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What's new

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

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.