Evidente 2.0

This project was bootstrapped with Create React App.

Requirements

The project is running with the following requirements. Lower versions might work, but are not tested

• Node: v16.13.0
• npm: 8.1.3
• python: 3.7.4
• java: Java(TM) SE Runtime Environment (build 14.0.1+7)

Run Devolpment Version

1. Go to project folder
2. Run setup.sh to install all npm and python packages bash setup.sh
3. Activate virtual environment source env/bin/activate
4. Run development version of evidente npm run evidente
5. Open http://localhost:3000 to view it in the browser.

Run Deployment Version

1. Go to project folder
2. Create virtual environment python3 -m venv env
3. Activate virtual environment source env/bin/activate
4. Install python dependencies pip install -r requirements.txt
5. Install server package (setup.py) pip install .
6. Install npm packages npm install
7. Build deployment version of code npm run build
8. Run server npm run server
9. Access deployed version at http://localhost:5000/

Available Examples

Toy Example

Toy example with 38 taxa and 10 SNPs. The phylogenetic tree is a modified version of the one presented by Yokoyama et al (2008, Publication). The SNPs are based on the table of the Mycobacterim leprae by Schuenemann et al (2018, Publication). Hence, this example does not show any biological data, but it can still be used to get to know the GUI of Evidente.

Mini Example

Extract of the Toy Example with seven taxa. This example is used to initialize Evidente.

Mycobacterium leprae

From Schuenemann et al (2018, Publication). The study analyzed over 169 taxa of different species around the globe and identified 3155 SNPs. It provides a metadata file with the location and date of extraction of the samples.

Treponema pallidum

From Arora et al (2016, Publication). The study analyzed around 120 samples of different strains of the T. pallidum collected around the globe. It analyzed their antibiotic resistance and it was able to identified a correlation between the presence of SNP 235204 and a resistance to the antibiotic macrolide.

contents.txt

Contains a list of contents of the evidente2 repository including all files relevant during the extension of evidente2.0 together with a short description.

CLASSICO

To get more information on the module CLASSICO visit its repository