18th of March:

Social activities:

• 19:00: Dinner.

19th of March:

Morning session:

• 08:45 – 10:45: Opening Symposium – session 1 (Room SV1717)
  • 08:45 – 09:00: Opening (Philipp Bucher and Martin Kuiper).
  • 09:00 – 09:35: Completing the collection of human TF motifs (Tim Hughes).
  • 09:35 – 10:10: A flexible algorithm for fitting accurate biophysical models of protein-DNA interaction directly to SELEX data (Harmen Bussemaker).
  • 10:10 – 10:45: A comprehensive Drosophila melanogaster transcription factor interactome (Sachi Inukai).
• 10:45 – 11:15: Coffee break.
• 11:15 – 13:00: Symposium – session 2 (Room SV1717)
  • 11:15 – 11:50: Predicting regulatory interactions from transcription factor ChIP-seq data (Tim Bailey).
  • 11:50 – 12:25: Fitting complementary motif sets to ChIP-seq data and dinucleotide weight tensors for TF specificities (Erik van Nimwegen).
  • 12:25 – 13:00: Use of variability across individuals to identify gene regulatory elements (Judith Zaugg).
• 13:00 – 14:00: Lunch break.

Afternoon session:

• 14:00 – 15:45: Symposium – session 3 (Room SV1717)
  • 14:00 – 14:35: From automated to curated annotation of regulatory elements and interactions in Ensembl (Daniel Zerbino).
  • 14:35 – 15:10: Characterising mammalian regulatory elements in the light of evolution (Maša Roller).
  • 15:10 – 15:45: Articulating the high throughput (epi)genomics data knowledge commons (Colin Logie).
• 15:45 – 16:15: Coffee break.
• 16:15 – 18:00: Break-out sessions:
  • TF specificity models break-out 1 – Predicting the precise location of TF binding at regulatory DNA (Moderators: Philipp Bucher and Ivan Kulakovskiy) (Room SV17171):
    • Part 1 (20 min): TFBS as a component of DNA-centric annotation: what is unclear. Ljubljana keypoints revisited.
    • Part 2 (15 min): TFBS prediction and annotation: performance measures and descriptive quality criteria.
    • Part 3 (10 min):(TFBS BE-IN 1) TFBS models open benchmarking initiative: current status (Ivan Kulakovskiy).
    • Part 4 (30 min): (TFBS BE-IN 2) Benchmarking protocols: which are there and which are missing (Philipp Bucher).
    • Part 5 (10 min): (TFBS BE-IN 3) Ensuring benchmarking re-usability by containerization of protocols (Ivan Kulakovskiy and Ilya Vorontsov).
    • Part 6 (15 min): Proposed deliverables for DNA-centric annotation, and questions to DNA-centric group.
  • DNA-centric annotation 1 – Regulatory elements for GREEKC (Moderators: Astrid Lægrid and Martin Kuiper) (Room AI153):
    • Part 1 (15 min): How do regulatory elements fit in the main GREEKC use cases/cartoons?
    • Part 2 (30 min): Review of available ontologies and proposed terms (GO/MSO/GRAO).
    • Part 3 (45 min): Develop a short list of needed terms.
    • Part 4 (15 min): Broad Yes/No proposals are voted upon and dissent is noted.

Social activities:

• 20:00: Dinner.

20th of March:

Morning session:

• 09:00 – 10:45: Break-out sessions:
  • TF-specificity models break-out 2 -From the experimental data to TF binding models and TFBS annotations (Moderators: Vsevolod Makeev and Tim Hughes) (Room INR219):
    • Part 1 (15 min): Introducing the table of DNA-protein interaction data (basing on https://doi.org/10.1016/j.cell.2018.01.029). Possible additions after one year?
    • Part 2 (10 min): (TFBS BE-IN 4) TF and data selection: the strategy and key sources of experimental data (Oriol Fornes, Skype).
    • Part 3 (35 min): Motif discovery. Model selection depending on the availability of the experimental data. Can we formulate guidelines for prudent use of models of appropriate complexity?
    • Part 4 (30 min):Motif finding / Pattern matching. TFBS occupancy as a function of site accessibility, TF concentration, and TF affinity. Competition between TF. What is to annotate?
    • Part 5 (15 min): Which TFBS model and prediction descriptors should be included in TFBS prediction ontology?
  • DNA-centric annotation 2 – Biochemical properties of regulatory elements. (Moderators: Judith Zaug, Maša Roller and Colin Logie) (Room DIA004).
• 10:45 – 11:00: Coffee break.
• 11:00 – 12:30: Joint session (Room INR219).
• 12:30 – 13:30: Lunch.

Afternoon session:

• 13:30 – 15:00: Break-out session:
  • TF-specificity models break-out 3 (Moderators: Vsevolod Makeev and Anthony Mathelier) (Room INR219):
    • Part 1 (45 min): (TFBS BE-IN 5) Roadmap: setting the stage for the open challenge (deadlines, key participants, invitation emails). Subtopics: standard representation of basic TFBS models (file formats, etc), and other technical questions.
    • Part 2 (30 min): Lessons from joint sessions. TFBS annotation viewed as a part of DNA-centric annotation.
    • Part 3 (15 min): Future plans + wrap-up for the final joint session.
  • DNA-centric annotation 3 – Measurable properties of regulatory elements. (Moderators: Daniel Zerbino, Camille Berthelot and Tim Hughes) (Room DIA004):
    • Part 1 (45 min): What are the measurable properties of a regulatory element, and what assays are available to measure them?
    • Part 2 (30 min): What are the existing data sets? Which data types are linked to which WG1 terms defined in this workshop?
    • Part 3 (15 min): Data sets to benchmark the GRAO.
• 15:00 – 15:15: Coffee break.
• 15:15 – 17:00: Wrap-up session, action points (Room INR219).

Social activities:

• 19:00: Dinner.