

======================= ======================================
filename                used by 
======================= ======================================
adjacency_matrix.csv    adj2sif
adjacency_names.csv     adj2sif
data.sop                sop2sif
kinetic.csv             kinexus
MD-ToyMMB.csv           general
metabolites             Metabolites
PKN-ToyMMB.net          sif2asp
PKN-ToyMMB.sif          general
reactions               Reactions
test.sif
MD-one_exp              MIDAS with single experiment
MD-one_stimulus         MIDAS with single stimuli
MD-one_inhiibitor       MIDAS special case  
MD-unnorm.csv           MIDAS to test normalisation(time)
MD-unnorm_exp.csv       MIDAS to test normalisation(exp)
MD-Test.csv             Same as MD-ToyPB with NA
MD-Test2.csv            same as aboe with 2 cell lines
PKN-Test.sif            same as PKN-ToyPB but with nonc
MD-average.csv          test average over time
======================= ======================================

metabolites_samples:
    ExampleNetwIdent
    ExampleNetwIdentNoCrossT
    FasTnfTrail
    FusedLDPSN
    HepatHCCs
    LDPSN-DREAM
    LDPSN-DREAM-simpler
    LDPSN-Ingenuity
    LDPSN-IngenuityFourHCC
    LDPSN-IngenuityNeg
    LDPSN-Ingenuity-NoNeg
    LDPSN-Ingenuity-NoNeg-Extend
    LDPSN-Ingenuity-NoNeg-Extend1b
    LDPSN-Ingenuity-NoNegIns
    LDPSN-Ingenuity-NoNegIns4Rec
    LDPSN-IngenuityOldMod
    SchlatterApopt
    sigtoynet
    TcellReduced
    TcellSmall
    U937Signaling
