Add new tool: PyDrugLogics

colomoto · Nov 20, 2024 · 1782b5a · 1782b5a
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diff --git a/.idea/.gitignore b/.idea/.gitignore
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
diff --git a/Dockerfile b/Dockerfile
@@ -154,6 +154,7 @@ RUN AUTO_UPDATE=1 conda install --no-update-deps -y \
         mpbn=3.8=py_0 \
         nordic=2.5.0=py_0 \
         pyactonet=1.0=py_0 \
+        szlaura::pydruglogics=0.1.8=py_0 \
         pymaboss=0.8.9=py_0 \
         pypint=1.6.3=py_0 \
         pystablemotifs=3.0.6=py_0 \

diff --git a/tools/pydruglogics.md b/tools/pydruglogics.md
@@ -0,0 +1,34 @@
+---
+name: Tool Name
+homepage: https://...
+release_url: https://github.com/YYY/XXX/releases/tag/v{}
+summary: Short summary
+interface: Python module [`xxx`](https://API)    # xxx=Python module to import, API=url for documentation
+package_contact: Name <email>
+pyface_package: pyxxx    # pyface: secondary package for python interface
+pyface_name: PyXXX       # remove pyface_* lines if none.
+pyface_release_url: https://github.com/YYY/pyXXX/releases/tag/v{}
+---
+
+# Tool Name
+
+:::admonition
+Webpage: https://github.com/druglogics/pydruglogics
+:::
+
+PyDrugLogics is a Python package designed for constructing, optimizing Boolean Models and performs in-silico perturbations of the models.
+
+Core Features
+- Construct Boolean model from .sif file
+- Load Boolean model from .bnet file
+- Optimize Boolean model
+- Generate perturbed models
+- Evaluate drug synergies
+
+````{admonition} Notebooks
+:class: seealso
+
+```{tableofcontents}
+```
+
+````
diff --git a/tutorials/PyDrugLogics/example_models/e10_s1.bnet b/tutorials/PyDrugLogics/example_models/e10_s1.bnet
@@ -0,0 +1,80 @@
+# 2024_11_10, 2019
+# Evolution: 10 Solution: 1
+# Fitness Score: 0.998
+Antisurvival, ((CASP3) | FOXO_f)
+CASP3, ((CASP8) | CASP9)
+FOXO_f, !((AKT_f) | NLK)
+Prosurvival, ((CCND1) | MYC)
+CCND1, ((TCF7_f) | RSK_f)
+MYC, (TCF7_f)
+RAC_f, ((DVL_f) | mTORC2_c)
+mTORC2_c, (TSC_f) | !(S6K_f)
+DVL_f, (FZD_f)
+MAP3K4, (RAC_f)
+MAP3K11, (RAC_f)
+MAP2K4, ((((GRAP2) | MAP3K7) | MAP3K11) | MAP3K4)
+MAP3K7, (TAB_f)
+GRAP2, !(MAPK14)
+MAP2K7, ((GRAP2) | MAP3K7)
+JNK_f, ((MAP2K4) | MAP2K7) & !(DUSP1)
+DUSP1, ((MAPK14) | MSK_f)
+MAPK14, ((MAP2K4) | MAP2K3) | !(DUSP1)
+MAP2K3, ((MAP3K5) | MAP3K7)
+MAP3K5, !(AKT_f)
+AKT_f, ((PDPK1) | mTORC2_c)
+TAB_f, !(MAPK14)
+MSK_f, ((MAPK14) | ERK_f)
+RTPK_f, ((MMP_f) | RTPK_g) | !((MAPK14) | MEK_f)
+RTPK_g, (FOXO_f)
+MEK_f, ((MAP3K8) | RAF_f) | !(ERK_f)
+SHC1, (RTPK_f) & !(PTEN)
+PTEN, (PTEN_g) & !(GSK3_f)
+GRB2, (SHC1)
+SOS1, (GRB2) & !(ERK_f)
+ERK_f, (MEK_f) | !(DUSP6)
+KRAS, ((PTPN11) | SOS1)
+PTPN11, (GAB_f)
+RAF_f, (KRAS) | !(((ERK_f) | AKT_f) | RHEB)
+RHEB, !(TSC_f)
+MAP3K8, (IKBKB)
+DUSP6, ((ERK_f) | mTORC1_c)
+mTORC1_c, ((RSK_f) | RHEB) & !(AKT1S1)
+GAB_f, (GRB2) | !(ERK_f)
+RSK_f, ((ERK_f) | PDPK1)
+PDPK1, (PIK3CA) | !(PTEN)
+PIK3CA, (((GAB_f) | IRS1) | KRAS)
+IRS1, !(((ERK_f) | IKBKB) | S6K_f)
+S6K_f, ((PDPK1) | mTORC1_c)
+IKBKB, (MAP3K7) | !(TP53)
+PTEN_g, (EGR1)
+GSK3_f, !(((((((MAPK14) | AKT_f) | RSK_f) | S6K_f) | ERK_f) | LRP_f) | DVL_f)
+TSC_f, (GSK3_f) & !((((ERK_f) | AKT_f) | IKBKB) | RSK_f)
+TP53, (MAPK14) & !(MDM2)
+AKT1S1, !(AKT_f)
+MDM2, ((AKT_f) | MDM2_g) | !(S6K_f)
+MDM2_g, ((NFKB_f) | TP53)
+BAX, (TP53)
+CYCS, (BAX) & !(BCL2)
+BCL2, !(BAD)
+BAD, !((AKT_f) | RSK_f)
+NLK, (MAP3K7)
+CASP9, (CYCS)
+CASP8, !(CFLAR)
+CFLAR, (AKT_f) | !(ITCH)
+ITCH, (JNK_f)
+FZD_f, !(SFRP1)
+SFRP1, (SFRP1_g)
+LRP_f, ((((ERK_f) | MAPK14) | JNK_f) | FZD_f) | !(DKK_f)
+DKK_f, (DKK_g)
+AXIN1, !(LRP_f)
+CK1_f, !(LRP_f)
+BTRC, (((GSK3_f) | CK1_f) | AXIN1)
+CTNNB1, (CHUK) & !(BTRC)
+CHUK, (AKT_f)
+TCF7_f, (CTNNB1) | !(NLK)
+EGR1, !(TCF7_f)
+DKK_g, (TCF7_f) | !(MYC)
+SFRP1_g, !(MYC)
+NFKB_f, (((CHUK) | IKBKB) | MSK_f)
+LEF, (CTNNB1)
+MMP_f, (LEF)
diff --git a/tutorials/PyDrugLogics/example_models/e10_s2.bnet b/tutorials/PyDrugLogics/example_models/e10_s2.bnet
@@ -0,0 +1,80 @@
+# 2024_11_10, 2019
+# Evolution: 10 Solution: 2
+# Fitness Score: 0.957
+Antisurvival, ((CASP3) | FOXO_f)
+CASP3, ((CASP8) | CASP9)
+FOXO_f, !((AKT_f) | NLK)
+Prosurvival, ((CCND1) | MYC)
+CCND1, ((TCF7_f) | RSK_f)
+MYC, (TCF7_f)
+RAC_f, ((DVL_f) | mTORC2_c)
+mTORC2_c, (TSC_f) | !(S6K_f)
+DVL_f, (FZD_f)
+MAP3K4, (RAC_f)
+MAP3K11, (RAC_f)
+MAP2K4, ((((GRAP2) | MAP3K7) | MAP3K11) | MAP3K4)
+MAP3K7, (TAB_f)
+GRAP2, !(MAPK14)
+MAP2K7, ((GRAP2) | MAP3K7)
+JNK_f, ((MAP2K4) | MAP2K7) | !(DUSP1)
+DUSP1, ((MAPK14) | MSK_f)
+MAPK14, ((MAP2K4) | MAP2K3) & !(DUSP1)
+MAP2K3, ((MAP3K5) | MAP3K7)
+MAP3K5, !(AKT_f)
+AKT_f, ((PDPK1) | mTORC2_c)
+TAB_f, !(MAPK14)
+MSK_f, ((MAPK14) | ERK_f)
+RTPK_f, ((MMP_f) | RTPK_g) | !((MAPK14) | MEK_f)
+RTPK_g, (FOXO_f)
+MEK_f, ((MAP3K8) | RAF_f) | !(ERK_f)
+SHC1, (RTPK_f) | !(PTEN)
+PTEN, (PTEN_g) | !(GSK3_f)
+GRB2, (SHC1)
+SOS1, (GRB2) | !(ERK_f)
+ERK_f, (MEK_f) | !(DUSP6)
+KRAS, ((PTPN11) | SOS1)
+PTPN11, (GAB_f)
+RAF_f, (KRAS) & !(((ERK_f) | AKT_f) | RHEB)
+RHEB, !(TSC_f)
+MAP3K8, (IKBKB)
+DUSP6, ((ERK_f) | mTORC1_c)
+mTORC1_c, ((RSK_f) | RHEB) | !(AKT1S1)
+GAB_f, (GRB2) | !(ERK_f)
+RSK_f, ((ERK_f) | PDPK1)
+PDPK1, (PIK3CA) | !(PTEN)
+PIK3CA, (((GAB_f) | IRS1) | KRAS)
+IRS1, !(((ERK_f) | IKBKB) | S6K_f)
+S6K_f, ((PDPK1) | mTORC1_c)
+IKBKB, (MAP3K7) | !(TP53)
+PTEN_g, (EGR1)
+GSK3_f, !(((((((MAPK14) | AKT_f) | RSK_f) | S6K_f) | ERK_f) | LRP_f) | DVL_f)
+TSC_f, (GSK3_f) | !((((ERK_f) | AKT_f) | IKBKB) | RSK_f)
+TP53, (MAPK14) | !(MDM2)
+AKT1S1, !(AKT_f)
+MDM2, ((AKT_f) | MDM2_g) | !(S6K_f)
+MDM2_g, ((NFKB_f) | TP53)
+BAX, (TP53)
+CYCS, (BAX) & !(BCL2)
+BCL2, !(BAD)
+BAD, !((AKT_f) | RSK_f)
+NLK, (MAP3K7)
+CASP9, (CYCS)
+CASP8, !(CFLAR)
+CFLAR, (AKT_f) | !(ITCH)
+ITCH, (JNK_f)
+FZD_f, !(SFRP1)
+SFRP1, (SFRP1_g)
+LRP_f, ((((ERK_f) | MAPK14) | JNK_f) | FZD_f) | !(DKK_f)
+DKK_f, (DKK_g)
+AXIN1, !(LRP_f)
+CK1_f, !(LRP_f)
+BTRC, (((GSK3_f) | CK1_f) | AXIN1)
+CTNNB1, (CHUK) | !(BTRC)
+CHUK, (AKT_f)
+TCF7_f, (CTNNB1) | !(NLK)
+EGR1, !(TCF7_f)
+DKK_g, (TCF7_f) | !(MYC)
+SFRP1_g, !(MYC)
+NFKB_f, (((CHUK) | IKBKB) | MSK_f)
+LEF, (CTNNB1)
+MMP_f, (LEF)
diff --git a/tutorials/PyDrugLogics/example_models/e10_s3.bnet b/tutorials/PyDrugLogics/example_models/e10_s3.bnet
@@ -0,0 +1,80 @@
+# 2024_11_10, 2019
+# Evolution: 10 Solution: 3
+# Fitness Score: 0.915
+Antisurvival, ((CASP3) | FOXO_f)
+CASP3, ((CASP8) | CASP9)
+FOXO_f, !((AKT_f) | NLK)
+Prosurvival, ((CCND1) | MYC)
+CCND1, ((TCF7_f) | RSK_f)
+MYC, (TCF7_f)
+RAC_f, ((DVL_f) | mTORC2_c)
+mTORC2_c, (TSC_f) | !(S6K_f)
+DVL_f, (FZD_f)
+MAP3K4, (RAC_f)
+MAP3K11, (RAC_f)
+MAP2K4, ((((GRAP2) | MAP3K7) | MAP3K11) | MAP3K4)
+MAP3K7, (TAB_f)
+GRAP2, !(MAPK14)
+MAP2K7, ((GRAP2) | MAP3K7)
+JNK_f, ((MAP2K4) | MAP2K7) | !(DUSP1)
+DUSP1, ((MAPK14) | MSK_f)
+MAPK14, ((MAP2K4) | MAP2K3) | !(DUSP1)
+MAP2K3, ((MAP3K5) | MAP3K7)
+MAP3K5, !(AKT_f)
+AKT_f, ((PDPK1) | mTORC2_c)
+TAB_f, !(MAPK14)
+MSK_f, ((MAPK14) | ERK_f)
+RTPK_f, ((MMP_f) | RTPK_g) | !((MAPK14) | MEK_f)
+RTPK_g, (FOXO_f)
+MEK_f, ((MAP3K8) | RAF_f) | !(ERK_f)
+SHC1, (RTPK_f) | !(PTEN)
+PTEN, (PTEN_g) | !(GSK3_f)
+GRB2, (SHC1)
+SOS1, (GRB2) | !(ERK_f)
+ERK_f, (MEK_f) | !(DUSP6)
+KRAS, ((PTPN11) | SOS1)
+PTPN11, (GAB_f)
+RAF_f, (KRAS) | !(((ERK_f) | AKT_f) | RHEB)
+RHEB, !(TSC_f)
+MAP3K8, (IKBKB)
+DUSP6, ((ERK_f) | mTORC1_c)
+mTORC1_c, ((RSK_f) | RHEB) | !(AKT1S1)
+GAB_f, (GRB2) | !(ERK_f)
+RSK_f, ((ERK_f) | PDPK1)
+PDPK1, (PIK3CA) | !(PTEN)
+PIK3CA, (((GAB_f) | IRS1) | KRAS)
+IRS1, !(((ERK_f) | IKBKB) | S6K_f)
+S6K_f, ((PDPK1) | mTORC1_c)
+IKBKB, (MAP3K7) | !(TP53)
+PTEN_g, (EGR1)
+GSK3_f, !(((((((MAPK14) | AKT_f) | RSK_f) | S6K_f) | ERK_f) | LRP_f) | DVL_f)
+TSC_f, (GSK3_f) & !((((ERK_f) | AKT_f) | IKBKB) | RSK_f)
+TP53, (MAPK14) & !(MDM2)
+AKT1S1, !(AKT_f)
+MDM2, ((AKT_f) | MDM2_g) | !(S6K_f)
+MDM2_g, ((NFKB_f) | TP53)
+BAX, (TP53)
+CYCS, (BAX) | !(BCL2)
+BCL2, !(BAD)
+BAD, !((AKT_f) | RSK_f)
+NLK, (MAP3K7)
+CASP9, (CYCS)
+CASP8, !(CFLAR)
+CFLAR, (AKT_f) | !(ITCH)
+ITCH, (JNK_f)
+FZD_f, !(SFRP1)
+SFRP1, (SFRP1_g)
+LRP_f, ((((ERK_f) | MAPK14) | JNK_f) | FZD_f) | !(DKK_f)
+DKK_f, (DKK_g)
+AXIN1, !(LRP_f)
+CK1_f, !(LRP_f)
+BTRC, (((GSK3_f) | CK1_f) | AXIN1)
+CTNNB1, (CHUK) & !(BTRC)
+CHUK, (AKT_f)
+TCF7_f, (CTNNB1) | !(NLK)
+EGR1, !(TCF7_f)
+DKK_g, (TCF7_f) | !(MYC)
+SFRP1_g, !(MYC)
+NFKB_f, (((CHUK) | IKBKB) | MSK_f)
+LEF, (CTNNB1)
+MMP_f, (LEF)
diff --git a/tutorials/PyDrugLogics/example_models/e1_s1.bnet b/tutorials/PyDrugLogics/example_models/e1_s1.bnet
@@ -0,0 +1,80 @@
+# 2024_11_10, 2019
+# Evolution: 1 Solution: 1
+# Fitness Score: 0.998
+Antisurvival, ((CASP3) | FOXO_f)
+CASP3, ((CASP8) | CASP9)
+FOXO_f, !((AKT_f) | NLK)
+Prosurvival, ((CCND1) | MYC)
+CCND1, ((TCF7_f) | RSK_f)
+MYC, (TCF7_f)
+RAC_f, ((DVL_f) | mTORC2_c)
+mTORC2_c, (TSC_f) & !(S6K_f)
+DVL_f, (FZD_f)
+MAP3K4, (RAC_f)
+MAP3K11, (RAC_f)
+MAP2K4, ((((GRAP2) | MAP3K7) | MAP3K11) | MAP3K4)
+MAP3K7, (TAB_f)
+GRAP2, !(MAPK14)
+MAP2K7, ((GRAP2) | MAP3K7)
+JNK_f, ((MAP2K4) | MAP2K7) | !(DUSP1)
+DUSP1, ((MAPK14) | MSK_f)
+MAPK14, ((MAP2K4) | MAP2K3) & !(DUSP1)
+MAP2K3, ((MAP3K5) | MAP3K7)
+MAP3K5, !(AKT_f)
+AKT_f, ((PDPK1) | mTORC2_c)
+TAB_f, !(MAPK14)
+MSK_f, ((MAPK14) | ERK_f)
+RTPK_f, ((MMP_f) | RTPK_g) & !((MAPK14) | MEK_f)
+RTPK_g, (FOXO_f)
+MEK_f, ((MAP3K8) | RAF_f) | !(ERK_f)
+SHC1, (RTPK_f) | !(PTEN)
+PTEN, (PTEN_g) & !(GSK3_f)
+GRB2, (SHC1)
+SOS1, (GRB2) & !(ERK_f)
+ERK_f, (MEK_f) | !(DUSP6)
+KRAS, ((PTPN11) | SOS1)
+PTPN11, (GAB_f)
+RAF_f, (KRAS) & !(((ERK_f) | AKT_f) | RHEB)
+RHEB, !(TSC_f)
+MAP3K8, (IKBKB)
+DUSP6, ((ERK_f) | mTORC1_c)
+mTORC1_c, ((RSK_f) | RHEB) | !(AKT1S1)
+GAB_f, (GRB2) | !(ERK_f)
+RSK_f, ((ERK_f) | PDPK1)
+PDPK1, (PIK3CA) | !(PTEN)
+PIK3CA, (((GAB_f) | IRS1) | KRAS)
+IRS1, !(((ERK_f) | IKBKB) | S6K_f)
+S6K_f, ((PDPK1) | mTORC1_c)
+IKBKB, (MAP3K7) | !(TP53)
+PTEN_g, (EGR1)
+GSK3_f, !(((((((MAPK14) | AKT_f) | RSK_f) | S6K_f) | ERK_f) | LRP_f) | DVL_f)
+TSC_f, (GSK3_f) & !((((ERK_f) | AKT_f) | IKBKB) | RSK_f)
+TP53, (MAPK14) | !(MDM2)
+AKT1S1, !(AKT_f)
+MDM2, ((AKT_f) | MDM2_g) | !(S6K_f)
+MDM2_g, ((NFKB_f) | TP53)
+BAX, (TP53)
+CYCS, (BAX) | !(BCL2)
+BCL2, !(BAD)
+BAD, !((AKT_f) | RSK_f)
+NLK, (MAP3K7)
+CASP9, (CYCS)
+CASP8, !(CFLAR)
+CFLAR, (AKT_f) | !(ITCH)
+ITCH, (JNK_f)
+FZD_f, !(SFRP1)
+SFRP1, (SFRP1_g)
+LRP_f, ((((ERK_f) | MAPK14) | JNK_f) | FZD_f) | !(DKK_f)
+DKK_f, (DKK_g)
+AXIN1, !(LRP_f)
+CK1_f, !(LRP_f)
+BTRC, (((GSK3_f) | CK1_f) | AXIN1)
+CTNNB1, (CHUK) | !(BTRC)
+CHUK, (AKT_f)
+TCF7_f, (CTNNB1) | !(NLK)
+EGR1, !(TCF7_f)
+DKK_g, (TCF7_f) & !(MYC)
+SFRP1_g, !(MYC)
+NFKB_f, (((CHUK) | IKBKB) | MSK_f)
+LEF, (CTNNB1)
+MMP_f, (LEF)