SimBiology extends MATLAB with tools for modeling, simulating, and analyzing biochemical pathways. You can create your own block diagram model using predefined blocks. You can manually enter in species, parameters, reactions, rules, kinetic laws, and units, or read in Systems Biology Mark-Up Language (SBML) models. SimBiology lets you simulate a model using stochastic or deterministic solvers and analyze your pathway with tools such as parameter estimation and sensitivity analysis.First get the following MATLAB ISO images at ftp://pxe/software/Matlab2006b (perhaps only available for LAN of USTC)
mount these images and enter the directory where you want to install matlab, create a matlab directory ($MATLAB).
Copy the license file from the first CD. There two license files in CD1/crack license_locked.dat license_server.dat. I copy license_locked.dat to $MATLAB and rename it license.dat. Enter $MATLAB
run CD1/install. The graphic interface is easy to complete.
When I finished the normal install and tried to run matlab. It poped a very lengthy error message java.lang.ExceptionInInitializerError at com.mathworks.mde.filebrowser.FileBrowser.(FileBrowser.java:92) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
and collapsed thereafter. But if I run matlab -nojvm, it worked normally.
Solution: the java compiler that comes together with MATLAB caused the above error. Replace it with my own version of java (jre1.5.0_06)
PS: kkk recommended another standalone software, Copasi, to build and simulate biomedical networks. Have a look at it.
run CD1/install. The graphic interface is easy to complete.
When I finished the normal install and tried to run matlab. It poped a very lengthy error message java.lang.ExceptionInInitializerError at com.mathworks.mde.filebrowser.FileBrowser.
and collapsed thereafter. But if I run matlab -nojvm, it worked normally.
Solution: the java compiler that comes together with MATLAB caused the above error. Replace it with my own version of java (jre1.5.0_06)
cd $MATLAB/sys/javaAnd then MATLAB works now. Bingo!
mv java java-backup
ln -s path_of_your_own_java java
PS: kkk recommended another standalone software, Copasi, to build and simulate biomedical networks. Have a look at it.
COPASI is a software application for simulation and analysis of biochemical networks. COPASI — a COmplex PAthway SImulator. Bioinformatics 22, 3067-74.
Current Features:
- Stochastic and deterministic time course simulation
- Steady state analysis (including stability)
- Metabolic control analysis / sensitivity analysis
- Elementary mode analysis
- Mass conservation analysis
- Calculation of Lyapunov exponents
- Parameter scans
- Optimization of arbitrary objective functions
- Parameter estimation using data from time course and/or steady state experiments
- Sliders for interactive parameter changes
- Global parameter to change multiple kinetic rates at once
- Imports and exports SBML (export only in level 2 version 1, import all levels)
- Loads Gepasi files
- Export in Berkeley Madonna format and C source code of the ODE system generated from the chemical reactions
- Versions for MS Windows, Linux, OS X, and Solaris SPARC
- Command line version for batch processing
- Visit this page often, new releases will contain many more features!
No comments:
Post a Comment