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Web Lab Workshop 2018

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Jonathan Cooper edited this page May 25, 2018 · 4 revisions

Introduction

The ‘Cardiac Electrophysiology Web Lab’ project is running our first annual workshop on the 20th – 21st June 2018, in Oxford, UK. It is part of HARMONY2018, the annual hackathon for the COmputational Modelling in BIology NEtwork (COMBINE). Further details and registration can be found at https://www.co.mbine.org/events/HARMONY_2018 - you can sign up just for the two days of the Web Lab workshop itself, or come for the whole week. Several of the Web Lab team will be present throughout. There will also be a workshop dinner on the Wednesday evening.

The focus this year is on developers and eager early adopters, rather than typical end users. There's a preprint describing our plans for the project in biorxiv as background reading. Attendees will be able to help steer the direction taken for the remaining two years of the project, and get involved ‘hacking’ on the software. The exact format of the event will thus depend on the final set of people attending, and will be adapted on the day. Likely activities include:

  • An overview of the project, current status and planned directions
  • Designing the user interface - how do modellers & experimentalists want to interact with the system (and each other!)
  • Comparing approaches to parameter fitting for cardiac models
  • Tools & libraries for working with CellML
  • Representing in silico protocols - comparing our language, SED-ML, Tellurium, JupyterLab, etc. and deciding on the way forward for Web Lab 2. In particular, we’re looking to branch out from the restricted post-processing language we’ve been using and probably support at least arbitrary numpy operations, possibly arbitrary Python similarly to Tellurium.
  • Other standards support and development, e.g. metadata annotation, ontologies
  • Linking the Web Lab to other tools and resources, e.g. the Physiome Model Repository, data archives
  • Result visualisation - what kinds of plots/graphics are needed? What tools can we build upon to provide these?

Agenda

We are starting to flesh out a more detailed agenda for the workshop, although we hope to leave plenty of time for hacking (whether on code or documents) in smaller groups on topics of mutual interest. Wednesday morning will thus consist of:

  1. Introduction to the Web Lab
  2. Introductions by other participants
  3. Discussion of workshop goals
  4. Organising into smaller working groups

For your introduction, please could you prepare in advance up to 3 slides covering: what you are working on (relevant to the workshop), your goal(s) for the workshop, and what you see as the key issues around building mathematical models of biology from experimental data. There will also be time for you to give a brief demo of any tools you are building, if you wish. Please could you send Jonathan your slides and what you propose to demo by Monday 18th June.

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