add biosim_class

Products from Bio Simulation course
Kyoto model with Lambeth Glycogenolysis model

CytoplasmAssigmentProcess.cpp was updated to calculate and assign
concentrations of NAD and NADH in cytoplasm. Please use
amano_et_al_2009_121029.em and set @{Glycolysis = 'OFF'} to exclude
Lambeth model from the Kyoto model.
Minor change

Set oxygen concentration to 0.24 mM. Please set it to 0 to simulate
anoxic condition.
Minor change

Value of kfCK was fixed.
Bug fix
Bug fix
Luo-Rudy model update

Added IKATP, IKNa, and I_ns_Ca to the model.
chalhoub_2007 update

implement flux between upstream (Ci*) and blood. represented the steady
state of Table 1.
CrossFireProcess added (incomplete)
CrossFireProcess works now.
CrossFireProcess README corrected
CrossFireProcess README minor revision
CrossFireProcess README correction
CrossFireProcess_Test.em minor revison

Process name changed.
AGSProcess.cpp
AGSProcess.cpp reviewed
Adjust kuzumoto_et_al_2007_2.5Hz.em to CytoplasmAssignmentProcess

Change kuzumoto_et_al_2007_2.5Hz.em to adjust
CytoplasmAssignmentProcess revison by ducky-sfc in commit
ca6da9fde4188d1037cc2899e08d83bdb5b971ae
Discharge gsl_root_fsolve in IsotonicContraction

Replace gsl_root_fsolve with differential equations of motion in
IsotonicContraction module.
IsotonicContractionモデル中で、hSMLを代数方程式の求根で求めるのを廃止。代わりに運動方程式を微分方程式で解くようにした。バ
ネの質量に相当するパラメータKmは従来のモデルのシミュレーション結果から概算して 0.01 としているが、最適ではないかもしれない。
Fix NaN occurence in Mitochondria

Modify MitochondriaAssignmentProcess.cpp and Mitochondria.em. NaN
occurence is fixed.
Modify IsotonicContractionAssignmentProcess.cpp

Modify IsotonicContractionAssignmentProcess.cpp to avoid NaN generation
when X value is low.