Welcome to Noctua

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Noctua is a web-based tool for collaborative editing of models of biological processes.

You must Login to create or edit models. Models may be viewed without login.

Find Existing Models

Title Contributors State Date Mod Tmpl Dep GH Operations
Title Contributors State Date Mod Tmpl Dep GH Operations

Browse

Using AmiGO 2 Labs, search a somewhat recent (once or twice a week) scan of the models created using Noctua/Minerva.

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Create new model from the æther

You must be logged in to create a new model. You will jump directly to the graph editor UI for the new empty model.

Seed a new model from process and taxon

You must be logged in to create a new model from a taxon. If successful, you will jump directly to the graph editor UI for the new seeded model.

Create new model from the æther (prototype form) ALPHA

You must be logged in to create a new model. You will jump directly to the prototype form editor UI for the new empty model.

Load model using ??? format ALPHA

You do not want to be using this right now.

Welcome to Noctua

Noctua is a web-based tool for collaborative editing of models of biological processes.

About Noctua

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 Current development is very rapid, so some of these docs may be out of date.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

Capella Bootstrap

Various test methods to look at how capella kick-ins behave.

(blank)
(test payload)

JSON Debugging

Noctua Client Administration

Barista Administration

No admin available here--did you remember to login?
A configuration error is also possible.