# accusyn

**Repository Path**: chens1209/accusyn

## Basic Information

- **Project Name**: accusyn
- **Description**: AccuSyn: An Accurate Web-based Genome Synteny Browser
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-08-11
- **Last Updated**: 2020-12-20

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# AccuSyn
Website: [https://accusyn.usask.ca/](https://accusyn.usask.ca/)

<p align="center">
  <img src="https://accusyn.usask.ca/images/after.svg" width="500" height="500">
  <br />
  <i>AccuSyn providing a complete overview of the conserved synteny blocks in the Wheat genome.</i>
</p>

## Description

We apply Simulated Annealing, a well-known heuristic for obtaining near-optimal solutions to optimization problems, to discover conserved synteny relations (similar features) in genomes. As even simple organisms have huge numbers of genetic features, syntenic plots present an enormous clutter of connections, making the structure difficult to understand. Our interactive software, AccuSyn, visualizes syntenic relations with circular plots of chromosomes and draws links between similar blocks of genes, using Simulated Annealing to minimize link crossings. This provides geneticists with insights into the evolutionary history of species or functional relationships between genes. AccuSyn is actively used in the research being done at the University of Saskatchewan and has already produced a visualization of the recently-sequenced Wheat genome.

## Development

AccuSyn is a client-side-only application created using JavaScript. These three main libraries made this project possible: [D3.js](https://github.com/d3/d3), [CircosJS](https://github.com/nicgirault/circosJS), and [React.js](https://github.com/facebook/react).

To interact with AccuSyn locally, first install all the project dependencies using the Node Package Manager (`npm`):
```
  npm install
```
Then, run a development server inside the `accusyn` directory using `webpack-dev-server`, which also watches for changes and re-compiles the local bundle automatically:
```
  npm run start
```
Finally, go to [http://localhost:8080/](http://localhost:8080/) using Google Chrome (our recommended browser for the best app experience).

To build a production-ready minified JavaScript file, run:
```
  npm run build
```

**Note:** AccuSyn has been created using `node v6.11.3 (LTS)` and `npm v3.10.10`.

## Contact

Jorge Nunez Siri - jorge.nunez@usask.ca

AccuSyn has been created as part of the research being done by [P<sup>2</sup>IRC](https://p2irc.usask.ca) at the [University of Saskatchewan](https://www.usask.ca).

> Copyright &copy; 2018 - 2019 Jorge Nunez Siri. All rights reserved.