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Metabolic Pathways

Brian White (Massachusetts Institute of Technology),
John W. Moon, Jr. (Harding University),
Jülyet Benbasat (University of British Columbia),
Presley Martin (Drexel University), and
Allen Place (Center of Marine Biotechnology, University of Maryland Biotechnology Institute)
Screen Shots | What's New | System Requirements

The Metabolic Pathways module is designed to allow the user to model multistep pathways of enzymatic and non-enzymatic chemical reactions. The model allows the user to change kinetic and thermodynamic properties and observe their effects on the concentrations of the compounds in a pathway over time.

In the simple example model shown below, the enzyme (whose thermodynamic and kinetic parameters are shown) converts Compound A to Compound B. The plotter on the right monitors the concentration of A and B as a function of time, shown in the graph below.

 

Models in Metabolic Pathways can include six types of blocks, grouped into two types:

Compounds

  • Molecule: models a compound in a pathway whose concentration depends on how much has been synthesized or degraded by the reactions in the pathway.
  • Constant source or drain: models a compound whose concentration in a pathway is constant regardless of how much is synthesized or degraded. This is meant to model a constant source or sink of materials in a particular pathway.
  • Pulsatile source: models a compound whose concentration in a pathway varies with time, regardless of how much is used up or produced. It is intended to model an infinite source or sink whose concentration varies regularly.

Reactions

  • Non-enzymatic reaction: models a non-enzymatic reversible chemical reaction.
  • Enzyme: models an enzymatically catalyzed reversible chemical reaction. It is designed to model reactions where the enzyme is not subject to regulation.
  • Regulated Enzyme: models a regulated enzymatically catalyzed reversible chemical reaction.

The parameters of all of these blocks can be modified. Double-clicking on the icon will open a dialog box which gives the user access to many of the parameters.

 

What's New?

Metabolic Pathways is now available for both the Macintosh and Windows operating systems.

 

System Requirements

Macintosh or Power Macintosh

  • System 7 or later. System 7.5 recommended.
  • At least 8 megabytes of RAM.
  • 68020 processor or greater (will not run on 68000 computers like MacPlus or SE).

Windows 3.1, Windows 95, or Windows NT

  • Windows 3.1 or later and DOS 5.0 or later (and Win32s 1.25 if using Windows 3.1), or Windows 95, or Windows NT 3.5 or later.
  • 80486, Pentium, or Pentium Pro.
  • At least 8 megabytes of RAM.


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