Commit eb8dd30d authored by FAGES Francois's avatar FAGES Francois
Browse files

mise à jour des TDs de C2-19 et ajout comme tests dans nbrefs mais pas de...

mise à jour des TDs de C2-19 et ajout comme tests dans nbrefs mais pas de conversion automatique en .bc ?
parent 67c3c96b
...@@ -53,7 +53,7 @@ KERNEL_DIR=$(JUPYTER_DIR)/kernel/biocham_kernel ...@@ -53,7 +53,7 @@ KERNEL_DIR=$(JUPYTER_DIR)/kernel/biocham_kernel
WORKFLOWS_DIR=$(JUPYTER_DIR)/guinbextension/src/config/workflows WORKFLOWS_DIR=$(JUPYTER_DIR)/guinbextension/src/config/workflows
# NOTEBOOKS=$(shell find . -type f -name '*.ipynb' -print) # NOTEBOOKS=$(shell find . -type f -name '*.ipynb' -print)
NOTEBOOKS=library/examples/C2-19-Biochemical-Programming/TD1_lotka_volterra.ipynb library/examples/doctor_in_the_cell/diagnosis.ipynb NOTEBOOKS=library/examples/C2-19-Biochemical-Programming/TD1_lotka_volterra.ipynb library/examples/C2-19-Biochemical-Programming/TD2-enzyme_kinetics.ipynb library/examples/C2-19-Biochemical-Programming/TD4_genetic_switch.ipynb library/examples/C2-19-Biochemical-Programming/TD5_protein_switch.ipynb library/examples/C2-19-Biochemical-Programming/TD6_oscillators.ipynb library/examples/C2-19-Biochemical-Programming/TD7_switches.ipynb library/examples/C2-19-Biochemical-Programming/TD7_rate_independence.ipynb library/examples/C2-19-Biochemical-Programming/TD8_mapk_signalling.ipynb library/examples/C2-19-Biochemical-Programming/TD9_doctor_in_the_cell.ipynb library/examples/doctor_in_the_cell/diagnosis.ipynb
REFDIR=nbrefs REFDIR=nbrefs
all: biocham biocham_debug quick doc/index.html pldoc install_kernel install_gui all: biocham biocham_debug quick doc/index.html pldoc install_kernel install_gui
......
present(A,a). present(B,b). present(A,a). present(B,b).
k1*A*B for A+B => 2*B. k1*A*B for A+B => 2*B.
......
...@@ -5,11 +5,14 @@ ...@@ -5,11 +5,14 @@
"metadata": {}, "metadata": {},
"source": [ "source": [
"# TD1: Lotka-Volterra's prey-predator enzymatic model\n", "# TD1: Lotka-Volterra's prey-predator enzymatic model\n",
"- reaction network\n", "\n",
"<img src=\"PreyPredator.jpg\" alt=\"PreyPredator.jpg\" style=\"width: 600px;\"/>\n",
"\n",
"- modelled here with a reaction network\n",
"- differential, stochastic and boolean semantics\n", "- differential, stochastic and boolean semantics\n",
"- addition of immigration/emigration reactions\n", "- addition of immigration/emigration reactions\n",
"\n", "\n",
"F. Fages, 18 Jan. 2019, 24 Jan. 2020" "F. Fages, 18 Jan. 2019, 24 Jan. 2020, 19 Jan. 2021"
] ]
}, },
{ {
...@@ -2304,7 +2307,7 @@ ...@@ -2304,7 +2307,7 @@
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"### 5) Can you make a general conjecture about state reachability properties between the stochastic and continuous semantics of CRNs in presence of synthesis and degradation reactions ?\n", "### 5) Subsidiary question: can you make a general conjecture about state reachability properties between the stochastic and continuous semantics of CRNs in presence of synthesis and degradation reactions ?\n",
"\n", "\n",
"To my knowledge there is no known theorem ensuring that property --> a nice internship subject proposed with us to formulate and prove it\n", "To my knowledge there is no known theorem ensuring that property --> a nice internship subject proposed with us to formulate and prove it\n",
"\n", "\n",
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