Displaying 1 to 11 from 11 results

cytoscape

  •    Javascript

Cytoscape.js is a fully featured graph theory library. Do you need to model and/or visualise relational data, like biological data or social networks? If so, Cytoscape.js is just what you need. Cytoscape.js contains a graph theory model and an optional renderer to display interactive graphs. This library was designed to make it as easy as possible for programmers and scientists to use graph theory in their apps, whether it's for server-side analysis in a Node.js app or for a rich user interface.

dash-bio - Open-source bioinformatics components for Dash

  •    Python

Dash Bio is a suite of bioinformatics components built to work with Dash. Learn more about Dash at https://plotly.com/products/dash/.

pv - WebGL protein viewer

  •    Javascript

pv is a WebGL-based protein viewer whose goal is to once-for-all end the reign of Java applets on websites that require visualisation of protein structures. It's not you Java, it's all the annoying security popups and slow loading times. pv implements all major render modes that you would expect, and supports custom color schemes. Because there is nothing worse than an unresponsive website, pv has been implemented with maximum performance in mind. Even very large macromolecules can be visualised at interactive framerates.

dnaism - Horizon chart js library for DNA data.

  •    CSS

Main site here. Paper here. Please open a ticket and we will be happy to help you.




GRNsight - Web app and service for modeling and visualizing gene regulatory networks.

  •    Javascript

GRNsight is an open source web application and service for visualizing models of small- to medium-scale gene regulatory networks. GRNsight is a joint project of the Loyola Marymount University Bioinformatics and Biomathematics Groups, headed by Dr. Kam Dahlquist, Dr. John David N. Dionisio, and Dr. Ben G. Fitzpatrick. Undergraduate students initiated the development of GRNsight in Spring 2014, including Britain Southwick (Computer Science, ’14) and Nicole Anguiano (Computer Science, ’16), with consultation from Katrina Sherbina (Biomathematics, ’14). For current contributors, please see our People page. A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them, which govern the level of expression of mRNA and protein from those genes. GRNs can be mathematically modeled and simulated by applications such as GRNmap, a MATLAB program that estimates the parameters and performs forward simulations of a differential equations model of a GRN. Computer representations of GRNs, such as the models output by GRNmap, are in the form of a tabular spreadsheet (adjacency matrix) that is not easily interpretable. Ideally, GRNs should be displayed as diagrams (graphs) detailing the regulatory relationships (edges) between each gene (node) in the network. To address this need, we developed GRNsight.

muts-needle-plot - A needle plot for mutation data

  •    Javascript

A needle-plot (aka stem-plot or lollipop-plot) plots each data point as a big dot and adds a vertical line that makes it appear like a needle. This library is can be found as npm-library in the BioJS registry.

NtSeq - JavaScript (node + browser) bioinformatics library for nucleotide sequence manipulation and analysis

  •    Javascript

NtSeq is an open source Bioinformatics library written in JavaScript that provides DNA sequence manipulation and analysis tools for node and the browser. More specifically, it's a library for dealing with all kinds of nucleotide sequences, including degenerate nucleotides. It's built with the developer (and scientist) in mind with simple, readable methods that are part of the standard molecular biologist's vocabulary.


msa - Modular BioJS compoment for a multiple sequence alignment

  •    Javascript

Multiple Sequence Alignment Viewer - the MSAViewer - a BioJS component. Yes you can either link to the minified, gzipped CDN version or download the dev version from S3 .

biojs-io-newick - Newick Parser in JS - parses newick strings into JSON and JSON into newick

  •    Javascript

Now include biojs-io-newick.min.js in the build folder into your html (see example.html). Just call method parse_newick(string) for parsing a newick string into JSON. Call the method parse_nhx(string) for parsing an extended newick formats into JSON.

exelixis - Interactive and easy-to-use phylogenetic tree viewer for the web

  •    Javascript

Interactive and easy-to-use phylogenetic tree viewer for the web build on TnT.tree. Following default settings can be customized.






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