- Download and install the Systems Biology Workbench (SBW) from sbw.sourceforge.net. Read some background information about what it is and how it works.
This is a modular software system
designed to allow separate modelling and simulation tools to
work together in a unified way using a central broker for
passing massages from one software component to another. It
is conventional to use SBML for passing models from one
component to another, but not compulsory.
- If the JDesigner module is not included with the installation,
download that from the SBW modules page and install that
too. Load up SBW and JDesigner to see if they work. Read any
documentation/help you can find.
JDesigner is a graphical model-building tool that imports and exports
models in SBML. It can be used stand-alone, but is also
designed to work as a SBW module, and can be used in
conjunction with both deterministic and stochastic SBW
simulation modules.
- Use JDesigner to build the auto-regulatory network example from
Lecture 2. Build and save both the simple version given in the
lectures and the more detailed version you developed
later.
- Save both models as SBML. Load up the SBML into a text editor and
understand the code. Also understand the additional tags that
JDesigner uses to annotate the SBML with information about the
graphical representation.
Compare and contrast the generated SBML with the hand-crafted
example from the lecture, available here with either a local or global parameter list (you may need to
shift-click to download) - note that these models are SBML Level 1 - see my book web site for Level 2 (first edition) and 3 (second edition) versions.
- Go to the SBML home page (www.sbml.org), try out the on-line
model-validation tool, and download some other model-building tools
(CellDesigner and COPASI are very popular). Try using them to build models - compare and contrast
with JDesigner. Save the models as SBML and compare it with that
generated by JDesigner. Also try loading models from JDesigner into
the new tools and try importing models from the new tools into
JDesigner. If it doesn't work, try fixing the SBML code by hand so it
does. Try importing the above hand-crafted SBML files into the various
packages.
- Try downloading and importing some SBML models from the BioModels Database if you
have time. Also look at/try out some example models from my
book.