wiki:FunctionalCuration/Workshop2015

2015 Workshop on the Cardiac Electrophysiology Web Lab

The Web Lab is a new online system developed in the Computational Biology Group at Oxford that supports easy definition of experimental protocols, and allows any CellML model to be tested under these protocols. This enables comparison of the behaviours of cellular models under different experimental protocols: both to characterise a model’s behaviour, and comparing hypotheses by seeing how different models react under the same protocol.

Aims

This workshop will train attendees in how to make the most of the facilities provided by the Web Lab (and the underlying Chaste software) in order to practice open, reproducible science in cardiac electrophysiology modelling. We aim to equip people with the tools that are necessary to make not only their models, but also their training and validation simulations well defined, reproducible, and applicable to any model of the same system.

Sessions will include:

  • Using the Web Lab for comparing simulated experiments
  • Uploading your own models for analysis
  • Developing your own protocol descriptions
  • Building on the underlying software directly
  • Providing feedback to influence future development of these tools.

We are delighted that Professors Peter Hunter, Alan Garfinkel, Denis Noble and Yoram Rudy have accepted our invitation to join our Expert Panel, and will be presenting their views on the Web Lab and future directions during the final session.

Logistics

  • Dates & times: 10th & 11th September 2015, 9.30-5pm each day.
  • Location: Department of Computer Science, University of Oxford, UK
  • Cost: Thanks to the generous support of the 2020 Science project, registration for this workshop is free. Lunches on both days and a conference dinner (at St Anne's College, Oxford on the 10th) will also be provided.
  • Accommodation: Attendees are responsible for organising and funding their own travel and accommodation. Good places to look are University Rooms Oxford and Oxford B&Bs.
    • Partial bursaries for travel and accommodation costs are possible, and those attendees eligible have been contacted directly regarding this.

Programme

The tasks for the practical sessions can be found at https://goo.gl/jl62gh

Thursday 10th September

  • 09:00-09:45 Registration
  • 09.45-11.00 Welcome, introduction and demonstrations (slides video)
  • 11.00-11.30 Break
  • 11.30-13.00 Using the Web Lab for comparing simulated experiments
  • 13.00-14.00 Lunch
  • 14.00-15.00 Uploading your own models for analysis (video)
  • 15.00-15.30 Break
  • 15.30-17.00 Developing your own protocol descriptions, part 1 (slides video)
  • 19:00-21:00 Workshop dinner at St Anne's College

Friday 11th September

  • 09.30-11.00 Developing your own protocol descriptions, part 2 (slides video)
  • 11.00-11.30 Break
  • 11.30-13.00 Developing your own protocol descriptions, part 3 (practicals only, no talk)
  • 13.00-14.00 Lunch
  • 14.00-14.45 Building on the underlying software directly (slides video)
  • 14.45-15.15 Break
  • 15.15-17.00 Future directions expert panel and feedback session

About the Web Lab

Modellers have adopted XML-based markup languages to describe mathematical models over the past decade. This is great, as it means that models can be defined unambiguously, and shared easily, in a machine-readable format. We have been trying to do the same thing with 'protocols' - to define what you have to do to replicate/simulate an experiment, and analyse the results. We can then curate models according to their functional behaviour under a range of experimental scenarios. For the first time, we can thus easily compare how different models react to the same protocol, or compare how a model behaves under different protocols. The Web Lab brings together models encoded using CellML and virtual experiment protocols encoded in our own language, using standardised tags to generate interfaces between them, doing all the necessary units conversions, and running the experiments: any protocol applied to any compatible model. The stored results can then be viewed and compared.

The key idea underpinning our work is that when mathematical and computational models are being developed, a primary goal should be the continuous comparison of those models against experimental data. When computational models are being re-used in new studies, it is similarly important to check that they behave appropriately in the new situation to which you're applying them. To achieve this goal, it's a prerequisite to be able to replicate in-silico precisely the same protocols used in an experiment of interest, and this is what our protocol descriptions aim to do. As the Web Lab evolves, we want to link directly to databases of corresponding wet-lab experimental data, to allow comparison of simulated and real experiments. This will allow us to provide support for validating models, and begin to incorporate parameter fitting and model identifiability.

For more information, see a preprint of our publication about the Web Lab.

Last modified 4 years ago Last modified on Oct 29, 2015, 11:32:17 AM

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