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Agenda 

Current status and overview of features

Collaboration plans with bio.tools 

Creation of new workflows. Could be of 3 ways. 

  • Through workshops with domain experts 
  • By individuals/small groups
  • Conversion of existing guides into TeSS format (e.g. Terris EMBER bioinformatics guide)

Workflow creation guide

Attending

Oscar, Hedi, Sarah, Terri, Rita, Milo, Niall, Lorenza, Jure, Florian, Alex + others (please email me and I'll add you, I couldn't see the attendees list unfortunately!)

Apologies Celia, Jon Ison

Minutes

Current status and overview of features

Current features are visible here https://tess.elixir-europe.org/workflows

Put briefly - Training workflows in TeSS are visual, step-by-step protocols that allow users to navigate materials in TeSS in topic- or task-related ways.

Uses jQuery so can be integrated into other websites e.g Bio.tools

Allow users to create workflows, add/edit nodes and connect nodes together in TeSS, then view selected ones in bio.tools.

In workflow create mode - you can add a workflow stage - add text to it (which can be formatted using markdown) and then create associations with Training materials, events, tools from bio.tools, and databases, standards and policies from Biosharing.org

The current implementation status is not bad. The features we do have are robust and stable but there are many other features to implement (integration with other registries to assign associations, and annotation of stages and vertices with EDAM ontology terms)

 

Collaboration with bio.tools 

Bio.tools is the ELIXIR tools registry. They have a filterable table with lots of Life science tools. Their roadmap includes developing another view to make it easier for people to discover tools. This fits in with TeSS work on conceptual workflows so we will be developing further together rather than them reinventing the wheel. 

Their requirements are to annotate each workflow stage with an EDAM operation term, and a format or data term on connecting vertices. This will allow them to use the annotations already given to tools to automatically suggest tools for each stage. Slightly different to TeSS's requirements but manageable under the framework.

Hedi: There are plans to automatically extract topics of abstracts to help create workflows. The workshop in Tallinn can discuss this further (1st-3rd March)

EDAM Map and the Bioportal Annotator allow us to annotate resources in bio.tools and TeSS with more specific EDAM terms much easier.

 

Workflow Creation

Structural Bioinformatics Workflow

Lorenza from Basel has some PMs and can work on the Structural Bioinformatics workflow with Christine Orengo, Cath Brooksbank, Sarah Morgan and co, who have previously drafted the struct bioinformatics workflow https://tess.elixir-europe.org/workflows/structural-bioinformatics-workflow

Another workshop bringing together these people could be a great way to complete this workflow. Add useful text to guide the trainee through, add associations with training materials, tools, and other resources, and refactor. Plus create new workflows of other typical things.

During this we can be reflective about the process which will help inform the construction of a guide to developing workflows. This should be a document explaining exactly how to create workflows as well as advice to keep scoping and granularity correct. 

 

Other workflow strategy

Assigning personal responsibility for the continued construction of a workflow could be a good idea. Workshops have a 'fire and forget' effect where after the 6-8 hours or so of work, the group disbands and it is never completed, refactored, or maintained.

Workshops good way of sourcing workflows. Great to get different opinions from domain experts but can be hard to get concensus. Difficult to manage, but valuable. Hopefully the guide can help align people. 

 

Then there was a fire in the building next to me so the meeting ended.

 

 

 

 

 

 

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