feat: allow for multiple Myokit simulations #366
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## data-upload #366 +/- ##
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+ Coverage 76.69% 76.78% +0.09%
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martinjrobins
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Mar 12, 2024
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hi @eatyourgreens, this mostly looks right, but the number of simulations is not quite right:
You should perform 1 simulation for each distinct subject group. Each group of subjects will have 1 or more protocols associated with them (each dosing into a different variable). For each of those groups you want to gather the protocols for that group then run a simulation using all of the protocols for that group (you wont get an error since they will all be dosing into separate variables)
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Refactor the Myokit model mixin to allow multiple simulations to be run. Each simulation has its own dosing protocols and dosing events. Update the simulate API to return multiple simulations.
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Refactor the Myokit model mixin to allow multiple simulations to be run. Each dataset subject group has its own simulation, with subject dosing protocols and dosing events. Update the simulate API to return multiple simulations. Show multiple plots in the Simulations tab Test simulations with a project and dataset
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Upload a CSV dataset, set units (time, amount and observation), map CSV columns to model variables (dosing compartments and outputs), then run simulations and compare observation data with simulations in the Simulations tab. * Map data to model variables Show a table of dose amount data (and units), with select menus to map these to model inputs. Show a table of observation variables (and units), with select menus to map those to model outputs. * Add a mapped qname to biomarkers Store the mapped variable qname on biomarker types. Read it from OBSERVATION_VARIABLE in a dataset. * Allow for multiple variable mappings Map each Administration ID to a dosing compartment. Map each Observation ID to a model output. Add new columns to the CSV data, with mappings and optional units. * Save modified dataset to backend - load or create a dataset when we start an upload. - save the dataset when we finish an upload. - modify the `/datasets/:dataset_id:/csv` endpoint to accept a JSON string. * Allow for a single unit column - When there's a single unit column, use that column for both dosing and observations. - Split the CSV data into dosing rows and observation rows. - Add administration route to the Map Dosing screen. - Allow for dimensionless observation units. - Filter mapped observation variables for compatibility with the observation unit value. * feat: data stratification (#361) - Replace the tabbed interface for data uploads with a stepper. - Add utilities to group subjects by protocol. - Add stratification to the stepper. - Stratify by dose protocols for the time being. - Display each protocol group as a MUI data grid. - Display protocol groups as tabs in the trial design view. - Add the dosing compartment qname to the protocol model. - Add a 'cohort' field to the CSV. * refactor: optional simulation dosing protocols (#367) - break `create_myokit_simulator` up into smaller methods. - break `simulate` up into smaller methods. - add optional `dosing_protocols` to `create_myokit_simulator`. If set, it overrides the default dosing variable protocols. * feat: subject groups Add a subject group model to the Django app and the API. Subject groups have a list of subjects and a list of protocols associated with those subjects. Datasets have a list of subject groups in `dataset.groups`. Refactor the Data and Trial Design views to use `dataset.groups` for tabbed views. * feat: allow for multiple Myokit simulations (#366) Refactor the Myokit model mixin to allow multiple simulations to be run. Each dataset subject group has its own simulation, with subject dosing protocols and dosing events. Update the simulate API to return multiple simulations. Show multiple plots in the Simulations tab Test simulations with a project and dataset * feat: plot biomarker data in Simulation tab (#371) - add biomarker data to the dataset serialiser. - add biomarker data to the `useDataset` hook. - display the dataset as data grids in the Data tab. - show biomarkers as scatter plots on simulation plots. * fix: handle missing observation units in the CSV (#372) When the uploaded CSV doesn't have an observation unit column, allow the user to pick a unit from a list of units, then pick a compatible variable for the selected unit. * refactor: handle missing units in CSV (#373) Better handling of missing unit columns in the CSV. - When time units are missing, prompt to choose a time unit. - Change the column headings in the submitted CSV to match headings that are expected by the Python data parser utility. - Add a preclinical flag to the dosing step during uploads. * fix: validate observation unit symbols Makes sure that observation units are valid symbols. Symbols loaded from a CSV sometimes have encoding issues. If the symbol isn't valid, show the unit menu instead, so that we can pick a valid unit and correct the uploading error. * fix: set Group ID when selected cohort changes Update the Group ID column when the selected cohort changes. Use the group column values as the group ID for each row eg. (1, 2, 3) or (Male, Female.) * fix: 'map observations' with no selected unit When there's no selected unit yet, the observation variables menu should show all possible model variables. * feat: handle additional doses from a data row (#374) Map ADDL and II columns, in the CSV, to repeat doses in the model and simulations. * feat: filter displayed data by groups (#375) Add checkboxes to control which subject groups are displayed in the simulations view. --------- Co-authored-by: martinjrobins <[email protected]>
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Refactor the Myokit model mixin to allow multiple simulations to be run. Each simulation has its own subject group, with subject dosing protocols and dosing events.