Tuesday, 18 February

Morning session:

Main Event 1: University Club

Plenary Session 1: Short Presentations and lengthy discussion

• 09:00 – 09:30: Welcome and Introduction: What do we hope to achieve
• 10 min talks + 20 min discussions. Chair: Sandra Orchard
• 09:30 – 10:00: Status Ontologies WG1, what next Update of the Brussels meeting.
• 10:00 – 10:30: Status report on DNA-level annotation, TFBS representation, modeling, and benchmarking
• 10:30 – 10:45: Coffee break
• 10:45 – 11:15: Development of GO subtree, annotation guidelines, a new list of (Db)TFs
• 11:15 – 11:45: Training School on Curation and tools: how to organize
• 11:45 – 12:30: WG cluster discussion to identify key progress obtained during the action. Can we use this to fill an issue of the journal BBA Gene Regulatory Mechanisms?
• 12:30 – 13:30: Lunch

Afternoon Sessions:

Main event 2: University Club

Chair: Luana Licata. Remaining issues and hands-on work

• 13:30 – 13:50: Progress in FAIRness assessment
• 13:50 – 14:10: Use cases to eCourse. What should be their format?
• 14:10 – 14:30: Training and Skills development: resources from the ELIXIR’s Training Platform
• 14:30 – 15:15: Use cases GRAO. Started at the Brussels meeting: based on the proposed design of GRAO, which questions could we address?
•  15:15 – 15:30: Coffee break
• 15:30 – 16:30: Use cases GRKC. Based on the list of available resources, which questions can we already answer?
• 16:30 – 17:30: Which use cases are best developed to serve as teaching material?

Event 3: University Club – DNA-level Breakout 1: GRECO TFBS-BE-IN
Room Library “BATS”

• 13:30-13:40: Benchmarking as a field-test for ontology, data representation standards, and reliability estimates. Status of the GRECO TFBS Benchmarking Initiative
• 13:40-14:25: Results of the TFBS Benchmarking Project Pilot Study. TFBS Benchmarking protocols
• 14:25-15:10: Utilizing new and upcoming experimental data
  Coordinating efforts with the data providers
• 15:10 – 15:30: Coffee break
• 15:30-16:15: Utilizing existing experimental data on TFBS. Selection of representative TFs and reliable data
• 16:15-17:00: Setting the stage for the open challenge. From technical engine to expected outcomes
• 17:00-17:30: Wrapping up key questions and decisions

Wednesday 19 February 

Morning sessions:

Main Event 4: University Club

Chair: Lejla Kapur-Pojskic. Short presentations and discussions.

• 9:00 – 10:00: Where are we with GREEKC deliverables. WP2
• 10:00 – 10:30: What actions should we take to wrap this up in papers
• 10:30 – 10:45: Coffee break
• 10:45 – 11:30: Training School – curation. Other lectures
• 11:30 – 12:30: Finalise action on use cases for training
• 12:30 – 13:30: Lunch

Event 5 – DNA-level Breakout 2: towards a GREEKC consensus on regulatory elements Room Library “BATS”

• 9:00-9:45: Part 1: Specificity models (representation, terminology, resources, metadata)
• 9:45-10:30: Part 2: Experimental data and technologies (technical terms, metadata, reliability)
• 10:30 – 10:45: Coffee break
• 10:45-11:45: Part 3: Ontology terms related to TFBS and gene regulatory regions
• 11:45-12:30: Part 4: GREEKC deliverables (potential papers, terminology recommendations, possibilities for a collaborative framework)
• 12:30 – 13:30: Lunch

Afternoon session:

Event 6 – Plenary meeting

Chair: Stefan Schulz. Discussion of DNA-level annotations

• 13:30 – 13:50: Summary from the DNA level
• 13:50 – 14:20: GTRD – Gene Transcription Regulation Database –
  an integrated view on transcription regulation
• 14:20 – 14:50: Upcoming experimental data on TF/TFBS,
  the Codebook Initiative
• 14:50 – 15:15: Joint Discussion
• 15.15 – 15:45: Coffee break
• 15:45 – 16:30: The Regulatory SO: Structure and use in Annotations. Lausanne Sandbox document with draft RSO
• 16:30 – 17:00: Update on the Regulatory SO work. How can we move the RSO forward?
• 17:00 – 17:15: Wrap-up, Action points