diff --git a/.gitignore b/.gitignore
index 39aa9026..f9bf9c80 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/
diff --git a/bionetgen/core/main.py b/bionetgen/core/main.py
index 32de2a9d..208a8980 100644
--- a/bionetgen/core/main.py
+++ b/bionetgen/core/main.py
@@ -233,7 +233,6 @@ def generate_notebook(app):
     app.log.debug(f"Writing notebook to file: {fname}", f"{__file__} : notebook()")
     notebook.write(fname)
     # open the notebook with nbopen
-    # TODO: deal with stdout/err
     app.log.debug(
         f"Attempting to open notebook {fname} with nbopen",
         f"{__file__} : notebook()",
@@ -242,4 +241,9 @@ def generate_notebook(app):
     stderr = getattr(subprocess, app.config["bionetgen"]["stderr"])
     if args.open:
         command = ["nbopen", fname]
-        rc, _ = run_command(command)
+        process = subprocess.Popen(command, stdout=stdout, stderr=stderr)
+        p_out, p_err = process.communicate()
+        if p_out:
+            app.log.info(p_out.decode("utf-8") if isinstance(p_out, bytes) else p_out)
+        if p_err:
+            app.log.error(p_err.decode("utf-8") if isinstance(p_err, bytes) else p_err)