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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.


Table of contents (sketchy)  --- * indicates changes from previous version

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?
	1.5) What should I read?
	1.6) What should I ask?
*	1.7) How should I format my messages and postings?
*	1.8) How should I format maths in my messages and postings?
Section 2 --- about MCT
*	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?
Section 3 --- about MCA
	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

	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.
	For further information please contact the acting chairman 
	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
	greatly in the newsgroup about this issue, and now I've had my
	say, further discussion is discouraged. :-)

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

1.6) What should I ask?
	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 
	paragraphs, either instead of (preferred) or in addition
	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:


= {{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}}
{\ {\rm\;\%change\;in\;E_p}} }}

Section 2 --- about MCT

2.1) What are the fundamental theorems of MCA?

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

Section 3 --- about MCA

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

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