Add new tool: PyDrugLogics (#154)

https://github.com/druglogics/pydruglogics

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 \

tools/pydruglogics.md

@@ -0,0 +1,30 @@
+---
+name: PyDrugLogics
+homepage: https://druglogics.github.io/pydruglogics/
+release_url: https://github.com/druglogics/pydruglogics/releases/tag/v{}
+summary:  Construct, optimize Boolean Models and perform in-silico perturbations of the models
+interface: Python module [`pydruglogics`](https://druglogics.github.io/pydruglogics/api.html)
+---
+
+# PyDrugLogics
+
+:::admonition
+Webpage: https://druglogics.github.io/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}
+```
+
+````

tutorials/PyDrugLogics/modeloutputs

@@ -0,0 +1,7 @@
+# Name	Weight
+RSK_f	1
+MYC	1
+TCF7_f	1
+CASP8	-1
+CASP9	-1
+FOXO_f	-1

tutorials/PyDrugLogics/network.bnet

@@ -0,0 +1,77 @@
+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)

tutorials/PyDrugLogics/network.sif

@@ -0,0 +1,149 @@
+CASP3	->	Antisurvival
+FOXO_f	->	Antisurvival
+CASP8	->	CASP3
+CASP9	->	CASP3
+AKT_f	-|	FOXO_f
+NLK	-|	FOXO_f
+CCND1	->	Prosurvival
+MYC	->	Prosurvival
+TCF7_f	->	CCND1
+RSK_f	->	CCND1
+TCF7_f	->	MYC
+mTORC2_c	->	RAC_f
+DVL_f	->	RAC_f
+TSC_f	->	mTORC2_c
+S6K_f	-|	mTORC2_c
+FZD_f	->	DVL_f
+RAC_f	->	MAP3K4
+RAC_f	->	MAP3K11
+MAP3K4	->	MAP2K4
+MAP3K11	->	MAP2K4
+MAP3K7	->	MAP2K4
+GRAP2	->	MAP2K4
+TAB_f	->	MAP3K7
+MAPK14	-|	GRAP2
+MAP3K7	->	MAP2K7
+GRAP2	->	MAP2K7
+MAP2K7	->	JNK_f
+MAP2K4	->	JNK_f
+DUSP1	-|	JNK_f
+MAPK14	->	DUSP1
+MSK_f	->	DUSP1
+MAP2K3	->	MAPK14
+MAP2K4	->	MAPK14
+DUSP1	-|	MAPK14
+MAP3K7	->	MAP2K3
+MAP3K5	->	MAP2K3
+AKT_f	-|	MAP3K5
+PDPK1	->	AKT_f
+mTORC2_c	->	AKT_f
+MAPK14	-|	TAB_f
+MAPK14	->	MSK_f
+ERK_f	->	MSK_f
+MMP_f	->	RTPK_f
+RTPK_g	->	RTPK_f
+MAPK14	-|	RTPK_f
+MEK_f	-|	RTPK_f
+FOXO_f	->	RTPK_g
+RAF_f	->	MEK_f
+MAP3K8	->	MEK_f
+ERK_f	-|	MEK_f
+RTPK_f	->	SHC1
+PTEN	-|	SHC1
+PTEN_g	->	PTEN
+GSK3_f	-|	PTEN
+SHC1	->	GRB2
+GRB2	->	SOS1
+ERK_f	-|	SOS1
+MEK_f	->	ERK_f
+DUSP6	-|	ERK_f
+SOS1	->	KRAS
+PTPN11	->	KRAS
+GAB_f	->	PTPN11
+KRAS	->	RAF_f
+AKT_f	-|	RAF_f
+ERK_f	-|	RAF_f
+RHEB	-|	RAF_f
+TSC_f	-|	RHEB
+IKBKB	->	MAP3K8
+ERK_f	->	DUSP6
+mTORC1_c	->	DUSP6
+RSK_f	->	mTORC1_c
+RHEB	->	mTORC1_c
+AKT1S1	-|	mTORC1_c
+GRB2	->	GAB_f
+ERK_f	-|	GAB_f
+ERK_f	->	RSK_f
+PDPK1	->	RSK_f
+PIK3CA	->	PDPK1
+PTEN	-|	PDPK1
+GAB_f	->	PIK3CA
+IRS1	->	PIK3CA
+KRAS	->	PIK3CA
+S6K_f	-|	IRS1
+ERK_f	-|	IRS1
+IKBKB	-|	IRS1
+PDPK1	->	S6K_f
+mTORC1_c	->	S6K_f
+MAP3K7	->	IKBKB
+TP53	-|	IKBKB
+EGR1	->	PTEN_g
+LRP_f	-|	GSK3_f
+RSK_f	-|	GSK3_f
+S6K_f	-|	GSK3_f
+ERK_f	-|	GSK3_f
+MAPK14	-|	GSK3_f
+DVL_f	-|	GSK3_f
+AKT_f	-|	GSK3_f
+GSK3_f	->	TSC_f
+IKBKB	-|	TSC_f
+AKT_f	-|	TSC_f
+RSK_f	-|	TSC_f
+ERK_f	-|	TSC_f
+MAPK14	->	TP53
+MDM2	-|	TP53
+AKT_f	-|	AKT1S1
+AKT_f	->	MDM2
+MDM2_g	->	MDM2
+S6K_f	-|	MDM2
+NFKB_f	->	MDM2_g
+TP53	->	MDM2_g
+TP53	->	BAX
+BAX	->	CYCS
+BCL2	-|	CYCS
+BAD	-|	BCL2
+AKT_f	-|	BAD
+RSK_f	-|	BAD
+MAP3K7	->	NLK
+CYCS	->	CASP9
+CFLAR	-|	CASP8
+AKT_f	->	CFLAR
+ITCH	-|	CFLAR
+JNK_f	->	ITCH
+SFRP1	-|	FZD_f
+SFRP1_g	->	SFRP1
+FZD_f	->	LRP_f
+ERK_f	->	LRP_f
+JNK_f	->	LRP_f
+MAPK14	->	LRP_f
+DKK_f	-|	LRP_f
+DKK_g	->	DKK_f
+LRP_f	-|	AXIN1
+LRP_f	-|	CK1_f
+AXIN1	->	BTRC
+GSK3_f	->	BTRC
+CK1_f	->	BTRC
+CHUK	->	CTNNB1
+BTRC	-|	CTNNB1
+AKT_f	->	CHUK
+CTNNB1	->	TCF7_f
+NLK	-|	TCF7_f
+TCF7_f	-|	EGR1
+TCF7_f	->	DKK_g
+MYC	-|	DKK_g
+MYC	-|	SFRP1_g
+CHUK	->	NFKB_f
+IKBKB	->	NFKB_f
+MSK_f	->	NFKB_f
+CTNNB1	->	LEF
+LEF	->	MMP_f