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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”.

Target Audience: Software developers, bioinformaticians

Workshop Objectives:

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

Related Documents:

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.

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

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.

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

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. 

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:

 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.

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:

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.

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: