498_systems_and_synthetic_biology_winter_2009

August 2009 Physiology Course

304 Engineering Physiology 2009

498 Systems and Synthetic Biology Spring 2008

304 Engineering Physiology

The role of Software and Standards in the Design and Construction of Synthetic Networks

The Sauro Lab meets regularly for group meetings. Since we have grown in size, they are split up into three focus groups. Have a look at the detailed schedule.

Sizes Of Things

See papers

Acerenza et al, Control Analysis of Time-dependent Metabolic Systems. JTB paper from 1989

Studies on Complex Enzyme Systems by J. A. Burns

Follow this link to download Jim Burns' Thesis.

From THE GROWTH OF BACTERIAL CULTURES BY JACQUES MONOD Annu. Rev. Microbiol. 1949.3:371-394.

“It has often been assumed that the over-all rate of a system of linked reactions may be governed by the slowest, or master, reaction. That this conception should be used, if at all, with extreme caution, has also been emphasized (17, 18). On theoretical grounds, it can be shown that the over-all rate of a system of several consecutive reversible enzymatic reactions depends on the rate and equilibrium constant of each. The reasons for this are obvious, and we need not go into the mathematics of the problem. A master reaction could take control only if its rate were very much slower than that of all the other reactions. Where hundreds, perhaps thousands, of reactions linked in a network rather than as a chain are concerned, as in the growth of bacterial cells, such a situation is very improbable and, in general, the maximum growth rate should be expected to be controlled by a large number of different rate-determining steps.”

Suárez Miranda, Viajes de varones prudentes, Libro IV, Cap. XLV, Lérida, 1658

Borges, J. L. 1998. On exactitude in science. P. 325, In, Jorge Luis Borges, Collected Fictions (Trans. Hurley, H.) Penguin Books.

“On Exactitude in Science

… In that Empire, the Art of Cartography attained such Perfection that the map of a single Province occupied the entirety of a City, and the map of the Empire, the entirety of a Province. In time, those Unconscionable Maps no longer satisfied, and the Cartographers Guilds struck a Map of the Empire whose size was that of the Empire, and which coincided point for point with it. The following Generations, who were not so fond of the Study of Cartography as their Forebears had been, saw that that vast Map was Useless, and not without some Pitilessness was it, that they delivered it up to the Inclemencies of Sun and Winters. In the Deserts of the West, still today, there are Tattered Ruins of that Map, inhabited by Animals and Beggars; in all the Land there is no other Relic of the Disciplines of Geography.”

Here the instructions on how to create a news entry:

1. Create a new page under: http://www.sys-bio.org/sbwWiki/sysbio-news/ (say http://www.sys-bio.org/sbwWiki/sysbio-news/someNews )

2. Fill this page with the paragraph for the news entry.

 NOTE: do not use fancy formatting for this one, as it will be stripped

out

 (say "Some new news here" )

3. When saving the page, put the NEWS title as comment for the edit of the page

 (say "Some News")

Wang's Latex Introduction

JabRef - Bibtex Reference Manager

Cambridge Latex Page Many useful links

Well presented tutorials on PSTricks

TeX showcase site

PSTricks: PsTricks Web Site Wikipedia PSTricks Site

Case Study(LaTeX) in Open Source Software

After having worked though many different approaches to adding good looking and relatively maintainable graphics in LaTeX I have settled on the following tools.

tikz/pgf: “PGF is a macro package for creating graphics. It is platform- and format-independent and works together with the most important TeX backend drivers, including pdftex and dvips. It comes with a user-friendly syntax layer called TikZ.”. I would also recommend looking at some add-ons to tikz by someone called Alain Matthes. He has a number of different and interesting extensions including additional plotting support and networks diagrams.

tikz/pfg

Alain Matthes

Asymptote: “Asymptote is a powerful descriptive vector graphics language that provides a natural coordinate-based framework for technical drawing. Labels and equations are typeset with LaTeX, for high-quality PostScript output.” Asymptote is a sort of easy to use version of metapost. The syntax is more straight forward than metapost.

Asymptote

Both tools allow one to include the graphics commands directly in the LaTeX script. Both tools are actively maintained and continue to improve.

Interesting site on Newton Methods: Nunerical Methods Institute

Home of NLEQ etc: zlib

Continuation Algorithms (Though may not work on windows): LOCA

Analog Computers

Building an Analog Computer

Commerical Analog Computer Site

DukiWiki

YACC/LEX for C# from Queensland University

YACC for C#

LEX for C#

NDoc for .NET 1.1

NDoc for .Net 2.0

SandcastleGUI

NDoc like GUI for running MS Sandcastle

and how to use it:

Using Sandcastle Help Builder

Source Documentation in .NET 2.0

QuickGraph

and a more bleeding edge library that uses WPF.

Dot2Wpf

Non-Graphviz graph layout library

GLEE

Network Enumeration

SCAMP

What is SCAMP? SCAMP is a general purpose simulator of metabolic and chemical networks. It is based around a simple metabolic language. The version of SCAMP available here is the PC version. Other versions may be available at other sites. The PC executable is a full 32-bit application that can be run from Windows or the DOS command line. A manual in LaTex format is also available here. Other text formats (e.g. Postscript) may be available at other sites.

To give you an idea of what a SCAMP command file looks like, here's an example:

Example model:

Title An example;

# Any text starting with a hash is a comment;

simulate;
dec A, B, C; # declare chemical species;

reactions
A + B - C; k1*A*B - k2*C;
C - A; k3*C;
eor;

initialise
A = 1.0; B = 0.2; C = 0;
k1 = 1.2; k2 = 0.6; k3 = 15;
ei;

print_sim TIME, A, B, C (results);
end

SCAMP's primary function is to enable users to carry out metabolic control analysis calculations, such as computing control coefficients and elasticities. A summary of features include:

• Specify reactions using natural biochemical notation, virtually any reaction mechanism can be specified in this manner.
• Use your own rates laws or use the predefined rate laws.
• Enter differential equations directly rather than using reaction mechanisms, i.e use SCAMP as a differential equation solver.
• No program limit to size of model, i.e. number of metabolites, reactions etc.
• Metabolite species may have non-unit volume spaces.
• Possible analyses: time simulation, steady-state and continuation (multi-steady state analysis)
• Conserved cycle analysis including auto-reduction of model dimensionality and mass parameters made available to user automatically.
• Compute elasticities and control coefficients with respect to any variable and any parameters. Evaluation either by modulation or Reder analysis.
• Internal Jacobian and elasticities can be computed numerically or by exact symbolic differentiation.
• Supports forcing functions which allows user to precisely control models' environment.
• Full monitoring and if/then controls within language
• All relevant model indices available to user, e.g. fluxes, rates of change….
• Large selection of built-in numerical methods which can be called up by user to make SCAMP adaptable to most problems
• Its free….

References:

OLD REF: Sauro, H. M & Fell, D. A (1991) SCAMP: A Metabolic Simulator and Control Analysis Program. Mathl. Comput. Modelling Vol 15, No. 12, pp. 15-28

Sauro, H. M (1993) SCAMP: a general-purpose simulator and metabolic control analysis program. CABIOS, Vol 9, no. 4, Pages 441-450

This page was last modified on July 25, 1999

Other Work