Herbert M. Sauro
Associate Professor
Department of Bioengineering
University of Washington |  |
At the group meetings each week there will be a dedicated discussion from one of the focus groups. Each group should self-organize and arrange a meeting when it is their turn. Discussion topics should include work accomplished or currently underway. The focus group may also mention any interesting or relevant papers related to the focus group and bring up topics of general interest to the focus group.
Group Members are as follows (in alphabetical order):
Computational Group
Frank Bergmann
Deepak Chandran
Lucian Smith
Alex Bratt
TBA
Experimental Group
Bryan Bartley
Wilbert Copland
Austin Day
Alec Nielsen
Sean Sleight
Theory Group
Alex Bratt
Deepak Chandran
Kyung Kim
Austin Day
TBA
Group Meeting Schedule for each Group:
| | Computational | Experimental | Theory |
| Dec 3rd | X | | |
| Dec 10th | | X | |
| Dec 17th | | | SNOW |
| Jan 9th | | | X |
| Jan 16th | X | | |
| Jan 23rd | | X | |
| Jan 30th | | | X |
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")
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.
QuickGraph
and a more bleeding edge library that uses WPF.
Dot2Wpf
Non-Graphviz graph layout library
GLEE
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
