You have found a collection of common chemical and biochemical reactions. The
reactions are described and are available for solving with modeling software.
Each reactant, intermediate and product in the equations can be simulated over
time. The models can be used i) to predict changes in species over time by varying
parameters of the equation, and ii) to determine rates of the equation by fitting
the models to observed data. For every model there are five sections:
1) Equations: The Equations section has a simple sketch of the reaction
and all the differential equations that describe it.
2) Graph: The Graph section has a detailed representation of the reaction.
3) Plot: The Plot section has plots of important reactants,products, enzymes
and intermediates concentrations over time.
4) Notes: The Notes section provides some helpful hints into how the model works.
5) Working model The working model is a text file in a format that can be solved
using the free software package, SAAM (see below).
Using the Models
To use a model, download the working model file using your software browser.The file
is a format that can be solved using SAAM, a free software package that can be
downloaded from the Internet at
http://www.saam.nci.nih.gov/saam.htm
Alternatively, from the main menu of the Library click on Modeling Resources then
SAAM: Free modeling software from NIH then SAAM/CONSAM and finally click onto free
compartmental modeling software for 386/486 DOS/WINDOWS based computers.
To solve a model, sart Consam, type 'DECK', then 'SOLVE'. Type 'PLOT Q(#)' where #
is the compartment number of the reactant/product of interest.
i) To view the effects of varying reaction rate constants
To change a parameter value type 'P(1)=x' where x is the new value, SOLVE, and then plot.
To change an intial condition, type "IC(n)=x" where n is the compartment number of
the species and x is the new initial condition.
ii) To fit the models to observed data
Select the approprate rection model, enter data under the heading for the product measured,
and free the parameter values, e.g., type "FREE P(1)", type "DECK", "SOLVE", "ITERATE",
then plot the results E.g., PLOT Q(3) if compartment 3 is the product compartment.
To save changes, type 'UPDATE'.
To exit the program type 'STOP'.
BEGINNERS GUIDE TO SAAM/CONSAM
To enter a new model:
A chemical reaction has reactants that over time go to products
as described by ordinary differential equations.
Each product and reactant is represented by a separate compartment, therefore
arbitrarily one should assign everything its unique # that will refer to its
compartment #.
To start a model, type "I".
Now the first line of the file has to read "A saam31".
Every line that begins with a "C" is a comment and they can be put
anywhere. The next section is for the parameter and it must read
"H PAR". Then starting four spaces in the initial conditions must be
written "IC(#for the compartment)" then starting on space 14 the value
must be entered. The file should now look something like this
A saam31
c comments
c the sky is blue
H Par
IC(1) 4.0
IC(2) 5.0
P(1) 3.0
Notice there is an extra line "P(1)....". This line is for a parameter,
i.e., a constant like a rate constant. One can put in as many initial
conditions as there are intended compartments and as many constants as
desired. Usually there is one rate constant per "arrow" drawn on a
balanced equation.
The next line must read "H DAT" for the data section.
This is where you give the equations for the compartments. The method
used is to write one equation per compartment. Each equation describes
the input into that compartment so that a loss is a negative input.
Take for example the reversible reaction of A to B. Say the forward
reaction has a rate constant equal to P(1) and the back reaction has a
rate constant equal to P(2). The equations are written in the following
format "UF(# for the compartment)=.....". "F(# for the compartment)"
is the concentration for the compartment, an asterisk acts as a
multiplier and a slash acts as a divisor. This example would look like
the following:
H DAT
C THE FOLLOWING DESCRIBES A
UF(1)=-P(1)*F(1)+P(2)F(2)
C THE FOLLOWING DESCRIBES B
UF(2)=P(1)*F(1)-P(2)F(2)
Then just copy the following for every compartment
101F(1)
0
2 5 20
2 20 20
The spacing is difficult, but one can use semicolon to help
Simply type :
102f(2)
;;0
2;;5;;20
2;;20;;20
Notice that 101f(1) is changed to 102f(2). This is the difference between
compartment one and two.
How to edit a model
Command: Function
I(1): insert in line one
P(5): go to line five
A R: to edit the line you are looking at
How to run a model:
After the model is written type "Deck" then type "Solve".
If no error messages are printed that you would have to fix then you can make plots.
Type "plot QC(1,2,..5)" you can plot up to five compartments at a time.
Remember, SAAM makes text files so quick changes can always be done in an editor.
To exit type STOP. Generally type "N", for no, when asked to "update" or "save history."