This is version 9 of kkit.
It is a minor upgrade since version 8, involving a few new features, but also
including the stochastic solver.

1. Stochastic solver included, with 3 new integration methods. The options
	dialog controls this.
2. Automatic dose-response calculation implemented.
3. Timestep calculation included. This is particularly useful for the mixed
	stochastic method. It is too conservative for the Exp Euler method.
4. Fixes made to database dumping.

5. Minor cleanups of the main menu controls.


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This is version 8 of kkit.
It is a major upgrade since version 7, involving large changes to the interface,
greatly expanded functionality, changes to file format,
and requirements for new binaries.

It requires GENESIS 2.2 or later, including the kinetics library.

Major changes since version 7:
1. Modularization. Organizational structure for very complex models.

2. Stochastic models (through a very inefficient algorithm)

3. Unlimited size for notes.

4. New file format, which is incompatible. A conversion utility is provided.

5. Major interface changes, geared towards modularization.

6. Snap-to-grid display option

7. Improvements to postscript dump, especially in b/w mode

8. Database dump feature for connecting to the DOQCS database.

Under the hood, the following changes have ocurred
- Display coordinates are now simply the x y z coordinates of the respective
	pools, etc.
- 'Mirrors' are now used extensively. This is a change to the pool code which
	effectively allows a pool to be in many places at once. Mirrors can
	participate in reactions etc, but it is as if the same master pool is
	represented in each place.


The change involved in modularization is based on a conceptual development
which is being prepared for publication. The key idea is that nearly all
signaling interactions can be represented by a single motif, that of 
duplication of structurally identical reactions involved in interactions.
The parameters of these interactions vary in individual cases, but the 
reaction structure is preserved. This generalization makes it possible to
make a library of modules and their interactions (links). Because links
can be represented in a stereotyped way, they can be set up at the
block-diagram level rather than through the detailed hooking up of individual
reactions. The modularization changes in kinetikit build on this to allow
setup of modules and links, and a still evolving system for managing them.
Access to the gory details of reactions and mechanisms is retained, but the
fully defined model can be set up at a higher block-diagram level.

Minor changes:
	There is a persistent 'feature' which happens when a user
	accidentally drags an enzyme onto its own parent, or vice-versa.
	The natural response is that the user now corrects the mistake
	by repeating the drag to delete the offending message.
	This sequence of actions causes a 
	subtle but disastrous change in the messaging such that the
	REAC eA B message becomes a REAC sA B message. This does horrible
	things like eat up all the enzyme. I have implemented two things
	to fix this. First, the action itself no longer is permitted. There
	is an error message that pops up when the user tries to make
	an enzyme act on itself. Second, the system automatically scans
	loaded files for such messages and warns the user so they can take
	corrective measures.


===========================================================================
This is version 7 of kkit. 
It requires Genesis version 2.1 or later, plus the kinetics library.
The new transporter object requires GENESIS 2.2 for proper operation.
Installation instructions are in the README of the parent
directory for kinetikit.

Major changes since version 6:

1 Addition of units
2 Addition of default volume settings
3 Addition of experimental parameters
4 Addition of transporter module
5 Fixes to the xtab object.
6 Pseudo-Variable timestep for integration.
7 Major update of help section. Please use it!

Minor changes:
8 Easier assignment of colors to objects
9 Automatic updating of pool concentrations
10 Plots delete correctly and prevent overwriting
11 Minor updates to copyright information

These changes are all backward compatible, so existing files will
load correctly. There may be some surprises in the volumes and concentrations,
as explained below.

1. Rates and concentrations now have a variety of time and concentration units
you can use in addition to the somewhat cumbersone #/cell default that
kinetikit originally used. The 'units' menu item allows you to select between
these. When units are changed the actual concentration does not change but the
display scales appropriately.

2. The default volume settings are in the 'units' menu item. They start
out at a volume of 1e-15 m^3 which is a 10 micron cube. THIS IS DIFFERENT
FROM THE PREVIOUS VERSION. The old 'volume' term in the pools and enzymes
was actually a conversion factor from #/cell into concentration units. 
For example, for a 10 micron cube the previous 'volume' term was 6e5 to
convert this into micromolar. Now the conversion is still done but it is
internal and the user is presented with familiar volume and concentration
terms. For reference, some simulations (such as the feedback.g example)
used a 'volume' scale factor of 1 in earlier versions. This converts
to an actual volume of 1.667e-21 m^3, which the reader can verify is the
volume for which 1 molecule gives a concentration of 1 micromolar. So the
example will still work, but the volumes look a bit odd at first sight.

3. Enzymes and reactions now have several additional dialog boxes for entering
and/or viewing conventional experimental parameters for reactions. The
reaction dialog incorporates a Kd and a tau which are read-only, since the
tau term is not simply defined for higher-order reactions. The enzyme dialog
has the Michaelis-Menten parameters Km and Vmax in conventional units, as
well as a ratio term to explicitly set the ratio between k1 and k2. These
values are read-write and convert immediately between the k1/k2/k3 terms.

4. There is a new module on the menu bar for doing transport. Its icon
is a molecule on a filament, with an arrow indicating movement. This
functions like a unidirectional reaction with a delay. The usual sort
of interaction arrows and click-and-drag apply to this. the transporter
is useful to model nuclear or axonal transport in which there is a
significant time-delay in the arrival of the molecule. Note that the
transporter itself accumulates molecules in transit, so the amount
available to reactions appears to decraese. 
The use of this module is shown in the example model
	transport.g

5. Fixes to xtab object.
xtab was seriously broken in version 6. It is now more functional. The 
file read/write now handles xy as well as y-only type ascii data files.
The selection of table options is hopefully a bit cleaner. It is now again
possible to create a table graphically, with many nifty options.

6. Pseudo-variable timestep.
The timestep at the start of a simulation can be set to a different value
than for the rest of the run. This is selected in the 'options' menu. This
can greatly speed up simulations while preserving numerical accuracy.
Transients at the start of simulations and at the time of addition of reactants
can lead to numerical errors. These are usually fixed by reducing the timestep,
but for most of the reaction a longer timestep usually suffices. So the
'variable timestep' allows the user to set a very tiny timestep (typically 10
times shorter than the regular dt) for the start of a simulation (usually a
couple of seconds). Once selected in the 'options' menu, the shorter timestep
comes into play whenever one presses the 'start' button. So user inputs to
the simulation which result in transients can also be accomodated by this
mechanism.

7. Help section.
Lots of new material added to reflect changes. 

8. Assignment of colors. A little rainbow-colored scale replaces the text
entry for color names.

9. Pool concentration updating. The Co and n dialogs in the pool parameter
window now update during the course of the simulation.

10. When objects with an attached plot are deleted, the plots are now also
deleted. There is also a warning issued when the user attempts to create
duplicate plots in the same graph. These fixes avoid a possible segmentation
violation, in addition to making things a bit smoother to work with.

11. I have made minor changes in the wording of the copyright notice, mainly
in the section about Models and Experiments. The message is the same, that
you cannot do biology without biological experiments. I hope it is a bit
more clearly stated.

