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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 Current development is very rapid, so some of these docs may be out of date.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 is a web-based tool for collaborative editing of models of biological processes.

Noctua screenshot

Quickstart

  • Noctua Users
  • Software Developers -- Development and technical documentation can be found on the GitHub repository.
  • Bioinformaticians -- See the Noctua models repository for access to the underlying models and explanation of the OWL representation

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
  • 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, Heiko, 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.