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What's new

What changed in each release of ProcessDB, newest first. Help → About shows the version you are running.

Unreleased

Built since 10.0.2 and not yet released.

New

  • An Effort menu in the Biology Agent. The agent window's toolbar sets how much the agent thinks before each step, from low to max; the default is medium. Higher effort is slower and usually pays off on hard problems. ProcessDB remembers your choice, and a change takes effect from the agent's next step. See Effort.

Changed

  • Stoichiometry is kept exactly as you type it. A coefficient can be any positive number — 2, 0.5, 2.50, 1e-3 — and it appears that way in the Properties tables and in the generated equations: 2.50 * P456 in a state's differential equation, ^2.50 as an exponent in a modular rate law. SBML import keeps fractional coefficients, which it used to round down (1.5 became 1, and 0.5 vanished), and SBML export now writes coefficients, which it left out. See Roles.
  • The Biology Agent runs on OpenAI's gpt-6-astra model.

10.0.2

October 14, 2026

ProcessDB 10 moves its data to a new database. Everything — models, realizations, experiments, data, Biology Agent conversations, and model history — was copied across on October 14, and your username and password are unchanged. 10.0.0 and 10.0.1 were built earlier the same day and replaced within hours; this entry covers all three. Versions before 10.0 point at the old database, so update to keep working with current data.

Changed

  • Model History follows the model's sharing. The version list, the differences between versions, and version comments are available only to people who can open the model; until now any signed-in user could read any model's history. See History.
  • A fractional coefficient entered before October 14 may read as unspecified. The copy to the new database kept only whole-number stoichiometry, so a coefficient such as 2.67 reads as blank — that is, as 1 — and has to be entered again.

Fixed

  • A note typed on a new model before its first commit was lost.
  • Committing a Model Realization you had not written a note on deleted everyone else's notes on it.
  • Deleting a model's last subdiagram did not persist; it was back at the next reload.
  • Creating a place or molecule with a name already in use appeared to save and was gone at the next reload. The save now reports the problem.
  • Adding a tracer molecule to an experiment could silently replace a tracer link in another experiment.
  • A save that failed after creating a Model Realization failed again on every retry.
  • The Biology Agent answered Status 500 to every message from October 14 until October 20. This was fixed on the server; no update is needed.

9.8.9

September 15, 2026

Changed

  • The Save Report also reports repairs. When the database no longer has a data set or measurement link that your session still holds — the cause of saves that kept failing at Experimental data points — the save puts the missing row back, or recreates it as a placeholder named Recovered … (rename me), and the report lists each repair even when everything then saved. Data points whose data set is gone for good are held back and listed as not saved, with what to do about them. See When a save fails.

Fixed

  • Saving experimental data failed, save after save, when the database had lost a data set or measurement link that this session still held; every other point in the same save was rolled back with it.
  • After Recover Unsaved Work, the Biology Agent's list of past conversations was stale and never refreshed, and every agent session brought the recovery prompt back at the next launch. The list now reloads each time the agent window opens, and keeps a conversation that only this computer has.

9.8.7

September 1, 2026

Changed

  • Properties is a panel. The Properties of a state, process, arrow, molecule, place, model, Model Realization, MOE, or experiment open in a sixth panel rather than a dialog. It still comes up in its own window, and closing that window still puts it away — but it now has a button in the panel bar and the View menu, and it can be docked on an edge like the Browser or Notes, where it follows the selection from tab to tab. It reopens wherever you last had it, docked or in a window. See Arranging the panels.
  • A popped-out panel's window keeps its size. It opens at the size you last dragged it to, remembered between sessions — the Properties window in particular used to snap back whenever its contents changed. Reset Layout restores the defaults.
  • The blank edge of a window resizes it. Every ProcessDB window and dialog can be resized by dragging the empty padding just inside its edges and corners, not only the thin frame the operating system draws; the pointer shows a resize arrow wherever a drag will work, and the main window has a narrow strip along its left and right edges for the purpose. Holding Alt (⌥ on macOS) resizes both sides at once. See Keyboard and mouse reference.

Fixed

  • Closing a tab in the Workspace could leave the wrong icons on the tabs after it — a model tab wearing the experiment icon, and after a few closes every tab wearing it. Each tab now keeps its own.

9.8.6

August 27, 2026

New

  • Panels. The Browser, Outline, Notes, Action Items, and Search Results are panels arranged around the diagram. Show or hide each from the panel bar at the bottom of the window or from the View menu, drag the dividers to resize, move a panel to another edge, or pop it out into its own window — onto a second monitor, say. The arrangement is remembered between sessions, and View → Layout offers Build, Simulate, and Write layouts plus Reset Layout. The Outline no longer comes and goes with the selected tab. See Arranging the panels.
  • Notes panel. Notes have left the diagram tab — the diagram/notebook view toggles are gone — for a panel that follows the model behind whichever tab is in front, including a Model Realization or MOE. Sections are in name order, and a section without a note offers Click to add a note instead of an empty box. See Notes.
  • Action Items panel. The Model Realization tab's action-items strip is now a panel along the bottom of the window. It opens on its own when a realization has rate laws or initial conditions still to fill in. See Action Items.
  • Search Results panel. Matches for the toolbar search box appear in a panel beneath it, one per line; the first hundred are shown, with a Show more… row for the rest. Double-click a match to open it. See Searching.
  • Export Model Bundle. File → Export Model Bundle… writes a folder and a zip holding the diagram as SVG and PNG, every open plot, the equations typeset as LaTeX and MathML, parameter values, simulation results and experimental data as CSV, and an HTML report that gathers them — the raw material for a paper. It works from a Model, Model Realization, or MOE tab. See The model bundle.
  • The Biology Agent works with experiments. It can list and create experiments, protocols, measurements, and data sets, choose the fit variable, and compare a simulation with the data. Its simulations are now plotted against the MOE's experimental data. It also reads this documentation, so a question about what ProcessDB can do is answered from the current pages. See What it can do.
  • A Processes tab in State Properties lists every process the state takes part in, with its role and — for a reactant or product — its stoichiometry, edited in the table. Double-click a row to open the process. See A state's properties.

Changed

  • A kinetic mechanism is chosen with the rate law, not drawn on the diagram. The competitive, non-competitive, partial, essential, non-essential, and specific roles introduced in 9.8.5 are gone. An edge's role is again one of the ten biological roles, and the mechanism is chosen per regulator in the Default Rate Law dialog when ProcessDB writes a modular law. Edges saved with one of the removed roles are read as Inhibitor or Activator, as are the corresponding SBO terms on SBML import. See How regulators enter a modular law.
  • Parameter set notes can be edited on the MOE tab's Parameter Sets tab. See Parameter sets.
  • A new MOE function parameter starts at 1 rather than blank, and its Value accepts only numbers. See MOE functions.
  • Molecule search in the Browser ranks exact matches first, then names that begin with what you typed, then the rest.
  • Dividers are wider, so they are easier to grab.

Fixed

  • The toolbar search box shows results again; 9.8.5 found matches but displayed none. Typing a ( or [ — as in Ca(2+) or [Ca2+] — no longer silences search for the rest of the session.
  • Diagrams open fitted to the window; a Model Realization's often opened at 100% in its top-left corner. Fit diagram to window fits the diagram it sits above rather than another tab's, and keeps it fitted as panels and the window change size until you pan or zoom. Closing a Model Realization tab no longer leaves a stale view behind for the next time it is opened.
  • A Model of Experiment's tracer equations follow the Tracers tab as shown. Until something was ticked, nothing was traced, and rows left from an earlier version of the model were traced silently; such rows are now marked [not in the model] or [not reachable from this tracer]. See Choosing what carries the label.
  • Regenerating equations no longer fails after the Biology Agent creates a rate law. The same fault broke selecting a newly created subdiagram beside a saved one, and comparing versions in Model History when the model had unsaved states or processes.
  • In the Model Realization tab, moving through the tree with the arrow keys updates the detail view, as clicking does.
  • The Browser's trees draw much faster, most noticeably the Molecules tab.
  • The Help button on the diagram toolbar and the Go to Documentation buttons in graph windows open this site; they opened dead links.
  • On Windows, a few icons drew as empty boxes: the remove button on a tag, the go-to-molecule button in the state Properties dialog, and the Biology Agent's text-size buttons.
  • Long identifiers.org references no longer push the molecule and state Properties dialogs wider than the window.
  • The splash screen is crisp on standard-resolution displays.