nightingale

Nightingale is a monorepo containing visualisation web components to use with biological data.

Documentation/Getting started

Documentation, getting started guide and examples for each of the components are available here https://ebi-webcomponents.github.io/nightingale

Contributing

Read our guide here as well as our code of conduct

Installing

Nightingale uses Lerna to manage its packages.

First run yarn to install root packages. Then run yarn bootstrap to install remaining modules and link dependencies.

Building the components

Run yarn build

Showcase application

Locally

Run yarn start to run the application locally.

Build

Run yarn build to build the application ready for deployment.

Components

ProtVista

Visualisation components

protvista-zoomable: A superclass providing zooming functionality (uses D3's zoom).

protvista-track: The base component to render features. Responds to zoom and allows highlights. Extends protvista-zoomable.

protvista-navigation: The main navigation component, allows zooming and shows the position of the visible window along the sequence.

protvista-sequence: Displays the amino-acid sequence. Responds to zoom and allows highlights. Extends protvista-zoomable.

protvista-variation: An adjacency graph to represent variation data, mapping amino-acids to position. Extends protvista-track.

protvista-variation-graph: a graph representing the number of variants at a given position. Extends protvista-track.

protvista-interpro-track: A specialisation of protvista-track to use in InterPro. Extends protvista-track.

protvista-datatable: an interactive table view of features. Can highlight/be highlighted by features from the protvista-track

protvista-coloured-sequence: Track that uses the sequence to paint a color depending on each residue. Extends protvista-sequence.

protvista-msa: an element displaying multiple sequence alignments. Extends. protvista-zoomable.

protvista-links: a track representing inter-residue contacts with arcs. Extends. protvista-track.

Data loading and adapters

Most components use the Proteins API

data-loader: this component can load json data given a url. It caches the results in the window so multiple calls

protvista-uniprot-entry-adapter: a superclass providing basic functionality for data transformation and handling of events.

protvista-variation-adapter: this component transforms data returned by the Proteins API Variation service so it can be displayed by the protvista-variation and protvista-variation-graph components. Extends protvista-uniprot-entry-adapter.

protvista-feature-adapter this component transforms data returned by the Proteins API Features service so it can be displayed by the protvista-track component. Extends protvista-uniprot-entry-adapter.

protvista-proteomics-adapter this component transforms data returned by the Proteins API Proteomics service so it can be displayed by the protvista-track component. Extends protvista-uniprot-entry-adapter.

protvista-structure-adapter this component transforms structure data returned by the Proteins API Proteins service so it can be displayed by the protvista-track component. Extends protvista-uniprot-entry-adapter.

protvista-topology-adapter this component transforms topological data returned by the Proteins API Features service so it can be displayed by the protvista-track component. Extends protvista-uniprot-entry-adapter.