noctua v0.0.10

• The Noctua (Editor + Barista + Minerva) Stack

  Previously the GO MME.

  Current development is very rapid, so some of these docs may be out of date.

  More docs/API to be found [http://geneontology.github.io/noctua].

  Prototype editor frontend (Noctua) and messenger server (Barista) for the Gene Ontology Molecular Modal Environment server (Minerva).

  It is based on BBOP(X) JS (using the AmiGO 2 environment) and jsPlumb. The backend is the OWLTools Molecular Model Manager.

  While the editor is generally developed with Firefox, the user experience using Chrome/Chromium is quite a bit smoother.

  The current alpha instance is available at: http://noctua.berkeleybop.org

** Installation

You must start with a modern version of Node.js (say >=0.12.3). All of the tooling is built around that and should install easily with:

: npm install : ./node_modules/.bin/gulp build

Or, if you have "./node_modules/.bin" in your paht:

: npm install : gulp build

Tha available gulp tasks are:

• doc - build the docs, available in doc/
• test - need more here
• build - assemble the apps for running
• watch - development file monitor
• clean - clean out /doc and /deploy

** Running

*** Minerva

TODO

Everybody is different, but mine is like: 

: GENEONTOLOGY="/home/sjcarbon/local/src/svn/geneontology.org/trunk/" make start-minerva-go-fast

*** Barista

TODO

Everybody is different, but mine is like: 

: make start-barista-dev

*** Graph Editor (previously "Noctua")

TODO

Everybody is different, but mine is like: 

: make start-noctua-dev

How to use demo * Generating/selecting a model

- Models that are currently known (either in memory or file) are
  found under [Current State] > select "Usable" > [Jump]
- To create a new model from a class and a DB, use [Wizard] >
  (fill out first sections) > [Generate]; this operation could
  take tens of minutes depending on the complexity
- To create a new model from just a DB, use [Wizard] > (fill out
  second section) > [Generate]; this operation may take minutes
  depending on the size of the GAF to be loaded
- Directly loading by copy-and-paste is not currently tested

*** Instances and edges

• A new instance can be created by filling in the form on the left side of the display
• Double clicking edges and instances allows the editing of evidence and comments
• Clicking on the green box upper-left of an instance allows you to view and edit the instance type information
• By dragging the blue circle in the upper-right of an instance to anywhere on a different instance will allow you to create a relation between the two

• A complex expression can be added by opening the instance type editor and

  • Selecting: enabled_by
  • Entering an expression of the form: "GO:0043234 and ('has part' some UniProtKB:P0002) and ('has part' some UniProtKB:P0003)"

*** Models

- Model meta information can be edited by selecting [Model] >
  [Edit annotations] from the top menu
- [Model] > [Soft refresh] gets a fully updated model from the
  server; this is what you'll use for the time being when another
  user makes a change to the model
- [Model] > [Reset] complete reloads everything from the server
  from scratch
- To export to a text file (Manchester syntax), use
  [Export]
- To save your current model, select [Model] > [Save]; your model
  should now be available from the landing page

*** General navigation

- Dragging on the background of the model allows you to pan around
  without using the scrollbars
- Under [Views], there are various zooming options
- To reduce clutter, the "part of" relation can be hidden by
  selecting [View] > [Show/hide "part of"]
- The minimum space you start with is 800x600px. If you need more,
  try reseting your model--the space you can use will grow with
  it.

** Known Issues

The bulk of major issues and feature requests are handled by the tracker (https://github.com/geneontology/noctua/issues). If something is not mentioned here or in the tracker, please contact Seth or Chris.

• Sometimes, when moving instance or relations near a boundary, the relations will fall out of sync; either move nearby instances or refresh the model
• Sometimes, when editing an instance, the relations (edges) will fall out of sync; either move nearby instances or refresh the model
• The endpoint scheme is reversed between creation and instantiation
• TODO, etc.

** Deployment +This should be deployable in most JS environments. It should be+ +noted that we do most development on Ubuntu 12.04 using Chris Lea's+ +[https://launchpad.net/~chris-lea/+archive/ubuntu/node.js]. Also, our alpha deployment environment is RedHat's OpenShift,+ +so we're hoping this is fairly flexible.+

We do have people who have run the whole stack easily on OS X.

*** Running Minerva The main/best way to run Minerva is with the "start-go-minerva.sh" script, found in the [https://code.google.com/p/owltools/] (in owltools/MolecularModelServer/bin). The only input parameter is the root directory for the local GO-SVN checkout.

In typical setup for running Minerva, you will have to:

- Build Minerva (only required after updates): build-server.sh
- Start server: start-go-minerva.sh /path/to/GO-trunk

*** Running Noctua and Barista The most important part of getting familiar with the setup is understanding the options in the Makefile. As well, besides the environmental variables, there are a couple of important files for configuration:

- config/app.json
- config/users.json

These are the backend mapping configuration and user authorization
files respectively.

Also, remember that Noctua cannot be run successfully until both
Minerva and Barista are running.

Also remember that Barista and Noctua are designed to be very
flexible about where they are pointing, so that configurations
like cloud -> server -> another server and perfectly fine. It is
important to look at the initial output of all the server to know
who that are trying to talk to and where they are--it is all
configurable, you just need the right option.

** Local testing make start-barista make start-noctua ** Local testing with copies of BBOP JS and BBOPX JS make start-barista-dev make start-noctua-dev ** OpenShift (currently noctua.js only) git push openshift master (currently at: http://go-genkisugi.rhcloud.com/) ** Heroku (currently noctua.js only) TODO