{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "## Boolean networks" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from pyboolnet.file_exchange import bnet2primes, primes2bnet\n", "from pyboolnet.prime_implicants import find_constants, create_variables\n", "from pyboolnet.repository import get_primes" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "# Manual model definition\n", "bnet = \"\"\"\n", "v1,\t!v1\n", "v2,\t1\n", "v3,\tv2 & (!v1 | v3)\n", "\"\"\"\n", "\n", "primes = bnet2primes(bnet)" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "{'v2': 1}" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# finding nodes\n", "find_constants(primes)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "v2, \n", "\n", "v1, !v1\n", "v3, v2 & v3 | !v1 & v2\n", "v4, v4 | v2\n", "\n", "v5, !v1 & !v2 & v3 | !v1 & v2 & !v3 | v1 & !v2 & !v3\n", "\n" ] } ], "source": [ "# modifying networks\n", "create_variables(primes, {\"v4\": \"v4 | v2\"})\n", "create_variables(primes, {\"v5\": lambda v1,v2,v3: v1+v2+v3==1})\n", "\n", "print(primes2bnet(primes))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### From repository\n", "\n", "See https://github.com/hklarner/pyboolnet/blob/master/pyboolnet/repository/README.md" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "DNA_damage, DNA_damage\n", "EGFR_stimulus, EGFR_stimulus\n", "FGFR3_stimulus, FGFR3_stimulus\n", "Growth_inhibitors, Growth_inhibitors\n", "\n", "AKT, PI3K\n", "ATM_high, ATM_medium & DNA_damage & E2F1_medium\n", "ATM_medium, ATM_high & ATM_medium | DNA_damage\n", "Apoptosis_high, Apoptosis_medium & E2F1_high & E2F1_medium\n", "Apoptosis_medium, E2F1_high & E2F1_medium | Apoptosis_high & Apoptosis_medium | TP53\n", "CDC25A, !CHEK1_2_medium & E2F3_medium & !RBL2 | !CHEK1_2_medium & E2F1_medium & !RBL2\n", "CHEK1_2_high, ATM_medium & CHEK1_2_medium & E2F1_medium\n", "CHEK1_2_medium, CHEK1_2_high & CHEK1_2_medium | ATM_medium\n", "CyclinA, CDC25A & E2F3_medium & !RBL2 & !p21CIP | CDC25A & E2F1_medium & !RBL2 & !p21CIP\n", "CyclinD1, RAS & !p16INK4a & !p21CIP | AKT & !p16INK4a & !p21CIP\n", "CyclinE1, CDC25A & E2F3_medium & !RBL2 & !p21CIP | CDC25A & E2F1_medium & !RBL2 & !p21CIP\n", "E2F1_high, ATM_high & ATM_medium & CHEK1_2_high & CHEK1_2_medium & E2F1_medium & E2F3_high & E2F3_medium & !RB1 & !RBL2 | ATM_high & ATM_medium & CHEK1_2_high & CHEK1_2_medium & E2F1_medium & RAS & !RB1 & !RBL2\n", "E2F1_medium, RAS & !RB1 & !RBL2 | E2F3_medium & !RB1 & !RBL2 | E2F1_high & E2F1_medium\n", "E2F3_high, CHEK1_2_high & CHEK1_2_medium & E2F3_medium & RAS & !RB1\n", "E2F3_medium, RAS & !RB1 | E2F3_high & E2F3_medium\n", "EGFR, !FGFR3 & !GRB2 & SPRY | EGFR_stimulus & !FGFR3 & !GRB2\n", "FGFR3, !EGFR & FGFR3_stimulus & !GRB2\n", "GRB2, FGFR3 & !GRB2 & !SPRY | EGFR\n", "MDM2, !ATM_medium & !RB1 & TP53 & !p14ARF | AKT & !ATM_medium & !RB1 & !p14ARF\n", "PI3K, GRB2 & !PTEN & RAS\n", "PTEN, TP53\n", "RAS, GRB2 | FGFR3 | EGFR\n", "RB1, !CyclinA & !CyclinD1 & !CyclinE1 & !p16INK4a\n", "RBL2, !CyclinD1 & !CyclinE1\n", "SPRY, RAS\n", "TP53, E2F1_high & E2F1_medium & !MDM2 | ATM_medium & CHEK1_2_medium & !MDM2\n", "p14ARF, E2F1_medium\n", "p16INK4a, Growth_inhibitors & !RB1\n", "p21CIP, !AKT & !CyclinE1 & TP53 | !AKT & !CyclinE1 & Growth_inhibitors\n", "\n", "Growth_arrest, p21CIP | RBL2 | RB1\n", "Proliferation, CyclinE1 | CyclinA\n", "\n" ] } ], "source": [ "# reading from the repository\n", "primes = get_primes(\"remy_tumorigenesis\")\n", "print(primes2bnet(primes))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Trap spaces" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "from pyboolnet.trap_spaces import compute_trap_spaces, compute_steady_states" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "This notebook has been executed using the docker image `colomoto/colomoto-docker:2021-10-01`" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from colomoto_jupyter import tabulate" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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" ], "text/plain": [ " p21CIP p16INK4a p14ARF TP53 SPRY RBL2 RB1 RAS Proliferation PTEN \\\n", "0 0 0 0 0 0 1 1 0 0 0 \n", "19 0 0 1 0 1 0 0 1 1 0 \n", "18 0 0 1 0 1 0 0 1 1 0 \n", "10 0 1 1 0 1 0 0 1 1 0 \n", "8 0 1 1 0 1 0 0 1 1 0 \n", "1 1 0 0 0 0 1 1 0 0 0 \n", "17 1 0 0 0 1 1 1 1 0 0 \n", "16 1 0 0 0 1 1 1 1 0 0 \n", "3 1 0 0 1 0 1 1 0 0 1 \n", "2 1 0 0 1 0 1 1 0 0 1 \n", "13 1 0 0 1 1 1 1 1 0 1 \n", "12 1 0 0 1 1 1 1 1 0 1 \n", "15 1 0 0 1 1 1 1 1 0 1 \n", "14 1 0 0 1 1 1 1 1 0 1 \n", "5 1 1 0 0 0 1 0 0 0 0 \n", "11 1 1 0 0 1 1 0 1 0 0 \n", "9 1 1 0 0 1 1 0 1 0 0 \n", "4 1 1 0 1 0 1 0 0 0 1 \n", "7 1 1 0 1 1 1 0 1 0 1 \n", "6 1 1 0 1 1 1 0 1 0 1 \n", "\n", " PI3K MDM2 Growth_inhibitors Growth_arrest GRB2 FGFR3_stimulus FGFR3 \\\n", "0 0 0 0 1 0 0 0 \n", "19 0 0 0 0 0 1 1 \n", "18 0 0 0 0 0 1 1 \n", "10 0 0 1 0 0 1 1 \n", "8 0 0 1 0 0 1 1 \n", "1 0 0 1 1 0 0 0 \n", "17 0 0 1 1 0 1 1 \n", "16 0 0 1 1 0 1 1 \n", "3 0 0 0 1 0 0 0 \n", "2 0 0 1 1 0 0 0 \n", "13 0 0 0 1 0 1 1 \n", "12 0 0 0 1 0 1 1 \n", "15 0 0 1 1 0 1 1 \n", "14 0 0 1 1 0 1 1 \n", "5 0 0 1 1 0 0 0 \n", "11 0 0 1 1 0 1 1 \n", "9 0 0 1 1 0 1 1 \n", "4 0 0 1 1 0 0 0 \n", "7 0 0 1 1 0 1 1 \n", "6 0 0 1 1 0 1 1 \n", "\n", " EGFR_stimulus EGFR E2F3_medium E2F3_high E2F1_medium E2F1_high \\\n", "0 0 0 0 0 0 0 \n", "19 0 0 1 0 1 0 \n", "18 1 0 1 0 1 0 \n", "10 0 0 1 0 1 0 \n", "8 1 0 1 0 1 0 \n", "1 0 0 0 0 0 0 \n", "17 0 0 0 0 0 0 \n", "16 1 0 0 0 0 0 \n", "3 0 0 0 0 0 0 \n", "2 0 0 0 0 0 0 \n", "13 0 0 0 0 0 0 \n", "12 1 0 0 0 0 0 \n", "15 0 0 0 0 0 0 \n", "14 1 0 0 0 0 0 \n", "5 0 0 0 0 0 0 \n", "11 0 0 1 0 0 0 \n", "9 1 0 1 0 0 0 \n", "4 0 0 0 0 0 0 \n", "7 0 0 1 0 0 0 \n", "6 1 0 1 0 0 0 \n", "\n", " DNA_damage CyclinE1 CyclinD1 CyclinA CHEK1_2_medium CHEK1_2_high \\\n", "0 0 0 0 0 0 0 \n", "19 0 1 1 1 0 0 \n", "18 0 1 1 1 0 0 \n", "10 0 1 0 1 0 0 \n", "8 0 1 0 1 0 0 \n", "1 0 0 0 0 0 0 \n", "17 0 0 0 0 0 0 \n", "16 0 0 0 0 0 0 \n", "3 1 0 0 0 1 0 \n", "2 1 0 0 0 1 0 \n", "13 1 0 0 0 1 0 \n", "12 1 0 0 0 1 0 \n", "15 1 0 0 0 1 0 \n", "14 1 0 0 0 1 0 \n", "5 0 0 0 0 0 0 \n", "11 0 0 0 0 0 0 \n", "9 0 0 0 0 0 0 \n", "4 1 0 0 0 1 0 \n", "7 1 0 0 0 1 0 \n", "6 1 0 0 0 1 0 \n", "\n", " CDC25A Apoptosis_medium Apoptosis_high ATM_medium ATM_high AKT \n", "0 0 0 0 0 0 0 \n", "19 1 0 0 0 0 0 \n", "18 1 0 0 0 0 0 \n", "10 1 0 0 0 0 0 \n", "8 1 0 0 0 0 0 \n", "1 0 0 0 0 0 0 \n", "17 0 0 0 0 0 0 \n", "16 0 0 0 0 0 0 \n", "3 0 1 0 1 0 0 \n", "2 0 1 0 1 0 0 \n", "13 0 1 0 1 0 0 \n", "12 0 1 0 1 0 0 \n", "15 0 1 0 1 0 0 \n", "14 0 1 0 1 0 0 \n", "5 0 0 0 0 0 0 \n", "11 0 0 0 0 0 0 \n", "9 0 0 0 0 0 0 \n", "4 0 1 0 1 0 0 \n", "7 0 1 0 1 0 0 \n", "6 0 1 0 1 0 0 " ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "steady = compute_steady_states(primes)\n", "tabulate(steady)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.1" } }, "nbformat": 4, "nbformat_minor": 4 }