A drawing tool for biochemical reaction networks. Draw species and reactions, shape the reactions with straight lines or Bézier curves, give them rate laws, lay the network out automatically, and exchange it with the rest of the systems biology world as Antimony or SBML with layout.
It is written in Rust with egui. The same code runs in the browser and as a desktop app for Windows, macOS and Linux.
Try it: https://sys-bio.github.io/PathwayDesigner-rs/
This software was developed with the assistance of Anthropic's Claude, an AI model, through Claude Code. Stop here if you aren't comfortable with AI assisted code generation.
The same model in the Escher theme (View ▸ Theme ▸ Escher), for metabolic maps:
An Escher map of E. coli core metabolism, opened
with File ▸ Open (Escher/e_coli_core.Core metabolism.json) and drawn as Escher
draws it:
This is a re-implementation of the Delphi PathwayDesigner. It does everything the Delphi version does, and some more (see Status).
- In the browser: open https://sys-bio.github.io/PathwayDesigner-rs/. Nothing to install, and it keeps working offline once it has been opened.
- On the desktop: download the installer for Windows, macOS or Linux from Releases. The packages are not signed, so the first time you start it, Windows asks you to choose More info ▸ Run anyway, and on macOS you right-click the app and choose Open.
- On your own web server: copy the website, a folder of plain files, as described in Host your own copy.
- What's new: what changed in each version is in RELEASE-NOTES.md, and with each download on the Releases page.
Drawing and editing
- Species, and reactions of any shape, with stoichiometry: tools for A → B, A + B → C, A → B + C and A + B → C + D, and A+… → B+… for any number of reactants and products (click the reactants, press Enter, click the products, press Enter again).
- Change a reaction's species afterwards from its right-click menu: Add Reactant…, Add Product… and Remove from Reaction. An automatic rate law follows, and a side left empty gets a null node.
- Three ways to draw a reaction: Straight (legs meet at a junction), Linear (one straight line, for A → B), and Bézier curves with handles you can drag, optionally with a smooth junction. A reaction can also have a stem, a straight centre line its reactants join at one end and its products leave from the other, as Escher draws reactions.
- Aliases (a second drawing of the same species), with commands to split a species into aliases, split off chosen reactions, and merge aliases back.
- Modifiers (drawn as dashed arcs, found from the rate law), and null nodes for sources and sinks. A modifier can be an activator (open arrowhead), inhibitor (blunt bar) or catalyst (open circle), carried to and from SBML (as SBO terms) and Antimony (in the diagram comment). Modifier lines, and reactants' and products' lines, can be routed round the diagram through corner points, carried in SBML Layout as curves of several segments.
- Compartments, drawn as boxes you can move and resize (by their corners, or by Width and Height in Properties); species move with their compartment, a box can be hidden, and its name can be any size.
- Free text for titles and notes, with typeface, size, bold, italic, colour, alignment and wrapping.
- A right-hand panel with Properties for what is selected (colours, line and border widths, values, boundary species, rate laws, with errors in a rate law shown as you type), the live Antimony text, and the saved Styles.
- A model tree listing every species, reaction and compartment, usable from the keyboard, with a Find box (Ctrl+F) that keeps only the items whose id or display name holds the words typed.
- Ids and display names: each species, reaction and compartment has an id, which can be typed in its Properties to rename it (rate laws follow), and can have a display name, a readable name such as D-Glucose 6-phosphate. View ▸ Display names labels the diagram with display names instead of ids; each item's Label setting can override that. A drawing can also have label text, shorter words shown in place of its display name: Reactome's maps, for example, label GPI dimer [cytosol] as GPI dimer, and opening one keeps those labels.
- Cut, Copy and Paste (Ctrl+X, Ctrl+C, Ctrl+V) parts of a network, within a
model or into another, in the same window or another one. A copied reaction
brings its species, and rate laws bring the parameters and rules they use. Ids
already in the model get
_2,_3, …, and the rate laws follow; display names stay as they were. - Undo and redo for every change.
Annotations
- Full support for model annotations: SBO terms, references to database entries (ChEBI, UniProt, Rhea, EC numbers, GO, KEGG, PubMed and others) and notes, on species, reactions, compartments, parameters and the model. They are read from and written to SBML and Antimony unchanged, so a curated model keeps them, and can be seen and edited in each item's Annotations part.
- Each reference shows what its entry is called (
CHEBI:16452— oxaloacetate), and opens the entry's page in the browser. Resting the pointer on an item shows its annotation. - Annotate a whole model from its names: Annotate Species from Names and Annotate Reactions from Names look the items up in BiGG, ChEBI, PubChem and Rhea and list what they find to check before anything is added.
- Find in ChEBI and Find in Rhea for one species or reaction at a time, and marks on the diagram for what is still to check (see How to annotate a model).
How things look
- Species shapes: rounded rectangle, rectangle, ellipse, circle or hexagon; resize them by their corners or by number, or fit them to their names. A name too long for its node is broken onto more lines, or drawn a little smaller, so it never spills out.
- Fill, border colour, border width (0 for no border), solid or dashed border, label colour and font size, for each item. A species' or compartment's fill can be left out (No fill), so what is behind shows through.
- The diagram's background colour (Properties, with nothing selected), on screen and in exported pictures.
- Names outside the node, as in Escher's metabolic maps: small circles with their names beside them, each name dragged where you want it.
- Reaction names: show a reaction's id beside it (Show Id in the Properties panel), placed clear of its lines, with its own size and colour; drag it where you want it.
- Copy Style and Paste Style (Ctrl+Alt+C, Ctrl+Alt+V) copy a look from one item to others, like a format painter; an alias can take its species' look.
- Saved styles: keep a look under a name and give it to other items, which then follow it, so changing the style changes them all. Styles are kept with the app ("My Styles") and saved in the model file for the styles it uses, so a model given to someone else carries them. Edit a style directly, and export and import styles to share them.
- Themes (View ▸ Theme): Escher restyles the whole diagram as a metabolic map, with orange circles, smaller circles for cofactors such as ATP and NADH, names placed clear of the lines, thick blue reactions curving smoothly through their junctions, and every reaction's name shown; new items follow the theme. Classic puts back the default look. Undo reverses either.
- Arrowheads grow with thick reaction lines.
Layout
- Force-directed auto-layout, animated, with an optional pass that shapes the Bézier curves. Locked nodes stay where they are.
- Align and distribute species and junctions, and Arrange in Circle.
- A grid to line things up, and Snap to grid: dragged items, new items, corners, Bézier handles, names and arrow-key moves land on grid points (hold Alt to place freely).
- Nudge the selection with the arrow keys.
- The pointer's position on the diagram is shown in the status bar.
- A random network generator, for trying things out.
Files
- PathwayDesigner's own JSON format. It reads the Delphi version's files, and a model that uses nothing new is still saved in the Delphi version's format.
- Antimony: import and export, with a live Antimony panel next to the drawing. The drawing goes with it, in a readable diagram format written as a comment after the model (docs/diagram-format.md), so any Antimony tool still reads the file: File ▸ Export Antimony writes it, and the panel's Get Antimony does with Diagram ticked. File ▸ Export Antimony with Layout Statements, or Layout statements in the panel, adds Antimony 3's own layout statements, for tellurium and SBMLNetwork. Import reads either, from PathwayDesigner or from libAntimony, and lays out what a diagram leaves out. What Antimony can't say of an SBML model (a rate law's own parameters, metaids and the like) goes in a second comment, so nothing is lost; Load Antimony keeps it from the diagram it replaces when the text has none (docs/antimony-full-support-design.md).
- The whole model is kept. Events, assignment, rate and algebraic rules, starting values from formulas, functions, units, constraints, a rate law's own parameters, other tools' annotations and other SBML packages are read, kept and written back, so a model opened and saved unchanged means what the file meant. Checked on all 1,062 curated BioModels and 1,823 SBML Test Suite cases, element by element against libSBML, through SBML and through Antimony (docs/sbml-full-support-design.md). The Events & Rules tab lists them as sentences ("When time ≥ 10: Glucose becomes 5") and edits them in place; a lightning bolt marks what they change on the diagram (docs/sbml-app-design.md).
- SBML Level 2 and Level 3: import and export, including the Layout package, so positions, aliases, curves, reaction stems and reaction names survive the round trip, and the Render package, so colours, line widths, dashes, shapes, fonts, arrowheads and modifier symbols do too. Other tools draw the file in PathwayDesigner's look (checked with COPASI and SBMLNetwork), and the Render that COPASI, SBMLNetwork and SBMLDiagrams write is read, with a warning for anything that can only be approximated (docs/render-design.md).
- Escher maps: File ▸ Open reads an Escher map
(
.json) and draws it as Escher does: its layout, each reaction's straight centre line and the map's own curves, its labels, and each extra drawing of a metabolite as an alias, in the Escher theme, each at the size the map gives it. Maps whose lines are routed through chains of markers (such as the BiGG maps drawn by MetaCarto) keep their routes as corner points. - KEGG maps: File ▸ Open reads a KEGG metabolic
pathway map (a KGML file,
.xml) at KEGG's positions: compounds as circles, enzymes as boxes catalysing their reactions, links to other maps as grey text. Compounds are labelled with names from PubChem (D-Glucose, notC00031), as display names; the KEGG numbers stay their ids. On the desktop, File ▸ Open from KEGG… fetches a map by its code (eco00010); KEGG doesn't let web pages fetch its files, so in the browser the map's file opens in a new tab, to be saved and opened. KGML gives no line routes, so reactions whose compounds don't line up are drawn as rounded elbows. Signalling and global maps aren't read yet. KEGG's data are free for academic use under KEGG's terms (docs/kegg-import-design.md). - Network structure (the Structure tab): the stoichiometry matrix (in a panel under the diagram), the flux null space and the conservation laws, computed as COPASI does (QR with column pivoting) and checked against libRoadRunner, with an optional sparse basis whose vectors are short routes. Clicking a vector or a law highlights it on the network; Copy and CSV export for each.
- Graphics: SVG, PNG at any resolution, and vector PDF (Letter, A4 or the drawing's own size), and printing.
- The Gallery: File ▸ Open from Gallery… opens example models, from small networks to E. coli central metabolism and Escher's E. coli core map. They are fetched from this repository when wanted, so new ones appear without a new release (see The Gallery).
In the browser
- Works offline once it has been opened. Saves straight back to the file you opened (in Chromium-based browsers), autosaves, and offers your changes back if the tab was closed or the app crashed.
- Says when a new version has been published.
On the desktop
- Opens files from the file manager, and keeps a list of recent files.
- Autosaves every 10 seconds while there are unsaved changes, and offers them back after a crash or a power cut.
- On macOS, the usual application menu (About, Settings, Hide, Quit) and Window menu, and Cmd for every shortcut.
Pick a tool on the left: Species adds a species where you click, and the reaction tools (A → B and the others) add a reaction when you click its species in turn; with A+… → B+…, press Enter after the reactants and again after the products. Select is for selecting, dragging and editing. Esc goes back to Select.
The toolbar shapes the selected reactions (Linear, Bézier, Straight, smooth junction, Make Nice) and runs the auto-layout. Right-click a species or a reaction for more: aliases, renaming, locking, alignment, styles. The View menu has the grid, Snap to grid, zoom, and switches for the alias indicator and modifier lines.
On macOS, Cmd takes the place of Ctrl and Option of Alt.
On the canvas, with the Select tool
| Action | What it does |
|---|---|
| Click | Select a species, reaction, compartment, text or name |
| Shift-click | Add to or take from the selection |
| Drag on empty canvas | Select everything the rectangle touches |
| Drag a species, junction, text, name or compartment border | Move it (a compartment carries what is inside it) |
| Drag a Bézier handle of a selected reaction | Reshape that line |
| Drag a corner of a selected species or compartment | Resize it; Shift keeps the proportions |
| Drag the small handle on a selected text's right edge | Set where its lines wrap |
| Drag a square at an end of a selected reaction's stem | Move that end of the stem; with Straight stem ticked (Properties), the stem pivots about the junction instead of bending |
| Drag the + by a selected reaction's junction onto a species | Add the species to the reaction as a product; hold Shift when letting go for a reactant |
| Alt while dragging | Place freely while Snap to grid is on |
| Double-click a species | Rename it |
| Double-click a text | Edit its words |
| Double-click a modifier line, or a reactant's or product's line | Add a corner point there, so the line can turn a corner; drag the small square to move it, right-click it to remove it |
| Right-click | The menu for what is under the pointer (Cut, Copy and Paste, aliases, Add Reactant…, Add Product…, Remove from Reaction, Add, Straighten or Remove Stem, Modifier Kind, corner points, styles, alignment, locking and more); on empty canvas, Paste puts the copy there |
| Rest the pointer on an item | A tooltip: a species' value, a reaction's rate law, a compartment's volume, and its display name and annotation |
Adding things
| Tool or command | How |
|---|---|
| Species, Text | Click where it should go |
| Compartment | Drag out its box (a click makes a 300 × 200 box) |
| A → B, A + B → C, A → B + C, A + B → C + D | Click the reactants, then the products, in turn |
| A+… → B+… | Click the reactants, press Enter, click the products, press Enter again |
| Add Reactant…, Add Product… (a reaction's right-click menu) | Click species to add them; Esc or a click on empty canvas stops |
| Any of these | A click on empty canvas, or Esc, cancels |
Getting around
| Action | What it does |
|---|---|
| Wheel, or two-finger scroll | Pan (Shift: sideways) |
| Ctrl + wheel, or pinch | Zoom, keeping the point under the pointer still |
| Middle-button drag, or Space + drag | Pan |
| The − / % / + at the right of the status bar | Zoom out, zoom to fit, zoom in |
In the model tree (left)
| Action | What it does |
|---|---|
| Click | Select that item |
| Ctrl-click | Add to or take from the selection |
| Shift-click | Select everything from the last item clicked |
| ↑ / ↓, Shift + ↑ / ↓ | Move through the list; extend the selection |
| Ctrl+F, then type | Keep only the items whose id or display name holds the words; Enter, or a click, selects one and brings it into view |
Keys
| Keys | What they do |
|---|---|
| Ctrl+Z | Undo |
| Ctrl+Shift+Z, Ctrl+Y | Redo |
| Ctrl+A | Select all (Edit also has Select All Species and Select All Reactions) |
| Delete, Backspace | Delete the selection |
| Ctrl+X, Ctrl+C, Ctrl+V | Cut, Copy, Paste the selection, between models and windows too; Ctrl+V pastes under the pointer |
| Arrow keys, Shift + arrow keys | Nudge the selection 1 unit, 10 units; with Snap to grid, one grid line, five (Alt for 1 and 10) |
| Arrow keys after clicking a corner point | Move that point instead, by the same steps; a click elsewhere or Esc goes back to the selection |
| Ctrl+Alt+C, Ctrl+Alt+V | Copy Style, Paste Style |
| Ctrl+F | Find in the model tree |
| Enter | With A+… → B+…: on to the products, then make the reaction |
| Esc | Cancel what is in progress (a drag, a reaction being picked, a layout) and go back to the Select tool |
| Ctrl+S, Ctrl+Shift+S | Save, Save As |
| Ctrl+O | Open |
| Ctrl+N | New (in a browser, Ctrl+N opens a new browser window: use File ▸ New) |
| Format | Extension | Read | Write |
|---|---|---|---|
| PathwayDesigner diagram | .json |
yes | yes |
| Antimony | .ant, .txt |
yes | yes |
| SBML Level 2 and 3, with Layout and Render | .xml |
yes | Level 3 Version 2 (Version 1 for a model with fast reactions) |
| Escher map | .json |
yes | |
| SVG, PNG, PDF | .svg, .png, .pdf |
yes |
Models/ holds the reference models in each format. The tests check every one,
so a model added there needs a stored image. File ▸ Open sample opens the JSON
ones directly, even in the browser. ExampleModels/ holds more example models;
the tests don't use it. Escher/ holds an Escher map of E. coli core metabolism.
Both are in the Gallery.
An annotation says what an item is: that the species G6P is
D-glucose 6-phosphate (ChEBI entry CHEBI:4170), or that the reaction PPC is
phosphoenolpyruvate carboxylase (EC number 4.1.1.31, Rhea entry 23072).
Annotations travel with the model in SBML and Antimony, and other tools and
databases read them. Select an item and open Annotations in its
Properties to see them; rest the pointer on it for a summary.
Species, all at once. Choose Edit ▸ Annotate Species from Names… (or
right-click a species). PathwayDesigner looks each species up by its display
name or id, in BiGG (which knows the abbreviations metabolic models use, such as
g6p and accoa), then ChEBI, then PubChem, and shows what it found in an
Annotate tab:
- Clear matches are ticked. The others are offered, unticked, with the
alternatives in a list: check them, since a short name can find the wrong
thing (
ASPis aspartate, but also the name of a peptide). - Click a species' name in the list to see it on the diagram, and the open link to see the entry's page.
- A second tick gives the species the full name found as its display name.
- Apply adds what is ticked, in one step you can undo. Nothing is changed before that.
Select some species first to look up only those.
Reactions, all at once. Edit ▸ Annotate Reactions from Names… works the same way. It looks each reaction up in BiGG by its id, which gives its EC numbers and its Rhea, KEGG and MetaNetX entries; failing that, it asks Rhea for the reactions that have all of its reactants and products (species without a ChEBI entry are looked up by name for this); failing that, it tries BiGG's search. Each match shows its equation: compare it with your reaction before ticking it. Annotating the species first gives better reaction matches.
One item at a time. In a species' Annotations, Find in ChEBI searches
for its name, or any words you type, and Add puts in the entry you choose.
In a reaction's, Search by Species finds the Rhea reactions with its
reactants and products, with no typing; or type an enzyme name (pyruvate
kinase) or an EC number and press Search. Add puts in the Rhea entry
and its EC numbers. A reference can also be typed directly, as a short
identifier such as CHEBI:15422 or ec-code:2.7.1.40.
What is left to do. After a lookup, the diagram marks the items still to check: an orange ring for one found but not ticked, a blue one for one where nothing was found. A mark goes as soon as its species gets a ChEBI reference, or its reaction an EC number or Rhea entry. View ▸ Annotation Marks turns each kind on or off, or clears them.
The lookups need a network connection; everything else works offline. On the Millard E. coli model in the Gallery, the species lookup ticks 17 of its 77 species, all correctly; most of the rest use abbreviations of the model's own.
File ▸ Open from Gallery… lists the example models named in
Gallery/index.json and opens the one you pick. The app
reads the list and the files from this repository's main branch on GitHub, in
the browser and on the desktop, so a model added or changed here reaches every
copy of the app once it is pushed: no new build or release. GitHub caches the
files for a few minutes, so a change can take about five minutes to show. With
no network the window says so; File ▸ Open sample still has a few models built
into the app.
To add a model:
-
Put the file anywhere in the repository;
ExampleModels/is the usual place. It can be a PathwayDesigner.jsonfile, an Escher map, or an SBML file. -
Add an entry to
Gallery/index.json:{ "file": "ExampleModels/my_model.json", "group": "Large models", "title": "My model", "description": "One line about it", "version": 4 }file: the path from the repository's root.group: the heading it is listed under. Groups appear in the order they first appear in the file; a new name makes a new group.title, and an optionaldescriptionshown under it.version: the"version"at the top of the model's file, or0for an Escher map or an SBML file. An app too old for that version shows the entry greyed out instead of failing to open it.
-
Run
cargo test -p pd-app gallery. It checks every entry: the file exists, opens, and has the version the entry says, and no file is listed twice. CI runs the same test, so a mistake fails the push that makes it. -
Commit and push to
main.
Changing a model is just steps 3 and 4, and step 2 if its version changed (saving it in a newer app can raise it). To remove one, delete its entry.
To try a Gallery before pushing it, build the app with PD_GALLERY_URL set to
another address that serves the same files, ending in /, for example
PD_GALLERY_URL=http://127.0.0.1:8080/ trunk serve from crates/pd-app with the
repository served on port 8080.
Version 1.0.0 (what changed: RELEASE-NOTES.md). All the milestones of SPEC-Rust.md are done: the browser version (R0 to R12) and the desktop version (D1). The conformance checklist and its evidence are in docs/release-checklist.md.
Still to do: try the macOS and Linux packages on those systems, and run the checklist there. So far they have been built and tested in CI, and the Windows installer has been tried by hand.
Beyond the Delphi version, this one adds SBML import, SVG export, a drawing-sized PDF page, the model tree, animated auto-layout, keyboard nudging, aligning junctions, Arrange in Circle, more alias commands, drawn compartments, free text, species shapes and resizing, names outside the node, Copy and Paste Style, saved styles, the grid and Snap to grid, themes, reaction names and stems, reactions with any number of species, corner points on reaction lines, Escher maps, SBML Render, Antimony layouts, the network's structure (conservation laws and flux null space) drawn on the network, transparent fills, a background colour, KEGG maps, display names, annotations and their lookup in BiGG, ChEBI, PubChem and Rhea, offline use and autosave, and fixes the defects listed in SPECIFICATION.md §15.
This work was supported by NIH Biomedical Imaging and Bioengineering award P41 EB023912 through HMS at the Center for Reproducible Biomedical Modeling.
MIT, see LICENSE. The bundled Noto Sans and Noto Serif fonts are under the SIL Open Font Licence (assets/fonts/NotoSans-OFL.txt). The bundled Hack font, for fixed-width text, is under the MIT and Bitstream Vera licences (assets/fonts/Hack-LICENSE.txt). The licences of the open-source crates PathwayDesigner is built from are in THIRD-PARTY.html, which the app also links to from its About box.
How the code is organised, built and tested.
| Crate | What it is |
|---|---|
pd-core |
The model, geometry, drawing, interaction, undo, layout, and the JSON, Antimony and SBML bridges. No user interface or platform code, so all of it is tested without a window. |
pd-app |
The egui application, for the browser and the desktop. |
pd-export |
Graphics output: SVG, PNG (through resvg) and PDF. |
antimony |
Reads and writes Antimony, all of the language, and converts it to SBML. Written to be reusable on its own, and checked case by case against a complete reference implementation. See its README. |
sbml-io |
Reads and writes SBML as plain Rust data. Written to be reusable on its own: Level 2 and 3 core plus Layout and Render, pure Rust, with everything it doesn't understand kept for a lossless round trip. See its README. |
You need Rust, the wasm32-unknown-unknown target
(rustup target add wasm32-unknown-unknown) and Trunk.
cargo test --workspace # the tests
cargo run -p pd-app # a desktop window
trunk serve # the browser version, at http://127.0.0.1:8080/
trunk build --release --public-url ./ # the web release, into dist/
On Windows, run Trunk from PowerShell, or from Git Bash with MSYS_NO_PATHCONV=1,
or Git Bash turns the --public-url path into a Windows path.
Desktop packages are made with cargo-packager
(cargo install cargo-packager --locked):
cargo packager --release -p pd-app --formats nsis # Windows installer
cargo packager --release -p pd-app --formats app,dmg # macOS
cargo packager --release -p pd-app --formats deb,appimage # Linux
The packages land in target/packages/. Pushing a version tag (v0.1.0, …) has
CI build all of them and attach them to a draft GitHub release. They are not
signed, so on first start Windows asks for More info ▸ Run anyway, and macOS for
a right-click on the app and Open.
Every push runs CI (.github/workflows/ci.yml):
formatting, Clippy for the desktop and for WebAssembly, licence checks, and the
tests; then
- SBML: every Level 2 and Level 3 model of the
SBML Test Suite is read and written
back by
sbml-io, and python-libsbml must find each one unchanged; every example model is exported and checked with libsbml'scheckConsistency(); - graphics: every example model's PDF is drawn by pdfium and compared with its PNG;
- web: the release build is served from a sub-path, as GitHub Pages serves it, and checked in headless Chromium: it starts, works offline, and shows the new-version notice;
- macOS: the desktop app is linted and tested on a Mac.
Pushes to main that pass are published to GitHub Pages, and the built website
is written to the gh-pages branch.
Three example programs in pd-core check things the tests don't, over every
model in the Gallery. They are run by hand, when a change might affect them.
export_sbml: exports models as SBML for checking with python-libsbml. CI
runs it on Models/ and, with --gallery, on the Gallery:
cargo run -p pd-core --release --example export_sbml -- out --gallery
python crates/pd-core/tests/scripts/check_sbml.py out
layout_report: what survives a round trip. Each model is exported as SBML
with Layout and Render and read back, as written and with PathwayDesigner's own
notes removed (what a program that reads only standard SBML sees), and compared
with the original field by field. With --antimony, the model alone is compared
after a trip through Antimony; with --antimony-layout, the whole drawing after a
trip through Antimony with its layout statements; with --diagram, after a trip
through Antimony with the drawing as a diagram comment (docs/diagram-format.md,
being implemented). Use it after changing an importer or exporter, to
see at once what a change keeps and loses. It prints a Markdown report; with
DETAIL=<part of a model's title> it also lists that model's every change (in
the round trip without the notes with DETAIL_STANDARD=1 too).
cargo run -p pd-core --release --example layout_report > sbml.md
cargo run -p pd-core --release --example layout_report -- --antimony > antimony.md
cargo run -p pd-core --release --example layout_report -- --antimony-layout > antimony-layout.md
cargo run -p pd-core --release --example layout_report -- --diagram > diagram.md
scripts/antimony_layout_check.py: compares PathwayDesigner's reading and
writing of Antimony's layout statements with libAntimony's, over the Gallery (it
needs the antimony Python package, and uses the export_sbml and
drawing_report examples). Use it after changing how those statements are read
or written. layout_report --antimony-layout checks that PathwayDesigner reads
its own Antimony export back as the same drawing.
python scripts/antimony_layout_check.py <work folder>
consistency_dump: everything the shared core makes from each model (the
saved file, the Antimony and SBML exports and what they read back as, SVG and PDF
drawings, and an automatic layout from a fixed seed), written to a folder. Build
it natively and for WebAssembly, run both, and compare the two folders: this
checks that the browser version computes what the desktop version does. Use it
after changing geometry, layout, drawing or the exporters, or after a new Rust or
dependency version. Expect the layouts and a few SBML coordinates to differ in
their last digits, because the platforms' maths libraries round hypot (used for
every length) differently; everything else should be identical. It needs the
wasm32-wasip1 target and Node (tried with Node 24).
cargo run -p pd-core --release --example consistency_dump -- . native
rustup target add wasm32-wasip1
cargo build -p pd-core --release --example consistency_dump --target wasm32-wasip1
node scripts/run_wasi.mjs target/wasm32-wasip1/release/examples/consistency_dump.wasm . wasm
diff -r native wasm
- SPECIFICATION.md: what the application does, written from the Delphi version, with every change made since recorded in it.
- SPEC-Rust.md: how it is built in Rust, the decisions taken, and the milestone plan.
- docs/release-checklist.md: the release checklist.
The web version is a folder of plain files: a page, the app compiled to WebAssembly, and a few small helpers. There is no server-side code and nothing to build, so hosting your own copy is a matter of copying that folder, as with MakeSBML.
1. Get the files. Either:
- download the
gh-pagesbranch of this repository: on GitHub, switch the branch menu togh-pages, then choose Code ▸ Download ZIP; or clone it:git clone --branch gh-pages --depth 1 https://github.com/sys-bio/PathwayDesigner-rs.git pathwaydesigner - or download
PathwayDesigner-web-<version>.zipfrom Releases.
The gh-pages branch always has the latest version (CI writes it after every
change); a release zip is a fixed version.
2. Copy them to your server. Put the files in any folder of your website, for
example pathwaydesigner/. Keep them together; the folder's name doesn't matter.
The files are:
| File | What it is |
|---|---|
index.html |
The page |
pathway-designer-<hash>.js and pathway-designer-<hash>_bg.wasm |
The app (the .wasm file is about 15 MB) |
sw.js |
Lets the app work offline |
THIRD-PARTY.html |
The licences of the software it is built from |
README.md |
These instructions |
3. Open it at the folder's address, for example
https://mysite.org/pathwaydesigner/.
What the server needs:
- to serve
.wasmfiles with the typeapplication/wasm. Almost every web server does this already. If the page stays on "Loading PathwayDesigner…", this is the first thing to check; - HTTPS, for working offline and for saving straight back to an opened file. Over plain HTTP the app still works, without those two.
To try it on your own computer, serve the folder with any local web server,
for example python -m http.server 8000 in the folder, then open
http://localhost:8000/. Opening index.html directly from disk (a file://
address) doesn't work, because browsers don't load WebAssembly that way.
To update your copy, replace all the files with the new ones. The names of the
.js and .wasm files change with each version, so delete the old ones. People
who have the page open are told a new version is available.