This is the Matlab automatization core script for simulationg metabolic networks. Under the auspecies of Dr. Ralf Steuer HU Berlin Master Bioinformatics student Raik Otto developt the software implementation as a whole while Dr. Ralf Steuer took care of the theoretical background.

Changelist

06_09_12
- Doc folder added

18_06_12
- added KMR, KMM
- Changed V0 to VM
- Deleted line "V0 = K;" in _Sim
- Changed all apparences of V0 to VM in the sim file
- Added the pertub_vec in order to force the network to find the fix point

01_04_12:
- added line '[J,EE] = Networkname_Jacobi() to the end'
- added copasi language binding for the jacobian
- second lsode is multiplied times 0.5 

26_03_12:
- Moved KREG vector to default
- Added header for default values
- Added spacer in the plot command
- Removed checks from scaled and unscaled simulation
- Excluded KREG_nh, vetors and or parameter links in the scaled part
- Added kernel check for N*V0'
- Wrote test file
- Changed check at the end of the ODE matlaf file according to Ralph

28_02_12:
- Changed error message on LibSBML
- switched EE*N to N*EE in Jacobi file
- Corrected Jacobian Matrix -> deleted REGA/REGI Terms in the product rule
- Inserted Parafile into Sim file and removed the Parafile from the network directory
- Removed KMR and KMM vectors from parafile
- Removed Jacobi link at the end of the simulation part
- Added checks for VM, S0, X0, concentration
- fixed the SBML stoichiometrical value different from kinetical bug. now it is correct like in the matlab file

29_01_12:
- added check if libSBML is installed, if not: error message
- Kix and Kax default in default.py added
- Kix and Kax modifiable by txt comman +n3S4_2 -> KAX = 2
- Fixed Kix and Kax reaction number problem
- SBML contains the manually set KAX and KIX values
- Added VM defaults - currently fixed to 1
- Added VM user defined values, appear in SBML and in the Sim file
- Added warning if a reaction contains an external metabolite and reaction type is nor irreversible, as well it changes the reaction type to reaction_type + 'IR'

To do list:
2. MA has only Keq, not Vm - unclear
5. Mysterious example with one liner does not work. double activation and inhibition
6. VM values dont appear in Parafile - okay?
7. Check for false input e.g. division by zero
9. Stoichiometry only works up to 9 -> change
10. KREG_nh part of default? - para in scaled simulation?