen Broekhuijsen, TNO
  • 10:30 – Test your knowledge (interactive session)
  • 10:35 – Panel discussion on the role played by digital twins on green deal & EU digital strategy
    • Jenni Kontkanen, CSC & Climate DT
    • Thomas Geenen, EMCWF & DestinE
    • Marina Tonani, Mercator Ocean & EDITO
  • 11:00 – Conclusion

MARCO-BOLO Kick-off Meeting

MARCO-BOLO Kick-off Meeting

Paris/Online, 14–15 March 2023.

The new MARCO-BOLO project’s hybrid kick-off meeting will take place in Paris from 14–15 March at the Pierre et Marie Curie Campus. The meeting will serve to plan the coordination between the different work pacakges and begin to plan ways of collaborating with similar projects in the field. In particular, two important plenary sessions will be held on data strategy and stakeholder engagement.

MARCO-BOLO, coordinated by EMBRC, aims to structure and strengthen European coastal and marine biodiversity observation capabilities, linking them to global efforts to understand and restore ocean health, hence ensuring that outputs respond to explicit stakeholder needs from policy, planning and industry. You can find out more about it on our Related Projects page.