Cell templates

Shown when: always — the last step before BIWT hands back its result.

The question

Each of your cell types can be assigned a cell template: a block of text describing how that cell behaves. For a PhysiCell host that block is a <phenotype> element — motility, mechanics, secretion, cycle, death rates — but BIWT never looks inside it.

One dropdown per cell type, plus (none) at the top of every dropdown. You can click Continue straight away, and you can click Skip instead — this step is never required. Skip leaves every type unassigned; so does picking (none) for individual types.

With nothing loaded, every type sits on (none) and the actions that need a library are disabled. This is a complete, valid answer — Continue and Skip both hand back an empty set.

Where the templates come from

BIWT ships none. Templates reach the dropdowns two ways:

From the host. An application embedding BIWT passes template files when it builds the widget, so they are present before you arrive — listed on the landing screen, where you can drop any of them.

From the landing screen. The Cell templates list on the first screen is the library every import starts from, so a library you work from all session is chosen once rather than at every run. The host's files seed it, and Remove file… takes any of them off for good.

From the wizard. The Add templates from file… button at the bottom of the screen loads template files on the spot, whether or not the host supplied any — pick several at once, or drop them onto the window. Load them at any point: the types you have not picked for yourself re-match against whatever the library now holds (see below). Remove templates from file… drops a file again, including the host's own library if you would rather work from yours.

Running BIWT remotely

Through a remote session — a Galaxy interactive tool, say — dropping will not work: your files are not on the machine BIWT is running on. The button always works; it browses that machine.

From the host's existing cell types. Cell types the application already defines appear too, tagged with its name — Tumor (Studio). Picking one assigns no template; it says this is the cell type you already have, and the host decides what to do about it. Where a name exists both ways, the host's wins.

Removing a file here removes it from this run only. The landing screen's list is what the next import starts from, so remove it there to be rid of it for good.

If nothing is supplied and you load nothing, every dropdown offers only (none).

Either way the file is TOML, mapping a template name to its content. For a PhysiCell host it looks like this:

"My Cell Type" = """
<phenotype>
  <cycle code="5" name="live">
    ...
  </cycle>
  ...
</phenotype>
"""

See templates and name matching for how a host wires that up, and what it gets back.

What gets pre-selected

Each type starts on a candidate whose name matches the type — case-insensitive, then a similarity match, preferring the host's own cell types where both name it equally well. Failing that, whatever is named default: the host's if it has one, else the library's. Failing that, (none).

Two libraries loaded, every type matched by name. The file each template came from is right-aligned in its own column, so the sources line up down the list rather than trailing each name. With a single library loaded the column is dropped — there is nothing to tell apart.

Three actions redo that for you, each with the same icon in two places: the Set all row at the top applies it to every cell type, the small button beside a dropdown to that type alone.

	Action	What it does
	Auto-match	Re-runs the matching above, overriding your picks
	Assign default	Assigns whatever is named default — the host's, else the library's
	Assign (none)	Clears the assignment

(none) on one type only. Unassigned types are simply absent from the result, so this is how you hand back some templates and not others.

If two sources offer the same name — tumor in one library and Tumor in another, or one of them the host's own cell type — that row is marked with an ⓘ. Hover it to see who else defines the name. Nothing is hidden: each is listed separately in the dropdown with its source. Click the ⓘ to dismiss it.

Set all → Assign (none) is Skip without leaving the step. Auto-match is greyed out if no templates are loaded at all, and Assign default if nothing is named default, or if two loaded files each define one and the host does not — then there is no single default to mean, so pick the one you want from the dropdown.

Changing the loaded files re-matches the types you have not touched. If a new file names a better match for a type whose dropdown you never used, that type takes it; a type you chose for yourself keeps your choice, including an explicit (none).

Removing a file works the same way, except for rows that were using it: their template no longer exists, so there is no choice left to preserve and they re-match with the rest rather than quietly picking up some other template.

Auto-match resets that, at either scope: a row you auto-match counts as untouched again.

Numbers in a name are treated as significant, so M1 Macrophage never matches M2 Macrophage, nor CD4 T Cell a CD8 one. A host can replace the whole rule by supplying its own predicate (the name_matches argument to create_biwt_widget).

Pre-selection is a hint: nothing stops you assigning Fibroblast parameters to a type you named something else.

Treat templates as starting points

A template library is generally literature-derived defaults, not calibrated parameters for your system. Expect to tune them in your config afterwards.

Sort templates reorders the dropdown entries by name, or groups them under a heading per source file. Either way names sort case-insensitively — default, Macrophage, t_cell, Tumor.

With a single file loaded, entries show the bare template name. Once two or more are loaded every entry is tagged with its source file. The host's own cell types are always tagged.

What happens with your choices

Your selections come back to the host as BiwtResult.cell_templates: a mapping from final cell-type name to (path, name, content) — the file the template came from, its name in that file, and its content verbatim. Assembling a config out of that is the host's job; BIWT generates no XML.

Where you picked one of the host's own cell types, path is HOST_SOURCE rather than a file and the content is empty.

Types left unassigned are absent from the mapping, so an empty mapping is a perfectly normal result — that is what Skip produces.

Next

Finishing up →.