Analysis Capabilities of ecellJ
ecellJ can currently
calculate the stoichiometric matrix, both incluing the fixed species, and
not including them. The matrix is output in Mathematica® format
and directly copied to the clipboard for pasting into Mathematica®
or any other application.
determine the conserved quantities from the stoichiometric matrix. This
is given by the nullspace or kernel of the matrix, which is converted into
a representation involving as many zero entries as possible to present
an easily readable format. Note: Currently, only non-negative conservation relations are calculated,
using the algorithm given By Heinrich and Schuster (1996).
create a Super-reactor from the presence of instances of "SlaveReactor".
The Super-reactor includes all slave reactors as unknown reactions, a list
of all substances involved in these reactors, and all reactions involving
these substances as known reactions. Currently, a check for connectedness
is performed, but the separation into multiple connected components is
not yet done.
Jörg R. Weimar 11.3.2003