Workshops & Training

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FAIRifying Metabolomics and Phenomics data in the EOSC

Venue: Leiden University (LU); Organiser: LU  Date: 9th – 10th March 2017

Workshop Synopsis:

The 2-day workshop was jointly organised by PhenoMeNal and the GO FAIR initiative and was focussed on establishing a metabolomics and phenomics node as one of the first nodes in the European Open Science Cloud. The programme of the workshop was designed in interaction with Claire o’Donovan (EBI), Chris Steinbeck (Jena), Jake Pierce (Imperial), Philippe Rocca-Serra and Susanna Sansone (UXOF) and Barend Mons (GOFAIR).

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As an outcome of the workshop, Professor Karel Luyben, chairman of the GO FAIR initiative, launched one of the very first Implementation Networks in the European Open Science Cloud on Metabolomics data and services. The initiative aims to collectively implement standards compliant with FAIR principles with the wider research community and to actively communicate these. According to the “Declaration of Leiden” signed by all the participants:

This group has set itself the following objectives:

  • Form and develop the open Metabolomics Implementation Network on Metabolomics data and services and we invite others to join
  • Collectively implement standards compliant with FAIR principles with the wider research community and to actively communicate these
  • Work closely together with other communities on better capturing and understanding phenotypes enabling integrated approaches
  • Support the GO FAIR initiative with the widespread implementation of the FAIR principles in the European Open Science Cloud, contributing to a global open internet of FAIR data and services

Related Documents:

Introduction to MetaboLights (Slides)

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PhenoMeNal Continous Testing Hackathon

Venue: EMBL-EBI, UK; Organiser: EMBL-EBI,UU and IPB; Date: 14th – 15th November 2016

Workshop Synopsis:

To establish PhenoMeNal testing at different levels including tool unit testing, container testing, workflow and infrastructure testing.

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Workshop Objectives:

Participants will participate in the establishment of PhenoMeNal testing at different levels:

  • Tool Unit testing is good software development practice
  • Container testing checks our tool packaging
  • Workflow testing checks that tools are still interoperable
  • Infrastructure testing checks that the PhenoMeNal infrastructure can be fired up and execute workflows of tools in containers.

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Industry Workshop

Venue: Dublin Conference Centre; Organiser: University of Leiden; Date:28th June 2016

Workshop Synopsis:

To create a lasting interaction with industry, in order to raise awareness of the PhenoMeNal initiative and to ensure optimal interoperability of PhenoMeNal infrastructure and instrument vendor’s data formats and tools.

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Workshop Objectives:

  • Interfacing with the industry
  • Understanding the technical requirements of industry

Related Documents:

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Computational Workflows and Workflow Engines

Venue: Metabolomics 2016 Conference; Organiser: PhenoMeNal consortium together with experts from the Metabolomics community Prof. Mark ViantRalf Weber and Warwick Dunn; Date: 27th June 2016

Workshop Synopsis:

Computational analysis of high-dimension and high-volume metabolomics data is a complex, time-consuming process including many steps, some of which still being the focus of intense research. Workflow management environments applied in metabolomics and cross-omics analyses are therefore an essential requirement to allow standardisation of bioinformatics analysis, provide access to the metabolomics community, and produce high- quality, reproducible results in a time-effective manner: on the one hand, experimenters should be able to easily select the tools via a graphical interface, choose the parameters, run the workflow and save/share the results; on the other hand, developers should be able to integrate new tools seamlessly into the environment. A few open-source workflows have recently been applied in different environments including Galaxy-M, Workflow4Metabolomics, MetaDB and MetaboAnalyst. There is a growing need for the international metabolomics community to understand the availability and capability of these workflow environments, and provide input into on-going development and interoperability.

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Target Audience: metabolomics data producers, researchers

Workshop Objectives:

  • Understanding different workflow environments
  • Current shortcomings and improvements that could help widen the adoption of these type of tools within the metabolomics community
  • Feedback from users

Metabolic Phenotyping in Clinics

Venue: Auditori Esteve. IDIBAPS Organiser: University of Barcelona; Date: 27th May 2016

Workshop Synopsis:

To define the state-of-the-art in Metabolic Phenotyping in the clinic. In this community workshops we aim to discuss with experts in the fields of biomedicine, government, ethics, and information technology how we can move forward with technically sound ethical, and law-abiding approaches to distribution and analysis of patient data.

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Target Audience: mixed audience from medical/clinical, industry or commercial, government, working or collaborating  using metabolomics data and tools and technologies related to clinic.

Workshop Objectives:

  • Which are the  application scenarios of metabolomics in the clinic?
  • What information do clinicians want from metabolomics analysis and how do they want it presented?
  • Which are IT infrastructure needs for clinicians?

Video recording of presentations from the workshop:

  • Ethics in genomics – Heidi Howard , Uppsala University

[embedyt] http://www.youtube.com/watch?v=3aqtmk4FtwM[/embedyt]

  • Challenges to the use of health data – Dipak Kalra, EuroRec Institute and UCL London
[embedyt] http://www.youtube.com/watch?v=erQ26WpBCqY[/embedyt]

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Microservice Infrastructure Workshop

Venue: Uppsala University BioMedical Center; Organiser: UU; Date: 12th May 2016

Workshop Synopsis:

Discussions around microservices architecture, with a focus on recent trends for virtual infrastructures and cloud-based provisioning. In focus were MANTL system (https://mantl.io/) and INDIGO-datacloud (https://www.indigo-datacloud.eu/) and the implications and opportunities with respect to PhenoMeNal.

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Target Audience: Software developers, system administrators and engineering students.

Workshop Objectives:

  • Discussions on state-of-the-art in microservices architectures.
  • How can we speed up provisioning?
  • How can we federate data and compute?
  • What will be the next development in the field?

Related Documents:

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 Integration of Galaxy W4M

Venue: CEA; Organiser: CEA; Date: 14th March – 16th March 2016

Workshop Synopsis:

Workshop on the integration of tools into Galaxy and interoperability between Galaxy/W4M and PhenoMeNal.

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Target Audience: Software developers, bioinformaticians

Workshop Objectives:

  • Practice integration of scripts or tools within Galaxy
  • Learn about the W4M infrastructure experience with the developer and user communities
  • Discuss about other Galaxy experiences (e.g. cloud computing)
  • Determine which local/remote tools could be integrated into W4M/Galaxy during the PhenoMeNal project and how both infrastructures could interoperate

Related Documents:

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e-Infrastructures in PhenoMeNal

Venue: Uppsala University BioMedical Center; Organiser: UU; Date: 29th Feb – 2nd March 2016

Workshop Synopsis:

This technical workshop was conducted to provide an opportunity to learn and gain hands-on experience with cloud computing environments and micro services. 

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Target Audience: PhenoMeNal e-infrastructure developers / people integrating tools (microservices) into the PhenoMeNal infrastructure.

Workshop Objectives:

  • Participants should learn and get hands-on experience with cloud computing environments and microservices.

Related Documents:

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Workshop on Ethical, Legal and Social Implications ELSI

Venue: ICL; Organiser: ICL; Date: 20th November 2015

Workshop Synopsis:

Patient and research subject data is very sensitive, and it is paramount to establish a robust governance framework for overall information management including sensitive data. The PhenoMeNal e-infrastructure will be able to cope with data generated from comprehensive clinical, genotypic, ‘omics and analytic sources including medical records, electronic health records, clinical measurements, genotypic data, phenotypic and metabolomics data from tissue and biofluid analysis, image and pathology data. Primarily, all data collected and held within the project will comply with all local laws, regulations and ethics. All personal information will be processed in accordance with accepted Data Protection Principles. Responsibility for data will be with the host institution/data provider.

In accordance with the above Ethical, Legal and Social Implications (ELSI) requirements,a workshop on best practices in handling sensitive human data was organised. The workshop included some lightning  presentations around the themes of ethics, data security, clinical phenotyping, legal frameworks and European data sharing efforts. Clear ways forward were identified to aid the implementation of state of the art privacy and ethics standards within the PhenoMeNal infrastructure.

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Target Audience: Software developers, bioinformaticians, ethicists

Workshop Objectives:

  • Understanding the policies around privacy and ethics
  • Identify models to aid the implementation of state of the art privacy and ethics within the PhenoMenal infrastructure

Related Documents:

First workshop on best practices in handling sensitive human data, taking into account National and Institutional legal policies – D7.1.1

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Virtual Research Community –  User Experience design workshop

Venue: EMBL-EBI; Organiser: EMBL-EBI; Date: 19th November 2015

Workshop Synopsis:

The PhenoMeNal Virtual Research Environment (VRE), aka. Virtual Research Community (VRC) will be the central access point for all users. This is the online portal enabling user interactions, virtual machine distribution, access to compute resources and information exchange. Users can search for existing public datasets and perform online analysis. The User Experience (UX) workshop was arranged to ensure a user centric design and usability of the VRC. Well-established UX design principles like creating personas, experience mapping, storyboarding, card-sorting and poker prioritisation were used to ensure that the design is intuitive and users know how to interact with the VRC.

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Target Audience: Potential VRC users from the community.

Workshop Objectives:

The workshop was focussed on finding answers to some pressing questions addressed through this User Experience workshop (UX) and will eventually help setting up a user focused PhenoMeNal Virtual Research Community (VRC). The key questions identified were:

  • Identify all users and the differences between them
  • Identifying major users
  • Gain an understanding of their current practices and workflow
  • Identify the services they use

Related Documents:

User Experience Document on VRC Design Guide – D6.1

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Software Standards Hackathon

Venue: EMBL-EBI; Organiser: EMBL-EBI; Date: 11th November 2015

Workshop Synopsis:

1 day hackathon with focus on software development and “containerisation standards” for PhenoMeNal. We should aim to come up with an initial draft of “The PhenoMeNal cloud”.

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Target Audience: Software developers, bioinformaticians

Workshop Objectives:

  • Development of software standards
  • Initial draft of the “PhenoMeNal Cloud”

Related Documents:

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