Merge pull request #275 from EbmeyerSt/OMICSINT_H24

rasools · web-flow · commit 01f9c5a68149 · 2024-10-21T15:26:18.000+02:00
GEMs lab update
diff --git a/session_gems/lab/03-Pathway-visualization.ipynb b/session_gems/lab/03-Pathway-visualization.ipynb
@@ -56,7 +56,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "escher.Builder('e_coli_core.Core metabolism')"
+    "b = escher.Builder('e_coli_core.Core metabolism')\n",
+    "escher.Builder.save_html(b, filepath='data/Ecoli_core_03')"
    ]
   },
   {
@@ -72,9 +73,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "escher.Builder('e_coli_core.Core metabolism',\n",
+    "b = escher.Builder('e_coli_core.Core metabolism',\n",
     "               reaction_data={'PGK': 100},\n",
-    "               metabolite_data={'ATP': 20})"
+    "               metabolite_data={'ATP': 20})\n",
+    "escher.Builder.save_html(b, filepath='data/Ecoli_core_031')"
    ]
   },
   {

Original file line number	Diff line number	Diff line change
`@@ -56,7 +56,8 @@`
`56`	`56`	`"metadata": {},`
`57`	`57`	`"outputs": [],`
`58`	`58`	`"source": [`
`59`		`- "escher.Builder('e_coli_core.Core metabolism')"`
	`59`	`+ "b = escher.Builder('e_coli_core.Core metabolism')\n",`
	`60`	`+ "escher.Builder.save_html(b, filepath='data/Ecoli_core_03')"`
`60`	`61`	`]`
`61`	`62`	`},`
`62`	`63`	`{`
`@@ -72,9 +73,10 @@`
`72`	`73`	`"metadata": {},`
`73`	`74`	`"outputs": [],`
`74`	`75`	`"source": [`
`75`		`- "escher.Builder('e_coli_core.Core metabolism',\n",`
	`76`	`+ "b = escher.Builder('e_coli_core.Core metabolism',\n",`
`76`	`77`	`" reaction_data={'PGK': 100},\n",`
`77`		`- " metabolite_data={'ATP': 20})"`
	`78`	`+ " metabolite_data={'ATP': 20})\n",`
	`79`	`+ "escher.Builder.save_html(b, filepath='data/Ecoli_core_031')"`
`78`	`80`	`]`
`79`	`81`	`},`
`80`	`82`	`{`