--- a
+++ b/docs/render_ipynb.bash
@@ -0,0 +1,48 @@
+#!/bin/bash
+#
+# Compile .md from .ipynb files for mkdocs
+
+# Names of ipynb files to convert (from /notebooks) are specified in ipynb_pages.txt
+set -e
+
+function sed_replace {
+  # https://stackoverflow.com/a/10467453/7529152
+  # sed_replace <from> <to> <file>"
+  sed -i "s/$(echo $1 | sed -e 's/\([[\/.*]\|\]\)/\\&/g')/$(echo $2 | sed -e 's/[\/&]/\\&/g')/g" $3
+}
+
+
+DIR=tutorials
+for file in $(cat ipynb_pages.txt); do
+
+    echo "converting: ${file}.ipynb"
+    # .ipynb -> .md
+    jupyter nbconvert --to markdown ../notebooks/${file}.ipynb --output-dir sources/${DIR}/
+
+    file_out=sources/${DIR}/${file}.md
+    dir_out=sources/${DIR}/${file}_files
+
+    # fix the paths for the original images
+    sed_replace '![img](../docs/theme_dir/img/' '![img](/bpnet/img/' $file_out
+    # prepend the original ipython notebook link
+    echo -e "Generated from [notebooks/${file}.ipynb](https://github.com/kundajelab/bpnet/blob/master/notebooks/${file}.ipynb)\n$(cat ${file_out})" > ${file_out}
+
+    if [ -d "${dir_out}" ]; then
+
+	# move the additional files <file>_files to theme_dir/img/ipynb/ (inline plots in ipynb)
+	if [ -d "theme_dir/img/ipynb/${file}_files" ]; then
+	    rm -r theme_dir/img/ipynb/${file}_files
+	fi
+	mv -f ${dir_out} theme_dir/img/ipynb/
+
+	# fix the path in the .md file
+	sed_replace '![png]('${file}'_files' '![png](/bpnet/img/ipynb/'${file}'_files' $file_out
+	sed_replace '![svg]('${file}'_files' '![svg](/bpnet/img/ipynb/'${file}'_files' $file_out
+    fi
+done
+
+if [ -d "theme_dir/bpnet" ]; then
+    rm -r theme_dir/bpnet
+fi
+mkdir -p theme_dir/bpnet
+ln -sr theme_dir/img theme_dir/bpnet/img