Date: December 1997
TALIS
----------------
Visual, interactive, real-time metabolic simulation
ANNOUNCEMENT: TALIS - Metabolic/Chemical Simulation Software
I am very pleased to announce the immediate availability of a beta
version of a new metabolic simulation package for Windows 95, codename
TALIS.
Main Features (not all necessarily available in beta version)
-------------
Talis has a number of unique features which will be of interest to
readers of this group:
1) Talis is entirely graphical in nature, that is metabolic pathways are
specified by drawing them on the screen using the mouse.
2) Talis offers live interaction with the simulated pathway. This means
you can modify parameters (Km, Vmax etc.) as the simulation runs and
observe the effect immediately.
3) Talis supports a number of so-called devices which allow specific
live interactions with the pathway under study.
4) Talis exposes much of its core functionality through a Tools Service
interface. This means anyone can write addon modules to enhance Talis'
feature set. Examples with complete source will be available upon
release of the final version.
Availability
------------
Talis is available now in a (very) pre-release version (0.8v) and is
freely available to all non-commerical application users. Commerical
users are free to evaluate Talis but may not use Talis for commercial
gain without express permission from the author (please read the licence
agreement in the readme file). Talis is a Windows 95, 32 bit
application, it has not been tested under Win NT. You will find the
program both computationally and graphically very demanding on your
computer hardware, I would therefore not recommend anything less than a
133MHz Pentium (although these days that's not much). I don't know what
the memory requirements are but I am sure 8MB must be a minimum, the
more the better - and it's not my fault.
A pre-release beta version of Talis is available now for download from:
http://www.fssc.demon.co.uk/Talis.htm
The .htm extension is VERY important, you won't get to the web site
without it. The WEB site is a bit thin on glitz so it's fairly basic.
You can also get it directly from the metabolic software ftp archive at:
ftp://bmsdarwin.brookes.ac.uk/pub/software/ibmpc/talis
Install Talis by executing the self-installing archive, tsetup.exe
Who is Talis aimed at?
----------------------
Version One of Talis is probably most suitable for introducing metabolic
dynamics to students. In it's present form it lacks many of the features
one would expect a full research package to offer, and also it not even
finished.
If you want a quick demonstration of what Talis can do then download it,
install it, and run it. Open the pathway called brus1.pth. Click on
the run button in the top right-hand corner of the screen and watch.
Features
--------
1. The drawing area for Talis pathways is virtually unlimited.
2. There is no limit to the number of reactions, metabolites or devices
in
a single model. The only thing that will limit the size of your model
is
therefore hardware, there are no software limits.
3. Two types of metabolite are supported (*), floating and fixed
boundary
pools. In the full version metabolites will have two visual
representations, either a simple name, e.g Fructose_6_Phosphate, or a
pictogram, e.g a green blob. Only the name representation is fully
implemented. There are a number of display characteristics of the
metabolites which can be changed including vertical or horizontal
mini-strips to display some state of the metabolite. If you've ever
played command and conquer or some similar game then you'll know what
I
mean.
(*) note: the term metabolite is used here in the general sense and
includes both 'metabolites', proteins or any entity which can be
represented by a concentration.
4. Four reactions types are currently supported (more will follow in
later
versions): UniUni, BiUni, UniBi and BiBi. Stoichiometries can however
be
freely modified, thus it is possible to model reactions such
as 2X + Y --> 3X. The limitation to BiBi is therefore not that
severe,
the only reason for this limitation is simply the time required to
write
necessary coding.
5. Reactions rate laws can be specified either from a list of pre-
defined laws
or you can enter your own.
6. Reactions arcs are drawn using one or more bezier curves, these have
selectable
control handles for fine adjustment.
7. Any thing on the display canvas can be dragged around until you're
happy with
the arrangement. Almost everything has right-mouse or double click
support.
This later point is actually very important as you'll notice that the
interface at start up appears quite minimal (this is intentional) and
some functions can only be accessed via the right-mouse popup menus.
8. Talis supports three types of devices, note that all devices can work
live:
a. Snoopers
b. Controllers
c. Injectors
In the current release the Injector series has not been implement, these
will become available as Talis approaches it's full version
specification.
9. Snoopers. As the name implies these devices can be used to display
the current states of the pathway. Three types are currently
available:
a. Simple, light-weight displays, eg bar strips and flow meters
(partially implemented)
b. A more elaborate bar-chart for displaying multiple charts
(not fully implmented)
c. Graph display. (very partially implemented!)
All snooper devices can display metabolite concentations, rates of
change,
fluxes or any combination expressed as an algebraic expression (e.g
S1+S2'+S3/Km)
10. Controllers. These devices (only one kind available at the moment)
can be used to control the values of model parameters. Thus you can
attach a controller to an enzyme reaction and use it to control the
amount of enzyme, a reaction's Km or a hill coefficient etc. In future
releases further controller types will be become available to enable
users to simulate experimental procedures (eg titration)
11. Injectors. Not yet implemented but when they are they will allow you
to add or remove mass from floating metabolite pools. Injectors will be
particuarly important for changing the mass in conserved moiety cycles.
12. Zoom and panning of the image.
13. Unlimited undo. What this means is if you accidently delete
glycolysis, you can get it back with a Ctrl Z.
14. Export SCAMP files (Import to be done soon).
15. Other things which I've forgotten or are too minor to mention here.
---------------------------
There is still much to be done to bring Talis up to its full release
state but I think the current version has enough functionality to make
it
a useful addition to the growing list of available metabolic software. I
also wanted to get something out by the end of Decemeber 1997 what ever
state it was in.
Things still to be implemented or completed:
1. Complete all devices, especially the Injectors.
2. New open-file dialog box with ability to preview pathways.
3. Include some addon example modules (with source), including a
reporting addon, an alignment addon and a stoichiometry analysis
addon.
4. Finalise the Tools Services interface - this will happen when I do
the above.
5. Import SCAMP files. I can probably do the same for other
simulators if I can get hold of their saved binary file formats.
6. Some sort of Help file.
7. Enhance the rate-law library with further built-ins and library
management
facility.
8. Visual indicators to show regulatory and signal pathways - if I can
sort out
a good algorithm - I think this is a must.
9. Elasticities for time simulation.
10. Control over the ODE integrator and ESPECIALLY initial condition
management
11. Access to raw simulation data for hard copy etc
12. Others things I've forgotten for the moment.
13. Suggestions from interested parties.
---------------------------------------------
Please note that the current release is NOT the final version, you will
find many things not working or only partially implmeneted, the current
release is definitely beta. There is much remaining work to do on the
program. I've been tinkering with it for almost a year and a half now
and rather than spend more time on it (which is very little at the best
of times) I've decided to distribute a pre-release version now.
Ccomments on usability and especially reports of bugs (!) will be much
appreciated - you may *even* find the program useful! If you do find a
bug then it is vital that you describe EXACTLY how you generated it
because if you want a fix then I need to be able to reproduce it on my
own machine. Bear in mind that no one has seen this program before other
myself so I'm probably in for many surprises and criticisms of interface
design - but that's one reason why I'm releasing it early for. There are
going to be some pretty obvious bugs and ommisions on first release,
some of these I am aware of already but report what ever you find.
Talis is a large and internally a very complex piece of software and
there are bound to be problems and interface inconsistencies. One thing
to bear in mind is that as I release updates I cannot guarantee that the
binary format of saved pathway files will remain the same from revision
to revision. I have build some redundancy into the saved format to try
to mitigate this problem, at this easrly stage I am sure I will have to
change the binary format of saved files. You can however export your
models as SCAMP files which you'll be able to import later on no matter
what version of Talis you have - so it's not quite the end of the world.
I have no plans to charge for Talis.
Version Two will commence once I've completed v1.0. The second version
will basically add all the metabolic control analysis support, so roll
on version One.
Have fun.
Herbert Sauro
December 1997
Comments, suggestions etc. to HSauro at fssc.demon.co.uk
The idea for Talis is something that has been on my mind for a long time
but I would like thank Dennis Bray for his interest and encouragement in
actually getting me started on this project a year and a half ago. I
would also of course like to thank the UK Science Funding establishment
for
their foresight, their immense generousity and unwavering support,
without which this project would never have got this far - ok, I lie,
that last sentence is not quite true.
------------------------------------------------------------------------
Permanent Address:
Herbert Sauro
Penrodyn
Pontrhydygroes
Ystrad Meurig
Ceredigion
United Kingdom
SY25 6DP
Current location (until May 98):
Herbert Sauro
2F3, 19 Yeaman Place
Polwarth
Edinburgh
Scotland
EH11 1BS
Tel: 0131 229 3383 (evenings); 0131 220 3993 (day time)
Permanent email:
HSauro at fssc.demon.co.uk
--
Herbert M Sauro
email: HSauro at fssc.demon.co.uk
Telephone: 01974 282428
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"He who cannot draw on 3000 years is living from hand to mouth" Goethe
"Ah, but a man's reach should exceed his grasp, or what's a heaven for?"
R Browning.
