[UPDATE] MEWpy

BioSystemsUM · Apr 11, 2023 · 3570c2f · 3570c2f
1 parent 3583d08
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diff --git a/.gitignore b/.gitignore
@@ -8,6 +8,7 @@ textbook.json
 ### Jetbrains
 # ignore idea
 .idea
+.DS_Store
 
 ### JupyterNotebooks template
 # gitignore template for Jupyter Notebooks

diff --git a/mewpy_tutorial/s2m2 - hands-on cobra - exercise 11.ipynb b/mewpy_tutorial/s2m2 - hands-on cobra - exercise 11.ipynb
@@ -6,7 +6,13 @@
    "source": [
     "# Advanced Modeling \n",
     "\n",
-    "In this exercice your aim is to increase the production of succinate in Yeast resorting to GECKO and ETFL formulations."
+    "Author: Vitor Pereira\n",
+    "\n",
+    "License: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)\n",
+    "\n",
+    "-------\n",
+    "\n",
+    "In this exercice your aim is to increase the production of succinate in Yeast resorting to GECKO and ETFL formulations.\n"
    ]
   },
   {
@@ -24,7 +30,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!pip install geckopy --upgrade --quiet"
+    "!pip install -U -q geckopy"
    ]
   },
   {
@@ -396,4 +402,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/mewpy_tutorial/s2m2 - hands-on mewpy - exercise 10.ipynb b/mewpy_tutorial/s2m2 - hands-on mewpy - exercise 10.ipynb
@@ -5,7 +5,15 @@
    "metadata": {},
    "source": [
     "\n",
-    "# Nutrient and proteome limited growth."
+    "# Nutrient and proteome limited growth\n",
+    "\n",
+    "Author: Vitor Pereira\n",
+    "\n",
+    "License: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)\n",
+    "\n",
+    "-------\n",
+    "\n",
+    "In this exercice you will learn the advantages of using enzyme constraints on genome-scale metabolic models."
    ]
   },
   {
@@ -219,9 +227,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "s2m2",
+   "display_name": "Python 3.9.6 64-bit",
    "language": "python",
-   "name": "s2m2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -233,9 +241,14 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.9.6"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6"
+   }
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/mewpy_tutorial/s2m2 - hands-on mewpy - exercise 8.ipynb b/mewpy_tutorial/s2m2 - hands-on mewpy - exercise 8.ipynb
@@ -6,6 +6,11 @@
    "source": [
     "# MEWpy Simulation \n",
     "\n",
+    "Author: Vitor Pereira\n",
+    "\n",
+    "License: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)\n",
+    "\n",
+    "-------\n",
     "This notebook exemplifies how MEWpy may be used for phenotype simulation."
    ]
   },
@@ -24,7 +29,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! pip install mewpy --upgrade --quiet"
+    "! pip install -U -q mewpy"
    ]
   },
   {
@@ -608,9 +613,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "'Python Interactive'",
+   "display_name": "Python 3.9.6 64-bit",
    "language": "python",
-   "name": "290eda42-6644-4090-8ab8-54482205eb0a"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -622,7 +627,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.9.6"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6"
+   }
   }
  },
  "nbformat": 4,

diff --git a/mewpy_tutorial/s2m2 - hands-on mewpy - exercise 9.ipynb b/mewpy_tutorial/s2m2 - hands-on mewpy - exercise 9.ipynb
@@ -6,6 +6,12 @@
    "source": [
     "# Strain Optimization in MEWpy\n",
     "\n",
+    "Author: Vitor Pereira\n",
+    "\n",
+    "License: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)\n",
+    "\n",
+    "-------\n",
+    "\n",
     "This notebook exemplifies how MEWpy may be used in strain optimization tasks.\n",
     "We will consider the as goal to increase the production of succinate in E. coli in anaerobic conditions."
    ]
@@ -469,7 +475,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.9.6 64-bit",
    "language": "python",
    "name": "python3"
   },
@@ -483,7 +489,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.9.6"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6"
+   }
   }
  },
  "nbformat": 4,