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.

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.

Notes for users of kkit 1.2
---------------------------

Changes from version 1.2  (provided with GENESIS 2.1)
1. Duplicate button added to make a copy of an object in the edit window.
2. Several improvements to the interface.  For example, graphs automatically
    extend the time axis when 'start' is clicked again for a further time run.
3. Several bug fixes.

kkit 6 and 7 should be compatible with dump files (saved models) created under
previous versions.

Notes for users of kkit 1.1
---------------------------

Changes from version 1.1
1. New tool added for comparing models
2. The 'Cooperative reactions' label has been corrected to 'Higher order'
        reactions.
3. Options added to directly modulate kf and kb for reactions.
4. Sundry updates to the 'Help' file, and minor bugfixes.
5. Tutorial document. This also appears in revised form in the Book
        of Genesis, 2nd edition.

Models saved using the kkit1.1 will load normally into this version, and
most files written with this version will load into kkit1.1 in the unlikely
event that you want to go backwards.

Notes for users of kkit 1.0
---------------------------

Changes from version 1.0
1. Added facility to allow batch-mode (no graphics) running for models.
2. Greatly improved documentation in the help file.
3. Improved implementation of the xtab, including file loading and more
        waveform manipulation options.
4. The kinetics library is now set up to compile as a user library, rather
        than as part of the main Genesis code tree.

Users of the earlier 1.0 release of kkit will not have to make any GENESIS
code changes to get it to run if they are in a hurry, but there are
recommended changes for some of the newer features to work properly.
Also, a number of bugs in the old code have been fixed.
Models saved using the old kkit will load normally into this version, and
most files written with this version will load into the old one.
