Tutorial: visual mode

[Jay Hannah]

Questions, trying to follow the tutorial

http://www.bioinformatics.org/chemchains/wiki/Main/Tutorial#ntoc13

I assume the official release is the same as this SVN code:

http://mathbio.unomaha.edu/svn/chemchains/cpp/branches/CC1_0-rc1

True? So I'm trying to run what the tutorial says:

./ChemChains \
-ilogic inFiles/exts/CChain/logic/sampleNet.txt \
-ispecs inFiles/exts/CChain/logic/sampleNet.txt \
-vis myFirstSimulation.txt

But I think maybe that should read

./ChemChains \
-ilogic inFiles/CChain/logic/sampleNet.txt \
-ispecs inFiles/CChain/specs/sampleSpecs.txt \
-vis myFirstSimulation.txt

Which successfully creates

../CCoutput/myFirstSimulation.txt

which is rather boring until the Output nodes are activated in
sampleSpecs.txt. So I think the wiki needs to be altered for the
correct files/paths and perhaps Output nodes should be activated by
default so the tutorial works straight out of the box?

Just my $0.02. Cheers,

j