TESTS

NamerxnconBioNetGenSBMLjSBGN-ERSBGN-ERSBGN-PDComments
#0Phosphorylation (P+)
Kinase_P+_Target
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#1Dephosphorylation (P-)
Phosphatase_P-_Target
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The autogenerated SBML file from BioNetGen is "empty" since the initial state of the Target is "unphosphorylated"
#2Autophosphorylation (AP)
Kinase_AP_Kinase
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The correct layout of the SBGN-ER currently cannot be saved in jSBGN since this requires edges to point to EdgeHandles of edges and not just the edges itself
#3Phosphotransfer (PT)
PDonor_PT_PAcceptor
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Currently Biographer only support the import of the jSBGN - ER for this reaction. Layout has to be applied manually. SBML cannot be created automatically since the initial state of both proteins is unphosphorylated (see P- reaction).
#4Guanine Nucleotide Exchange (GEF)
GEF_GEF_GProt
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#6Ubiquitination (Ub+)
UbLigase_Ub+_Target
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#8Proteolytic cleavage (CUT)
Protease_CUT_Target
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#9Protein-protein interaction (ppi)
A_ppi_B
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#10Intra-protein interaction (ipi)
ProtA_[a]_ipi_ProtA_[b]
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#11interaction (i)
Ligand_i_Receptor
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#12DNA-binding (BIND)
TF_BIND_DNA
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#13Transcription (Trsc)
PolII_Trsc_Target
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#14Translation (Trsl)
Rib_TRSL_Target
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#15Degradation (DEG)
Proteasome_DEG_Protein
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#16Nuclear import (NIMP)
NIMP_NIMP_ProteinA
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Biographer has some problems exporting nodes in compartments at the right position
#17Reduced Mig1 Example
! Nexp-{Cytoplasm};! Nimp-{Cytoplasm}
! Mig1DNASite-{Nucleus}
! PolII-{Nucleus};! SUC2mRNA-{Nucleus}
Nexp_Nexp_Mig1; x Mig1--Mig1DNASite
Nimp_Nimp_Mig1
Mig1_Bind_Mig1DNASite; ! Mig1-{Nucleus}  
PolII_Trsc_SUC2; K- Mig1--Mig1DNASite
[SucroseUtilisation] ! SUC2mRNA
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