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Tutorials

Registration
Attendance to tutorials is subject to the limitations listed below.
Registration for one or both tutorials can be done through the workshop registration form.

List of tutorials

Tutorial 1, Monday October 22, 2018, morning (09:00 – 12:30)
Bioschemas, a lightway approach to enable FAIRer data resources
Leyla Jael Garcia Castro, Ricardo Arcila, Rafael Jimenez, Victoria Dominguez del Angel
Registration fee: 10.00 €
Tutorial organized in collaboration with ELIXIR.

Tutorial 2, Wednesday October 24, afternoon (14:30 – 19:00)
The ELIXIR Data Stewardship Wizard – how to guide life science researchers towards FAIR data management
Rob Hooft, Vojtěch Knaisl, Jan Slifka
Registration fee: 10.00 €
Workshop/hackhathon organized by ELIXIR-NL and ELIXIR-CZ.


Tutorial 1, Monday October 22, 2018, morning (09:00 – 12:30)

Bioschemas, a lightway approach to enable FAIRer data resources
Bioschemas is an open community project aiming to contribute with Life Science specifications to schema.org. Schema.org provides an easy way to add structured markup to web pages thus corresponding resources become more findable and interoperable.
Building on schema.org, Bioschemas specifications include new types and properties, but also type customization and usage guidelines, a.k.a. profiles. Bioschemas approach relies on simplicity, with just enough guidelines in schemas such as ‘DataSet’, ‘BioChemEntity’ and ‘LabProtocol’ to enable FAIRer data resources.
During this half-day tutorial, people will learn about Bioschemas, its approach and its principles. Talks will be combined with hands-on activities so attendees can use Bioschemas profiles to better understand them, discuss on new specifications, and explore how extracted data can be used.
People bringing their own data can either:

Tutorial speakers

Leyla Garcia,
EMBL-EBI, UK
Ricardo Arcila,
ELIXIR Hub
Rafael Jimenez,
ELIXIR Hub
Victoria Dominguez del Angel,
ELIXIR-FR/IFB

Leyla Garcia is a Senior Software Engineer at the Protein Function Development team working mainly on web development, but also on training activities. She is involved in other projects related to semantic web, linked data, ontologies and machine learning. Before joining EMBL-EBI, eight years ago, she used to work as a lecturer and web developer in Colombia. She obtained her MSc in Software Engineering in Colombia and her PhD in Computer Science (artificial intelligence) in Spain.

Ricardo Arcila is a Software Engineer at ELIXIR, with theoretical and practical experience in the creation of innovative technology processes. He has experience in areas such as data science, semantic web, software and infrastructure design, front-end and back-end development. For the past six months, he has been actively involved on Bioschemas.org project, semantic web and data science. He joined ELIXIR team after five years of experience as a Software Engineer on several successful projects in the software industry.

Rafael Jimenez is the Chief Data Architect at ELIXIR. He has an active role in the technical design, coordination and implementation of the ELIXIR data infrastructure. He joined ELIXIR after four years at EMBL-EBI as a software engineer and technical lead in the Proteomics Services team. He is specialised in the coordination and management of bioinformatics services, and is interested in topics relating to data infrastructure, data integration, data federation, data visualisation and software development best practices. Rafael has experience coordinating technical projects, developing technical strategies, leading software development and managing community groups. He obtained his MSc in Molecular Biology in Spain and his MSc in Computer Science in South Africa.

Victoria Dominguez del Angel is the French ELIXIR Training coordinator. She comes to ELIXIR-FR (IFB) with over 15 years of experience in bioinformatic project management. Before joining ELIXIR-FR, Victoria worked as research scientist in UNAM Mexico, Pasteur Institute and INRA. More recently as CEO in a start-up bioinformatics company. Victoria has a PhD in Genome Analysis and Structural Genomics from University of Paris VII (Denis-Diderot) and is recently also rolling in a MBA in Management Research Infrastructures (Ritran) at the University of Milano-Bicocca (2017-2019). Victoria is also responsible of Sustainability Model of the software, databases, infrastructure and training produced by ELIXIR-FR.


Tutorial 2, Wednesday October 24, afternoon (14:30 – 19:00)

The ELIXIR Data Stewardship Wizard – how to guide life science researchers towards FAIR data management

Target audience
This workshop is for Data Stewards and Bioinformaticians who are assisting life science researchers with the data management and data management planning in their projects.

Organisers
Rob Hooft (DTL, ELIXIR NL), Robert Pergl (ELIXIR CZ), Vojtěch Knaisl (ELIXIR CZ), Jan Slifka (ELIXIR CZ), Celia van Gelder (DTL, ELIXIR NL).

The ELIXIR Data Stewardship Wizard (DSW, https://dsw.fairdata.solutions/) is a solution for “Smart Data Management Plans for FAIR Open Science”: incorporating expert knowledge on “FAIR” data management and data stewardship into daily practice, directly benefiting data-intensive research projects.
In this workshop participants will be shown how the ELIXIR Data Stewardship Wizard can guide researchers towards FAIR data stewardship, how it can help data stewards to stay organized, and how it can help data experts of all kinds to advertise their expertise.
We will walk together through:

  1. how the wizard works for researchers,
  2. what kind of knowledge is captured there,
  3. how the wizard can be customized.

We also briefly touch how to run your own copy of the Wizard. During the workshop, participants will have the opportunity to work with the authors of the wizard to contribute their own expertise to the knowledge model.
There will also be time to discuss what kinds of questions the workshop attendees are asked by researchers and how the wizard, in current or future form, will be able to contribute to answering such questions.

For the workshop organisers, this workshop will be a valuable occasion to get feedback on the current tool, and they will collect a list of suggestions for developments and improvements.

Tutorial speakers

 
Rob Hooft,
DTLS, NL
Vojtěch Knaisl,
ELIXIR CZ, CZ
Jan Slifka,
ELIXIR CZ, CZ
 

Rob Hooft was educated as a structural chemist at Utrecht University. He did his PhD studies modeling sweet tasting compounds. He spent 4 years at the EMBL in Heidelberg where he developed tools to verify the quality of protein structures in the group of Gert Vriend and Chris Sander.
Rob then worked in industry for 12 years, first as application software developer and later as manager of the R&D department. In 2009 he moved back to the academic world and joined the Netherlands Center for Bioinformatics, NBIC.
Via a two year excursion to the Netherlands eScience Center from where he ran the data program of the Dutch Techcenter for Life Sciences (DTL), he is now working for DTL itself managing the Dutch tasks in the European ELIXIR infrastructure for life science data. As part of these roles, Rob has been building up a body of knowledge on FAIR research data stewardship since early 2014.

Vojtěch Knaisl is a Ph.D. student at Faculty of Information Technology at Czech Technical University in Prague, where he also got a master degree in Software Engineering. His fields of study are evolvable software systems and functional programming languages. Further, he is a member of ELIXIR CZ Interoperability platform and one of the main developer of Data Stewardship Wizard in ELIXIR CZ. He has experiences from an industry while he worked as senior developer for telecommunication and big financial companies.

Jan Slifka got his Master’s degree in Software Engineering at the Czech Technical University in Prague. He is now Ph.D. student there, focusing on evolvable systems and functional programming. He acquired hands-on experience from the industry while working as a senior developer for several startups with wide range of technologies. He is also a member of ELIXIR-CZ Interoperability Platform where he works as a chief User Interface developer on the Data Stewardship Wizard.



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