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Welcome to the general public face of Noctua. Current development is very rapid, so some of these docs may be out of date.

Noctua screenshot

Quickstart

  • Noctua Users
  • Software Developers -- Development and technical documentation can be found on the GitHub repository.
  • Bioinformaticians and Systems Biologists -- See the Noctua models repository for access to the underlying models and explanation of the OWL representation
  • Biologists and end-users -- We are working on a number of ways to make the models easier to search and to use in data interpretation

How to use the beta

The current preview instance is available here; for a toy example model, see one of the scratch models.

This instance is configured for use with the Gene Ontology project.

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

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, Heiko, or Chris.

  • When editing large models, you may reach a point where almost anything you do will cause an error and hang (refresh to get back to where you were); if you want to make sure your model is saved, contact Seth #151
  • 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

Troubleshooting

  • Newer versions of Chrome and Firefox are supported, Safari is not supported
  • You need to have cookies allowed in your browser (for Persona)
  • Ad-blockers have been known to cause problems, please use a clean browser profile
  • You cannot save unless you have a title.
  • You cannot delete.
  • When weird things happen, this is pretty much what you should try:
  • Refresh your page
  • "Hard" refresh your page (probably by pressing "shift" or something when you refresh; the idea is to try and flush your cache, getting things freshly from the server)
  • Are you logged in? Are you sure? Try logging out and logging back in again--a bad session can cause all sorts of interesting things
  • Try going back to the main landing page, finding your model again, and trying again
  • Try contacting Seth, Chris, or Heiko

Noctua Resources