- Web Lab - The concept - and software for - a web-based tool that can combine model and experiment specifications to run simulations
- Cardiac Electrophysiology Web Lab (WL) - A Web Lab for the domain of cardiac electrophysiology.
- WL1 - The original WL implementation. Doesn't have any data or fitting. Uses the Functional Curation syntax for experiments, and runs simulations using either Chaste or a Cython simulation back-end.
- WL1 fitting prototype - An extension to WL1 created by Aidan, that uses a Python backend with CMAES and a custom adaptive MCMC routine to perform fitting on cardiac models.
- WL1 electrochemistry prototype - An extension to WL1 to show the concept works beyond cardiac electrophysiology, and can be applied to e.g. electrochemistry problems
- WL2 - A future implementation of the Cardiac Electrophysiology Web Lab, that includes experimental data and fitting capabilities
WL2 Demo versions
- WL2 Demo version: https://scrambler.cs.ox.ac.uk
- About WL2: https://scrambler.cs.ox.ac.uk/about
- Team/Contact: https://scrambler.cs.ox.ac.uk/contact
WL1 Live versions
- WL2 demo version: https://scrambler.cs.ox.ac.uk/
- WL1 pretty link: https://chaste.cs.ox.ac.uk/WebLab, which redirects to: https://travis.cs.ox.ac.uk/FunctionalCuration/
- WL1-fitting prototype: https://muck.cs.ox.ac.uk/FunctionalCuration/
- WL1-electrochemistry prototype: https://lofty.cs.ox.ac.uk/FunctionalCuration/
WL2 Code
- All new code: https://github.com/ModellingWebLab
- WL2 Django front-end: https://github.com/ModellingWebLab/WebLab
- WL2 issues: https://github.com/ModellingWebLab/project_issues
- WL2 project management: https://waffle.io/ModellingWebLab/project_issues
WL1 Code
- WL1 code: https://github.com/ModellingWebLab/fcweb
- WL1-fitting prototype code 1: https://github.com/ModellingWebLab/fcweb/tree/cardiac-fitting
- WL1-fitting prototype code 2: https://chaste.cs.ox.ac.uk/trac/browser/chaste/projects/AidanDaly
- WL1-electrochemistry prototype code: https://bitbucket.org/joncooper/fcweb/branch/echem
- WL1-fitting prototype code 3: https://github.com/ModellingWebLab/chaste-project-fitting-pints
Functional curation (FC)
- Wiki: https://chaste.cs.ox.ac.uk/trac/wiki/FunctionalCuration
- Code: https://chaste.cs.ox.ac.uk/trac/browser/chaste/projects/FunctionalCuration
- Oxmeta ontology: https://github.com/ModellingWebLab/ontologies/blob/master/oxford-metadata.ttl
- WL2 plans: Reproducible model development in the Cardiac Electrophysiology Web Lab. Daly, Clerx, Beattie, Cooper, Gavaghan, Mirams (2018) PBMB.
- WL1 description: The Cardiac Electrophysiology Web Lab. Cooper, Scharm, Mirams (2016) Biophysical Journal.
- FC: High-throughput functional curation of cellular electrophysiology models. Cooper, Mirams, Niederer (2011) Progress in Biophysics and Molecular Biology.
- Virtual experiments: A call for virtual experiments: Accelerating the scientific process. Cooper, Vik, Waltemath (2015) Progress in Biophysics and Molecular Biology (Open-access pre-print).