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# SCAMP for Unix or Mac ?

John Woods eanv20 at castle.ed.ac.uk
Tue Feb 1 04:01:50 EST 1994

a-kowald at nimr.mrc.ac.uk (Axel Kowald) writes:

>I am new to this list and have two questions.

>1. Where is the FAQ ?
>2. I heard about SCAMP but there seems to be only a version for IBMs.
>   Is there a mac or unix version available ??

2.  Yes.  SCAMP is written in C, so it runs on Unix.  (And presumably
on Mac --- you just have to compile it yourself).  Herbert Sauro (its
author) will be finalizing the new Unix version in a fortnight's time,
making it POSIX and ANSI compliant.

1.  I kind of gave up on the FAQ, as it generated very little
interest.  We didn't actually seem to have any questions for a period
of several consecutive months, let alone frequently asked ones!
Here's as far as it got.  If you want to make any suggestions (that
goes for *everybody*), please drop me a line.  I'm sorting out the
BTK-MCA archive listing any day now.

... John Woods

Contributions so far:
version 0.1 --- John Woods
version 0.2 --- Hans Westerhoff and John Woods
version 0.3 --- Joao Pedro Moniz Barreto, Simon Thomas, John Woods

(snip)-----8<-----8<-----8<-----8<-----8<-----8<-----8<-----8<----- (snip)

**********************************************************************
bionet.metabolic-reg/BTK-MCA FAQ --- version 0.3 930924103400

Discussion draft.  Please treat this document as the straw man it is
intended to be --- alterations and disccussion are urgently requested.

NB: I'm half-serious about the last sentence in point four.  If there
are enough objections I'll remove it, but I'd really rather not get
into philosophical nitpicking that might discourage future readers who
are more interested in biochemistry than semantics.  Not yet, anyway.

**********************************************************************

Section 1 --- about the newsgroup and mailing list
1.0) What is an FAQ?
1.1) Where can I get FAQs?
1.2) What is BTK-MCA/bionet.metabolic-reg for?
1.3) What is BioThermoKinetics?
1.4) What is Metabolic Control Analysis/Theory?
*	1.7) How should I format my messages and postings?
*	1.8) How should I format maths in my messages and postings?
*	2.1) What are the fundamentals of MCA?
*	2.2) What are the fundamental theorems of MCA?
*	2.3) What is the importance of the theorems in 2.1?
3.1) How do I make my yeast glycolize faster?  Pump up the PFK?
3.2) Is rubisco rate-limiting?

**********************************************************************

1.0) What is a FAQ?
An FAQ is a listing of Frequently Asked Questions.  It is
intended to prevent repeated discussion of certain points on
the newsgroup and to give newcomers a brief introduction to
the scope of the group.

1.1) Where can I get FAQs?
There is a machine around called rtfm.*.* (somebody fill in
the blanks please) which stocks the FAQs for most newsgroups.
But the one for this group isn't ready for inclusion yet, so
just watch for its sporadic posting in this group.

1.2) What is bionet.metabolig-reg for?
Discussion of topics concerning Metabolic Regulation/Control,
non-Equilibrium Thermodynamics, Kinetics, Biological Modelling,
Quantitative Bioenergetics, Biochemical Systems Theory and
Chanelling.

I quote form our initial charter:

 The International Study Group for BioThermoKinetics is an informal
group devoted to the quantitative understanding of the kinetics,
thermodynamics and control of biological processes at the cellular
level ... BTK meetings are aimed at providing a forum for a vivid
exchange of ideas between experimenters with a keen eye for
quantitative aspects, theoreticians with a keen eye for the
experimental practice and those in between.' (Preface, Programme for
5th BTK meeting) This mailing list [and newsgroup] is intended to
provide not only some continuity between the biennial meetings but
also to serve to propagate interest in the subjects covered.  Informal
participation is welcomed from all fields (and at all levels), and it
is particularly, but not exclusively, encouraged in the domain of
Metabolic Control Analysis --- the investigation of control in
biological systems.''

1.3) What is BioThermoKinetics?
Hans Westerhoff <hw at nki.nl> writes:

The International Study Group on BioThermoKinetics is a
loosely organized group of scientists interested in
the understanding of the energetics, kinetics, control and regulation
aspects of living cells.  The group started off with
the application of Non Equilibrium Thermodynamics
to Bioenergetics.  Much of its first interests was therefore
in mitochondria, chloroplasts and bacteria.  The interest was one
of doing more with experimental results than just plotting
them, i.e., view them in the light of theories based on sound
physical and chemical, 	and mathematical principles.  Also,
however, the intention is not to do theory just for theory's
sake;  the true challenge is felt to lie in the interface
between theory and experiment.

Soon it became clear that beyond equilibrium,
thermodynamics and kinetics are often two sides of the same
coin; kinetics of energy transducing systems (e.g., ion pumps)
became part of the field of interest. Subsequently the field
of metabolic control analysis began to flourish and as its
players had much the same interests in many the same
problems, it became an important topic of the BTK group.

The groups main activity is to organize a meeting every other year,
which is meant, above all, to stimulate discussion.  The most recent
meeting was in september 1992 near Bordeaux,  the next one will be
september 1994, near Innsbruck.
In principle, the group also organizes workshops.  One on
the modelling of cell physiology is in the makings.
of the BTK group: Hans V. Westerhoff:  HW at NKI.NL
FAX: +31 20 512 2029.

1.4) What is Metabolic Control Analysis/Theory?
Metabolic Control Analysis is the investigation into the mechanism
and distribution of control in metabolic, and conceivably other
biochemical systems.  Using certain theorems, it is possible
to relate the measurable *in vitro* properties of enzymes
and their effectors to the *in vivo* properties which
concern us.  As far as I am concerned, Metabolic Control
Analysis is the activity thus described, whilst Metabolic
Control Theory is the theoretical foundation on which it
rests.  (Very much like systems analysis is something done by
people who analyse systems, and systems theory is something
done by people who think more about systems analysis itself
than the analysis of particular systems).  Mileage differs
say, further discussion is discouraged. :-)

Try Fell, D. (1992) Biochem J. 286:313-330 for a recent review
and the references therein for more introductory material.

Anything related to metabolic regulation or BiothermoKinetics
as described above.  Give us a try!

* 1.7) How should I format my messages and postings?

Bear in mind that most people read news and mail items with
plain-text devices,  so only 7-bit ASCII in less than 80
columns is guaranteed to look the same to all people.

Do not assume that other  output devices will respond to tabs
in the same way that yours does --- use conventional spaces,
and rely on the fact that all characters are the same width.
Avoid wrap-aound problems --- unless you are sure that
your text-editor is putting explicit line ends in your
message, put them in yourself using the return key.
Do not assume a width any greater than 80 characters (70 for
preference) or any more than 24 lines of text to be
simulataneously visible.  And what looks like a
u-umlaut or e-acute to you will probably look like a Yen sign
or something horrible on devices configured to other
languages.  (German net.convention allows ue to be used in
place of u-umlaut (as in Muenchen), and a", o", u", e^, e', e
etc. are acceptable and reasonable obvious.

[Hint: use two spaces after periods (.) and colons (:), and
three dashes (---) to represent a long (em') dash for extra
readability.  For preference use a blank line to separate
to first line indentation.]

* 1.8) How should I format maths in my messages and postings?

Anything that is readily comprehensible, for preference well
spaced ASCII with any necessary explanations (such as saying
that d' stands for the partial delta, for example).

So, where Jq means J-subscript-q, Ep means E-subscript-p, and
d stands for the partial delta,  multiple definitions of the
Flux Control Coefficient for the Pth enzyme on the qth flux

could be written as:

Jq    d ln Jq    dJq Ep   dJq/Jq         %change in Jq
C   =  ------- =  --- -- = ------ = lim   -------------
Ep    d ln Ep    dEp Jq   dEp/Ep  %-->0  %change in Ep

A lot of MCA and BTK people use the LaTeX document processing
system.  Apart from the fact that braces ({}) group things together,
all you need to now is that underscore (_) means subscript and
circumflex (^) means superscript.  It's a lot easier than spacing
everything carefully in ascii.

or more simply as:

C_{E_p}^{J_q}

= {{d \ln J_q} \over {d \ln E_p}}

= {{dJ_q \over dE_p} {E_p \over J_q}}

= {{dJ_q/J_q} \over {dE_p/E_p}}

= {\lim_{\% \to 0} {{\ {\rm\;\%change\;in\;J_q}}
\over
{\ {\rm\;\%change\;in\;E_p}} }}

2.1) What are the fundamental theorems of MCA?

2.2) What is the importance of the theorems in 2.1?

3.1) How do I make my yeast glycolize faster?  Pump up the PFK?

3.2) Is rubisco rate-limiting?

--
"
Forsan et haec olim meminisse iuvabit (Virgil)
[approx] Tr: The time may come when we will look back on these days and laugh
"