diff --git a/notebook/nbconvert/handlers.py b/notebook/nbconvert/handlers.py
index 89995226e1..db001f0981 100644
--- a/notebook/nbconvert/handlers.py
+++ b/notebook/nbconvert/handlers.py
@@ -5,6 +5,7 @@
 
 import io
 import os
+import json
 import zipfile
 
 from tornado import web, escape
@@ -15,6 +16,8 @@
     path_regex,
 )
 from nbformat import from_dict
+import nbformat
+from traitlets.config import Config
 
 from ipython_genutils.py3compat import cast_bytes
 from ipython_genutils import text
@@ -41,16 +44,17 @@ def respond_zip(handler, name, output, resources):
     handler.set_attachment_header(zip_filename)
     handler.set_header('Content-Type', 'application/zip')
 
-    # Prepare the zip file
-    buffer = io.BytesIO()
-    zipf = zipfile.ZipFile(buffer, mode='w', compression=zipfile.ZIP_DEFLATED)
-    output_filename = os.path.splitext(name)[0] + resources['output_extension']
-    zipf.writestr(output_filename, cast_bytes(output, 'utf-8'))
-    for filename, data in output_files.items():
-        zipf.writestr(os.path.basename(filename), data)
-    zipf.close()
-
-    handler.finish(buffer.getvalue())
+    # create zip file
+    buff = io.BytesIO()
+    with zipfile.ZipFile(buff, mode='w', compression=zipfile.ZIP_STORED) as zipf:
+        output_filename = os.path.splitext(name)[0] + resources['output_extension']
+        zipf.writestr(output_filename, cast_bytes(output, 'utf-8'))
+        for filename, data in output_files.items():
+            zipf.writestr(filename, data)
+
+    # pass zip file back
+    buff.seek(0)
+    handler.finish(buff.getvalue())
     return True
 
 def get_exporter(format, **kwargs):
@@ -74,14 +78,11 @@ def get_exporter(format, **kwargs):
         raise web.HTTPError(500, "Could not construct Exporter: %s" % e)
 
 class NbconvertFileHandler(IPythonHandler):
-
     SUPPORTED_METHODS = ('GET',)
 
     @web.authenticated
     def get(self, format, path):
-
         exporter = get_exporter(format, config=self.config, log=self.log)
-
         path = path.strip('/')
         # If the notebook relates to a real file (default contents manager),
         # give its path to nbconvert.
@@ -92,15 +93,12 @@ def get(self, format, path):
             ext_resources_dir = None
 
         model = self.contents_manager.get(path=path)
+        nb = model['content']
         name = model['name']
+        self.set_header('Last-Modified', model['last_modified'])
         if model['type'] != 'notebook':
             # not a notebook, redirect to files
             return FilesRedirectHandler.redirect_to_files(self, path)
-
-        nb = model['content']
-
-        self.set_header('Last-Modified', model['last_modified'])
-
         # create resources dictionary
         mod_date = model['last_modified'].strftime(text.date_format)
         nb_title = os.path.splitext(name)[0]
@@ -110,7 +108,8 @@ def get(self, format, path):
                 "name": nb_title,
                 "modified_date": mod_date
             },
-            "config_dir": self.application.settings['config_dir']
+            "config_dir": self.application.settings['config_dir'],
+            "output_files_dir": nb_title+"_files",
         }
 
         if ext_resources_dir:
@@ -140,16 +139,93 @@ def get(self, format, path):
 
         self.finish(output)
 
+
+class NbconvertConfigHandler(IPythonHandler):
+    SUPPORTED_METHODS = ('POST',)
+
+    @web.authenticated
+    def post(self):
+
+        json_content = self.get_json_body()
+
+        c = Config(self.config)
+
+        # config needs to be dict
+        config = Config(json.loads(json_content.get("config",{})))
+        c.merge(config)
+
+        # We're adhering to the content model laid out by the notebook data model
+        # descriptor:
+        # http://jupyter-notebook.readthedocs.io/en/latest/extending/contents.html#data-model
+        # validate notebook before converting
+        nb_contents = json_content["notebook_contents"]
+        try:
+            nbformat.validate(nb_contents["content"])
+        except nbformat.ValidationError as e:
+            self.log.exception("notebook content was not a valid notebook: %s", e)
+            raise web.HTTPError(500, "notebook content was not a valid notebook: %s" % e)
+
+        nb = nbformat.from_dict(nb_contents["content"])
+        name = nb_contents["name"]
+        last_mod = nb_contents.get("modified_date","")
+        nb_title = os.path.splitext(name)[0]
+
+        export_format = c.NbConvertApp.get("export_format","")
+        if not export_format:
+            try:
+                export_format= json_content["export_format"]
+            except KeyError:
+                raise web.HTTPError(500, "No format specified for export.")
+
+        exporter = get_exporter(export_format, config=c, log=self.log)
+
+        metadata = {}
+        metadata['name'] = nb_title
+        if last_mod:
+            metadata['modified_date'] = last_mod.strftime(text.date_format)
+
+        resources_dict= {
+            "config_dir": self.application.settings['config_dir'],
+            "output_files_dir": nb_title+"_files",
+            "metadata": metadata
+        }
+
+        try:
+            output, resources = exporter.from_notebook_node(
+                nb,
+                resources=resources_dict
+            )
+        except Exception as e:
+            self.log.exception("nbconvert failed: %s", e)
+            raise web.HTTPError(500, "nbconvert failed: %s" % e)
+
+
+        if respond_zip(self, name, output, resources):
+            return
+
+        # Force download if requested
+        if self.get_argument('download', 'false').lower() == 'true':
+            output_filename = nb_title + resources['output_extension']
+            self.set_attachment_header(output_filename)
+
+        # MIME type
+        if exporter.output_mimetype:
+            self.set_header('Content-Type',
+                            '%s; charset=utf-8' % exporter.output_mimetype)
+
+        self.finish(output)
+
+
 class NbconvertPostHandler(IPythonHandler):
     SUPPORTED_METHODS = ('POST',)
 
     @web.authenticated
     def post(self, format):
-        exporter = get_exporter(format, config=self.config)
 
         model = self.get_json_body()
         name = model.get('name', 'notebook.ipynb')
         nbnode = from_dict(model['content'])
+        exporter = get_exporter(format, config=self.config)
 
         try:
             output, resources = exporter.from_notebook_node(nbnode, resources={
@@ -178,6 +254,7 @@ def post(self, format):
 
 
 default_handlers = [
+    (r"/nbconvert", NbconvertConfigHandler),
     (r"/nbconvert/%s" % _format_regex, NbconvertPostHandler),
     (r"/nbconvert/%s%s" % (_format_regex, path_regex),
          NbconvertFileHandler),
diff --git a/notebook/nbconvert/tests/test_nbconvert_handlers.py b/notebook/nbconvert/tests/test_nbconvert_handlers.py
index ebcfb4e9b8..27a75054e6 100644
--- a/notebook/nbconvert/tests/test_nbconvert_handlers.py
+++ b/notebook/nbconvert/tests/test_nbconvert_handlers.py
@@ -22,10 +22,8 @@
     from base64 import encodestring as encodebytes
 
 
-
-
 class NbconvertAPI(object):
-    """Wrapper for nbconvert API calls."""
+    """Wrapper for API calls to /nbconvert/<format>."""
     def __init__(self, request):
         self.request = request
 
@@ -43,11 +41,29 @@ def from_file(self, format, path, name, download=False):
 
     def from_post(self, format, nbmodel):
         body = json.dumps(nbmodel)
-        return self._req('POST', format, body)
+        return self._req('POST', format, body=body)
 
     def list_formats(self):
         return self._req('GET', '')
 
+class NbconvertConfigAPI(NbconvertAPI):
+    """Wrapper for API calls to /nbconvert"""
+
+    def _req(self, verb, body=None, params=None):
+        response = self.request(verb, 'nbconvert', data=body, params=params)
+        response.raise_for_status()
+        return response
+
+    def from_post(self, nbmodel, format="", config=None):
+        body = {}
+        body['notebook_contents'] = nbmodel
+        body['config'] = config
+        if format:
+            body['export_format'] = format
+
+        return self._req('POST', body=json.dumps(body))
+
+
 png_green_pixel = encodebytes(b'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00'
 b'\x00\x00\x01\x00\x00x00\x01\x08\x02\x00\x00\x00\x90wS\xde\x00\x00\x00\x0cIDAT'
 b'\x08\xd7c\x90\xfb\xcf\x00\x00\x02\\\x01\x1e.~d\x87\x00\x00\x00\x00IEND\xaeB`\x82'
@@ -56,7 +72,7 @@ def list_formats(self):
 class APITest(NotebookTestBase):
     def setUp(self):
         nbdir = self.notebook_dir
-        
+
         if not os.path.isdir(pjoin(nbdir, 'foo')):
             subdir = pjoin(nbdir, 'foo')
 
@@ -70,7 +86,7 @@ def cleanup_dir():
                 shutil.rmtree(subdir, ignore_errors=True)
 
         nb = new_notebook()
-        
+
         nb.cells.append(new_markdown_cell(u'Created by test ³'))
         cc1 = new_code_cell(source=u'print(2*6)')
         cc1.outputs.append(new_output(output_type="stream", text=u'12'))
@@ -79,12 +95,13 @@ def cleanup_dir():
             execution_count=1,
         ))
         nb.cells.append(cc1)
-        
+
         with io.open(pjoin(nbdir, 'foo', 'testnb.ipynb'), 'w',
                      encoding='utf-8') as f:
             write(nb, f, version=4)
 
         self.nbconvert_api = NbconvertAPI(self.request)
+        self.nbconvert_config_api = NbconvertConfigAPI(self.request)
 
     @onlyif_cmds_exist('pandoc')
     def test_from_file(self):
@@ -119,17 +136,32 @@ def test_from_file_zip(self):
     @onlyif_cmds_exist('pandoc')
     def test_from_post(self):
         nbmodel = self.request('GET', 'api/contents/foo/testnb.ipynb').json()
-        
+
         r = self.nbconvert_api.from_post(format='html', nbmodel=nbmodel)
         self.assertEqual(r.status_code, 200)
         self.assertIn(u'text/html', r.headers['Content-Type'])
         self.assertIn(u'Created by test', r.text)
         self.assertIn(u'print', r.text)
-        
+
         r = self.nbconvert_api.from_post(format='python', nbmodel=nbmodel)
         self.assertIn(u'text/x-python', r.headers['Content-Type'])
         self.assertIn(u'print(2*6)', r.text)
 
+    def test_config_from_post(self):
+        nbmodel = self.request('GET', 'api/contents/foo/testnb.ipynb').json()
+        html_config = json.dumps({"NbConvertApp":{"export_format": 'html'}})
+        python_config = json.dumps({"NbConvertApp":{"export_format": 'python'}})
+
+        r = self.nbconvert_config_api.from_post(config=html_config, nbmodel=nbmodel)
+        self.assertEqual(r.status_code, 200)
+        self.assertIn(u'text/html', r.headers['Content-Type'])
+        self.assertIn(u'Created by test', r.text)
+        self.assertIn(u'print', r.text)
+
+        r = self.nbconvert_config_api.from_post(config=python_config, nbmodel=nbmodel)
+        self.assertIn(u'text/x-python', r.headers['Content-Type'])
+        self.assertIn(u'print(2*6)', r.text)
+
     @onlyif_cmds_exist('pandoc')
     def test_from_post_zip(self):
         nbmodel = self.request('GET', 'api/contents/foo/testnb.ipynb').json()
@@ -137,3 +169,12 @@ def test_from_post_zip(self):
         r = self.nbconvert_api.from_post(format='latex', nbmodel=nbmodel)
         self.assertIn(u'application/zip', r.headers['Content-Type'])
         self.assertIn(u'.zip', r.headers['Content-Disposition'])
+
+    @onlyif_cmds_exist('pandoc')
+    def test_config_from_post_zip(self):
+        nbmodel = self.request('GET', 'api/contents/foo/testnb.ipynb').json()
+        latex_config = json.dumps({'NbConvertApp': {'export_format': 'latex'}})
+
+        r = self.nbconvert_config_api.from_post(config=latex_config, nbmodel=nbmodel)
+        self.assertIn(u'application/zip', r.headers['Content-Type'])
+        self.assertIn(u'.zip', r.headers['Content-Disposition'])
diff --git a/notebook/static/base/js/utils.js b/notebook/static/base/js/utils.js
index 8f54a6384b..54570ce1a6 100644
--- a/notebook/static/base/js/utils.js
+++ b/notebook/static/base/js/utils.js
@@ -1185,7 +1185,8 @@ define([
         js_idx_to_char_idx: js_idx_to_char_idx,
         char_idx_to_js_idx: char_idx_to_js_idx,
         _ansispan:_ansispan,
-        change_favicon: change_favicon
+        change_favicon: change_favicon,
+        _get_cookie:_get_cookie
     };
 
     return utils;
diff --git a/notebook/static/notebook/js/menubar.js b/notebook/static/notebook/js/menubar.js
index 450ce310cd..a4faed0311 100644
--- a/notebook/static/notebook/js/menubar.js
+++ b/notebook/static/notebook/js/menubar.js
@@ -1,7 +1,7 @@
 // Copyright (c) Jupyter Development Team.
 // Distributed under the terms of the Modified BSD License.
 
-define([
+define('notebook/js/menubar',[
     'jquery',
     'base/js/namespace',
     'base/js/dialog',
@@ -71,7 +71,7 @@ define([
             }
         );
     };
-    
+
     MenuBar.prototype.add_bundler_items = function() {
         var that = this;
         this.config.loaded.then(function() {
@@ -82,7 +82,7 @@ define([
                 ids.forEach(function(bundler_id) {
                     var bundler = bundlers[bundler_id];
                     var group = that.element.find('#'+bundler.group+'_menu')
-                    
+
                     // Validate menu item metadata
                     if(!group.length) {
                         console.warn('unknown group', bundler.group, 'for bundler ID', bundler_id, '; skipping');
@@ -91,7 +91,7 @@ define([
                         console.warn('no label for bundler ID', bundler_id, '; skipping');
                         return;
                     }
-                    
+
                     // Insert menu item into correct group, click handler
                     group.parent().removeClass('hidden');
                     var $li = $('<li>')
@@ -117,7 +117,7 @@ define([
             w.location = url;
         }
     };
-    
+
     MenuBar.prototype._bundle = function(bundler_id) {
         // Read notebook path and base url here in case they change
         var notebook_path = utils.encode_uri_components(this.notebook.notebook_path);
@@ -130,6 +130,162 @@ define([
         this._new_window(url);
     };
 
+    MenuBar.prototype._nbconvert_upload_conf = function(download) {
+      var body = $("<div>");
+      var notebook_path = utils.encode_uri_components(
+        this.notebook.notebook_path
+      );
+
+      var build_json_for_post = function(notebook, config, format) {
+        var json_to_pass = {
+          notebook_contents: {
+            content: notebook.toJSON(),
+            name: notebook.notebook_name,
+            last_modified: notebook.last_modified
+        },
+          export_format: format,
+          config: config
+        };
+        return json_to_pass;
+      };
+
+      var form = $("<form>");
+      var fileinput = $("<input>")
+        .attr("type", "file")
+        .attr("tabindex", "1");
+
+      var fileformat = $("<select>");
+
+      var export_opts = {
+        markdown: {
+          display_text: "Markdown",
+          exporter_name: "markdown"
+        },
+        html: {
+          display_text: "HTML",
+          exporter_name: "html"
+        },
+        rst: {
+          display_text: "reST",
+          exporter_name: "rst"
+        },
+        pdf: {
+          display_text: "PDF",
+          exporter_name: "pdf"
+        },
+        latex: {
+          display_text: "LaTeX",
+          exporter_name: "latex"
+        },
+        script: {
+          display_text: "script",
+          exporter_name: "script"
+        },
+        slides: {
+          display_text: "Reveal.js slides",
+          exporter_name: "slides"
+        }
+      };
+
+      for (var x in export_opts) {
+        fileformat.append(
+          $("<option/>")
+            .attr("value", export_opts[x]["exporter_name"])
+            .text(export_opts[x]["display_text"])
+        );
+      }
+
+      form.append(fileformat);
+      form.append(fileinput);
+      body.append(form);
+
+      var that = this;
+      var get_export_format = function() {
+        return fileformat.val();
+      }
+
+      var trigger_nbconvert_post = function() {
+        var filereader = new FileReader();
+        filereader.onload = function() {
+          var my_config_data = filereader.result;
+          that["json_content"] = build_json_for_post(that.notebook, my_config_data, get_export_format());
+          on_done();
+        };
+        if (fileinput[0].files.length > 0) {
+          filereader.readAsText(fileinput[0].files[0]);
+        } else {
+          that["json_content"] = build_json_for_post(that.notebook, "{}", get_export_format());
+          on_done();
+        }
+      };
+
+      var on_done = function() {
+        var url =
+          utils.url_path_join(
+            that.base_url,
+            "nbconvert"
+          ) +
+          "?download=" +
+          download.toString();
+        var xsrf_token = utils._get_cookie("_xsrf");
+        var xhr = new XMLHttpRequest();
+        xhr.open("POST", url, true);
+        xhr.responseType = "blob";
+        xhr.withCredentials = true;
+        xhr.setRequestHeader("X-XSRFToken", xsrf_token);
+        xhr.onreadystatechange = function() {
+          if (xhr.readyState === 4) {
+            var blob = xhr.response;
+            var content_disposition = xhr.getResponseHeader(
+              "Content-Disposition"
+            );
+            var filename = content_disposition.match(/filename\*=utf-8''(.+)/)[1];
+            saveData(blob, filename);
+          }
+        };
+        var data = JSON.stringify(that.json_content);
+        xhr.send(data);
+        return true; // close the dialog
+        // return false to keep it open.
+      };
+      var saveData = (function() {
+        var a = document.createElement("a");
+        document.body.appendChild(a);
+        a.style = "display: none";
+        return (
+          function(data, fileName) {
+            var blob = new Blob([data], { type: "octet/stream" });
+            var objectUrl = window.URL.createObjectURL(blob);
+            a.href = objectUrl;
+            a.download = fileName;
+            a.click();
+            window.URL.revokeObjectURL(objectUrl);
+            document.body.removeChild(a);
+          }
+        )
+      })();
+
+      var mod = dialog.modal({
+        notebook: this.notebook,
+        title: "Upload nbconvert config",
+        open: function() {
+          fileinput.focus();
+        },
+        body: body,
+        buttons: {
+          cancel: {
+            click: function() {
+              return true;
+            }
+          },
+          download: { click: trigger_nbconvert_post }
+        }
+      });
+
+      mod.modal("show");
+    };
+
+
     MenuBar.prototype._nbconvert = function (format, download) {
         download = download || false;
         var notebook_path = utils.encode_uri_components(this.notebook.notebook_path);
@@ -139,12 +295,12 @@ define([
             format,
             notebook_path
         ) + "?download=" + download.toString();
-        
+
         this._new_window(url);
     };
 
     MenuBar.prototype._size_header = function() {
-        /** 
+        /**
          * Update header spacer size.
          */
         console.warn('`_size_header` is deprecated and will be removed in future versions.'+
@@ -157,7 +313,7 @@ define([
          *  File
          */
         var that = this;
-        
+
         this.element.find('#open_notebook').click(function () {
             var parent = utils.url_path_split(that.notebook.notebook_path)[0];
             window.open(
@@ -184,7 +340,7 @@ define([
                 that._new_window(url);
             }
         });
-        
+
         this.element.find('#print_preview').click(function () {
             that._nbconvert('html', false);
         });
@@ -193,6 +349,10 @@ define([
             that._nbconvert(ev.target.parentElement.getAttribute('id').substring(9), true);
         });
 
+        this.element.find('#custom_download').click(function(){
+            that._nbconvert_upload_conf(true);
+        });
+
         this.events.on('trust_changed.Notebook', function (event, trusted) {
             if (trusted) {
                 that.element.find('#trust_notebook')
@@ -261,7 +421,7 @@ define([
             '#copy_cell_attachments': 'copy-cell-attachments',
             '#paste_cell_attachments': 'paste-cell-attachments',
             '#insert_image': 'insert-image',
-            '#edit_keyboard_shortcuts' : 'edit-command-mode-keyboard-shortcuts',
+            '#edit_keyboard_shortcuts' : 'edit-command-mode-keyboard-shortcuts'
         };
 
         for(var idx in id_actions_dict){
@@ -280,7 +440,7 @@ define([
             })(that, id_act, idx);
         }
 
-        
+
         // Kernel
         this.element.find('#reconnect_kernel').click(function () {
             that.notebook.kernel.reconnect();
@@ -296,33 +456,33 @@ define([
         this.element.find('#keyboard_shortcuts').click(function () {
             that.quick_help.show_keyboard_shortcuts();
         });
-        
+
         this.update_restore_checkpoint(null);
-        
+
         this.events.on('checkpoints_listed.Notebook', function (event, data) {
             that.update_restore_checkpoint(that.notebook.checkpoints);
         });
-        
+
         this.events.on('checkpoint_created.Notebook', function (event, data) {
             that.update_restore_checkpoint(that.notebook.checkpoints);
         });
-        
+
         this.events.on('notebook_loaded.Notebook', function() {
             var langinfo = that.notebook.metadata.language_info || {};
             that.update_nbconvert_script(langinfo);
         });
-        
+
         this.events.on('kernel_ready.Kernel', function(event, data) {
             var langinfo = data.kernel.info_reply.language_info || {};
             that.update_nbconvert_script(langinfo);
             that.add_kernel_help_links(data.kernel.info_reply.help_links || []);
         });
     };
-    
+
     MenuBar.prototype._add_celltoolbar_list = function () {
         var that = this;
         var submenu = $("#menu-cell-toolbar-submenu");
-        
+
         function preset_added(event, data) {
             var name = data.name;
             submenu.append(
@@ -346,7 +506,7 @@ define([
                 )
             );
         }
-        
+
         // Setup the existing presets
         var presets = celltoolbar.CellToolbar.list_presets();
         preset_added(null, {name: i18n.msg._("None")});
@@ -356,7 +516,7 @@ define([
 
         // Setup future preset registrations
         this.events.on('preset_added.CellToolbar', preset_added);
-        
+
         // Handle unregistered presets
         this.events.on('unregistered_preset.CellToolbar', function (event, data) {
             submenu.find("li[data-name='" + encodeURIComponent(data.name) + "']").remove();
@@ -377,7 +537,7 @@ define([
             );
             return;
         }
-        
+
         var that = this;
         checkpoints.map(function (checkpoint) {
             var d = new Date(checkpoint.last_modified);
@@ -393,13 +553,13 @@ define([
             );
         });
     };
-    
+
     MenuBar.prototype.update_nbconvert_script = function(langinfo) {
         /**
          * Set the 'Download as foo' menu option for the relevant language.
          */
         var el = this.element.find('#download_script');
-        
+
         // Set menu entry text to e.g. "Python (.py)"
         var langname = (langinfo.name || 'Script');
         langname = langname.charAt(0).toUpperCase()+langname.substr(1); // Capitalise
@@ -443,7 +603,7 @@ define([
             );
             cursor = cursor.next();
         });
-        
+
     };
 
     return {'MenuBar': MenuBar};
diff --git a/notebook/templates/notebook.html b/notebook/templates/notebook.html
index 7e627b1f92..9f0dc79c94 100644
--- a/notebook/templates/notebook.html
+++ b/notebook/templates/notebook.html
@@ -104,10 +104,11 @@
                         </li>
                         <li class="divider"></li>
                         <li id="print_preview"><a href="#">{% trans %}Print Preview{% endtrans %}</a></li>
+                        <li id="custom_download"><a href="#">{% trans %}Custom Download {% endtrans %}</a></li>
                         <li class="dropdown-submenu"><a href="#">{% trans %}Download as{% endtrans %}</a>
                             <ul id="download_menu" class="dropdown-menu">
                                 <li id="download_ipynb"><a href="#">{% trans %}Notebook (.ipynb){% endtrans %}</a></li>
-                                <li id="download_script"><a href="#">{% trans %}Script{% endtrans %}</a></li>
+                                <li id="download_script"><a href="#">S{% trans %}script{% endtrans %}</a></li>
                                 <li id="download_html"><a href="#">{% trans %}HTML (.html){% endtrans %}</a></li>
                                 <li id="download_slides"><a href="#">{% trans %}Reveal.js slides (.html){% endtrans %}</a></li>
                                 <li id="download_markdown"><a href="#">{% trans %}Markdown (.md){% endtrans %}</a></li>