diff --git a/src/jupyter_contrib_nbextensions/nbextensions/runtools/main.js b/src/jupyter_contrib_nbextensions/nbextensions/runtools/main.js
index 79b4cdbbe..427a8eaa6 100644
--- a/src/jupyter_contrib_nbextensions/nbextensions/runtools/main.js
+++ b/src/jupyter_contrib_nbextensions/nbextensions/runtools/main.js
@@ -11,10 +11,6 @@ define([
 ], function(Jupyter, $, require, events, configmod, utils, codecell) {
     "use strict";
 
-    var base_url = utils.get_body_data("baseUrl");
-    var config = new configmod.ConfigSection('notebook', {
-        base_url: base_url
-    });
     var run_list = []; /* list of cells to be run */
 
     // define default config parameter values
@@ -33,15 +29,6 @@ define([
         run_color: '#f30a2d'
     };
 
-    // updates default params with any specified in the provided config data
-    var update_params = function(config_data) {
-        for (var key in params) {
-            if (config_data.hasOwnProperty(key)) {
-                params[key] = config_data[key];
-            }
-        }
-    };
-
     /**
      * Add event if user clicks on codemirror gutter
      *
@@ -53,14 +40,11 @@ define([
             var cell = cells[i];
             if ((cell.cell_type === "code")) {
                 cell.code_mirror.on("gutterClick", changeEvent);
-
-                if (cell.metadata.run_control !== undefined) {
-                    if (cell.metadata.run_control.marked === true) {
-                        var g = cell.code_mirror.getGutterElement();
-                        $(g).css({
-                            "background-color": params.marked_color
-                        });
-                    }
+                if (is_marked(cell)) {
+                    var g = cell.code_mirror.getGutterElement();
+                    $(g).css({
+                        "background-color": params.marked_color
+                    });
                 }
             }
         }
@@ -70,9 +54,7 @@ define([
      * Initialize toolbar and gutter after config was loaded
      */
     function initialize() {
-        if (Jupyter.notebook.config.data.hasOwnProperty('runtools')) {
-            update_params(Jupyter.notebook.config.data.runtools)
-        }
+        $.extend(true, params, Jupyter.notebook.config.data.runtools);
 
         add_gutter_events();
 
@@ -93,11 +75,7 @@ define([
             help: 'Run cells above',
             help_index: 'xa',
             handler: function() {
-                var mode = Jupyter.notebook.get_selected_cell().mode;
-                Jupyter.notebook.execute_cells_above();
-                Jupyter.notebook.select_next();
-                var type = Jupyter.notebook.get_selected_cell().cell_type;
-                if (mode === "edit" && type === "code") Jupyter.notebook.edit_mode();
+                execute_cells_above();
                 return false;
             }
         };
@@ -105,10 +83,7 @@ define([
             help: 'Run cells below',
             help_index: 'aa',
             handler: function() {
-                var mode = Jupyter.notebook.get_selected_cell().mode;
-                Jupyter.notebook.execute_cells_below();
-                var type = Jupyter.notebook.get_selected_cell().cell_type;
-                if (mode === "edit" && type === "code") Jupyter.notebook.edit_mode();
+                execute_cells_below();
                 return false;
             }
         };
@@ -149,9 +124,7 @@ define([
             help_index: 'ra',
             handler: function() {
                 var pos = Jupyter.notebook.element.scrollTop();
-                var ic = Jupyter.notebook.get_selected_index();
-                Jupyter.notebook.execute_all_cells();
-                Jupyter.notebook.select(ic);
+                execute_all_cells();
                 Jupyter.notebook.element.animate({
                     scrollTop: pos
                 }, 100);
@@ -199,19 +172,23 @@ define([
         }
     }
 
+    function _show_input_output_of_marked(show, char) {
+        var cells = Jupyter.notebook.get_cells();
+        var ncells = cells.length;
+        for (var i = 0; i < ncells; i++) {
+            var _cell = cells[i];
+            if (is_marked(_cell))
+                showCell(_cell, char, show);
+        }
+    }
+
     /**
      * Hide or show input of all marked code cells
      *
      * @param show {Boolean} show (true) or hide (false) code cells
      */
     function show_input(show) {
-        var ncells = Jupyter.notebook.ncells();
-        var cells = Jupyter.notebook.get_cells();
-        for (var i = 0; i < ncells; i++) {
-            var _cell = cells[i];
-            if (_cell.metadata.run_control !== undefined && _cell.metadata.run_control.marked === true)
-                showCell(_cell, 'i', show);
-        }
+        _show_input_output_of_marked(show, 'i');
     }
 
     /**
@@ -220,13 +197,7 @@ define([
      * @param {Boolean} show show (true) or hide (false)
      */
     function show_output(show) {
-        var ncells = Jupyter.notebook.ncells();
-        var cells = Jupyter.notebook.get_cells();
-        for (var i = 0; i < ncells; i++) {
-            var _cell = cells[i];
-            if (_cell.metadata.run_control !== undefined && _cell.metadata.run_control.marked === true)
-                showCell(_cell, 'o', show);
-        }
+        _show_input_output_of_marked(show, 'o');
     }
 
 
@@ -235,18 +206,18 @@ define([
      *
      */
     function execute_next_marked_cell() {
+        var cells = Jupyter.notebook.get_cells();
+        var end = cells.length;
         while (run_list.length > 0) {
             var runcell = run_list.shift();
-            var end = IPython.notebook.ncells();
             for (var i = 0; i < end; i++) {
-                if (runcell === IPython.notebook.get_cell(i)) {
+                if (runcell === cells[i]) {
                     if (runcell.metadata.run_control !== undefined && runcell.metadata.run_control.marked === true) {
-                        IPython.notebook.select(i);
                         var g = runcell.code_mirror.getGutterElement();
                         $(g).css({
                             "background-color": params.run_color
                         });
-                        IPython.notebook.execute_cell();
+                        runcell.execute();
                         return;
                     }
                 }
@@ -254,18 +225,40 @@ define([
         }
     }
 
+    function _execute_without_selecting(idx_start, idx_end, stop_on_error) {
+        // notebook.execute_cells alters selection, this doesn't
+        var cells = Jupyter.notebook.get_cells();
+        idx_start = idx_start !== undefined ? idx_start : 0;
+        idx_end = idx_end !== undefined ? idx_end : cells.length;
+        for (var ii = idx_start; ii < idx_end; ii++) {
+            cells[ii].execute(stop_on_error);
+        }
+    }
+
+    function execute_cells_above() {
+        _execute_without_selecting(0, Jupyter.notebook.get_selected_index());
+    }
+
+    function execute_cells_below() {
+        _execute_without_selecting(Jupyter.notebook.get_selected_index(), undefined);
+    }
+
+    function execute_all_cells(stop_on_error) {
+        _execute_without_selecting(0, undefined, stop_on_error);
+    }
+
     /**
      * Run code cells marked in metadata
      *
      */
     function run_marked_cells() {
-        var end = IPython.notebook.ncells();
+        var cells = Jupyter.notebook.get_cells();
+        var end = cells.length;
         run_list = [];
-        /* Mark all selected cells as scheduled to be run with new gutter background color  */
+        /* Show all marked cells as scheduled to be run with new gutter background color  */
         for (var i = 0; i < end; i++) {
-            IPython.notebook.select(i);
-            var cell = IPython.notebook.get_selected_cell();
-            if (cell instanceof IPython.CodeCell) {
+            var cell = cells[i];
+            if (cell instanceof codecell.CodeCell) {
                 var last_line = cell.code_mirror.lastLine();
                 var cell_empty = ( last_line === 0 && cell.code_mirror.getLine(last_line) === "");
                 if (cell.metadata.run_control !== undefined && cell_empty === false) {
@@ -290,15 +283,11 @@ define([
     var finished_execute_event = function(evt, data) {
         var cell = data.cell;
         /* Reset gutter color no non-queued state */
-        if ((cell instanceof IPython.CodeCell)) {
-            if (cell.metadata.run_control !== undefined) {
-                if (cell.metadata.run_control.marked === true) {
-                    var g = cell.code_mirror.getGutterElement();
-                    $(g).css({
-                        "background-color": params.marked_color
-                    });
-                }
-            }
+        if (is_marked(cell)) {
+            var g = cell.code_mirror.getGutterElement();
+            $(g).css({
+                "background-color": params.marked_color
+            });
         }
         execute_next_marked_cell();
     };
@@ -309,6 +298,7 @@ define([
      * @param value
      */
     function setCell(cell, value) {
+        if (!(cell instanceof codecell.CodeCell)) return;
         if (cell.metadata.run_control === undefined) cell.metadata.run_control = {};
         if (cell.metadata.run_control.marked === undefined) cell.metadata.run_control.marked = false;
         if (value === undefined) value = !cell.metadata.run_control.marked;
@@ -326,41 +316,32 @@ define([
         }
     }
 
+    function setCellsMarked(cells, value) {
+        var ncells = cells.length;
+        for (var i = 0; i < ncells; i++) {
+            setCell(cells[i], value);
+        }
+    }
+
     /**
      * Toggle code cell marker
      */
     function toggle_marker() {
-        var cell = Jupyter.notebook.get_selected_cell();
-        setCell(cell, undefined);
-        cell.focus_cell();
+        setCellsMarked(Jupyter.notebook.get_selected_cells(), undefined);
     }
 
     /**
      *
      */
     function mark_all() {
-        var cell = Jupyter.notebook.get_selected_cell();
-        var ncells = Jupyter.notebook.ncells();
-        var cells = Jupyter.notebook.get_cells();
-        for (var i = 0; i < ncells; i++) {
-            var _cell = cells[i];
-            setCell(_cell, true);
-        }
-        cell.focus_cell();
+        setCellsMarked(Jupyter.notebook.get_cells(), true);
     }
 
     /**
      *
      */
     function mark_none() {
-        var cell = Jupyter.notebook.get_selected_cell();
-        var ncells = Jupyter.notebook.ncells();
-        var cells = Jupyter.notebook.get_cells();
-        for (var i = 0; i < ncells; i++) {
-            var _cell = cells[i];
-            setCell(_cell, false);
-        }
-        cell.focus_cell();
+        setCellsMarked(Jupyter.notebook.get_cells(), false);
     }
 
     /**
@@ -385,21 +366,10 @@ define([
      */
     function changeEvent(cm, line, gutter) {
         var cmline = cm.doc.children[0].lines[line];
-        var cell = Jupyter.notebook.get_selected_cell();
         if (cmline === undefined) {
             return;
         }
-
-        if (cell.code_mirror !== cm) {
-            var ncells = Jupyter.notebook.ncells();
-            var cells = Jupyter.notebook.get_cells();
-            for (var i = 0; i < ncells; i++) {
-                cell = cells[i];
-                if (cell.code_mirror === cm) {
-                    break;
-                }
-            }
-        }
+        var cell = $(cm.element).closest('.cell').data('cell');
         if (cell.metadata.run_control === undefined)
             cell.metadata.run_control = {};
         setCell(cell, !cell.metadata.run_control.marked);
@@ -411,12 +381,9 @@ define([
      * @returns {boolean} true if marked
      */
     var is_marked = function(cell) {
-        if (cell.metadata.run_control !== undefined) {
-            if (cell.metadata.run_control.marked === true) {
-                return true;
-            }
-        }
-        return false;
+        return (cell instanceof codecell.CodeCell) &&
+            cell.metadata.run_control !== undefined &&
+            cell.metadata.run_control.marked;
     };
 
     /**
@@ -458,11 +425,7 @@ define([
      *
      */
     var run_all_cells_ignore_errors = function() {
-        for (var i = 0; i < Jupyter.notebook.ncells(); i++) {
-            Jupyter.notebook.select(i);
-            var cell = Jupyter.notebook.get_selected_cell();
-            cell.execute(false);
-        }
+        execute_all_cells(false);
     };
 
     /**
@@ -512,8 +475,9 @@ define([
             'position': 'absolute'
         });
         $('#run_c').on('click', function(e) {
-                Jupyter.notebook.execute_cell();
-                e.target.blur()
+                var idx = Jupyter.notebook.get_selected_index();
+                _execute_without_selecting(idx, idx + 1);
+                e.target.blur();
             })
             .tooltip({
                 delay: {
@@ -522,9 +486,8 @@ define([
                 }
             });
         $('#run_ca').on('click', function(e) {
-                Jupyter.notebook.execute_cells_above();
-                Jupyter.notebook.select_next();
-                e.target.blur()
+                execute_cells_above();
+                e.target.blur();
             })
             .tooltip({
                 delay: {
@@ -533,8 +496,8 @@ define([
                 }
             });
         $('#run_cb').on('click', function(e) {
-                Jupyter.notebook.execute_cells_below();
-                e.target.blur()
+                execute_cells_below();
+                e.target.blur();
             })
             .tooltip({
                 delay: {
@@ -543,8 +506,8 @@ define([
                 }
             });
         $('#run_a').on('click', function(e) {
-                Jupyter.notebook.execute_all_cells();
-                e.target.blur()
+                execute_all_cells();
+                e.target.blur();
             })
             .tooltip({
                 delay: {
@@ -730,8 +693,8 @@ define([
      * Initialize all cells with new gutter
      */
     var initGutter = function() {
-        var ncells = Jupyter.notebook.ncells();
         var cells = Jupyter.notebook.get_cells();
+        var ncells = cells.length;
         for (var i = 0; i < ncells; i++) {
             var cell = cells[i];
             if (cell instanceof codecell.CodeCell) {
@@ -741,12 +704,9 @@ define([
                     cell.code_mirror.setOption('gutters', gutters);
                 }
             }
-        }
-        /**
-         * Restore hide/show status after reload
-         */
-        for (i = 0; i < ncells; i++) {
-            var cell = cells[i];
+            /**
+             * Restore hide/show status after reload
+             */
             if (cell.metadata.hasOwnProperty('hide_input') && cell.metadata.hide_input === true)
                 showCell(cell, 'i', false);
             if (cell.metadata.hasOwnProperty('hide_output') && cell.metadata.hide_output === true)
@@ -773,11 +733,9 @@ define([
                 events.one('notebook_loaded.Notebook', initGutter);
             }
         });
-        config.load()
+        Jupyter.notebook.config.loaded.then(initialize);
     };
 
-    Jupyter.notebook.config.loaded.then(initialize);
-
     return {
         load_jupyter_extension: load_extension,
         load_ipython_extension: load_extension