AI-Powered EcoGenomics

A web application that provides inexpensive computational methods of assessing biodiversity and both genomic and environmental components of resilience with genome skims.

This website is still in development and only available for local usage

Local Installation

Pythong 3.6 and up is required to install locally

Clone the repository

Navigate to your cloned repository and set up a virtual environment and install all dependencies:

Using conda:

conda env create -f environment.yml
conda activate env

Using pip:

python3 -m venv env
source env/bin/activate
pip install -r requirements.txt

Set up flask development server

export FLASK_APP=run.py
export FLASK_ENV=development

Local Usage

Follow this instruction whenever you want to run the web application on local computer (after installation)

For the application to run as expected, user must install all tools listed in the "tools" section. Please refer to the git repoistory linked in the description.

Go to the cloned local directory
Activate the virtual environment:
- Using conda:
```
conda activate env
```
- Using pip:
```
source env/bin/activate
```
Use following command line to run Flask application:
```
flask run
```
Once ran, development server will be running on localhost:5000 in your default web browser

Tools

CONSULT: Remove contamination by filtering extraneous reads

To install this tool in your local computer refer here.

RESPECT: Given the cleaned up reads, RESPECT will output the estimated genomic length of the species and the repeat spectrum.

To install this tool in your local computer refer here.

Skmer: Estimate distances between genomes from low-coverage sequencing reads (genome-skims), without needing any assembly or alignment step

To install this tool in your local computer refer here.

APPLE: Accurately phylogenetically place the reads into tree

Not integrated into the website yet

MISA: Analyze mixed samples of multiple species that are hard to physically separate before sequencing

Not integrated into the website yet

Online Usage

Home Page

When development server starts running, the home page looks like this:
- - First Look of the home page includes:
    - Navigation Bar:
      - Home: Allows users to navigate back to the home page wherever they in the website (this is the default of the website)
      - Flow Diagram: Since there are more than one way for the users to use each tools, there is a basic flowchart that shows the users the basic pipeline of the tools. There are 4 different pipeline that the users can use on this website: 1. Processing of Individual Query and References 2. Distance Estimation 3. Indication of Query 4. Mixture of Analysis. The diagram shows the relationship between one pipeline to the other.
      - App: This is a dropdown menu that allows user to navigate to any one of the tools that are described in the "Tools" section. When any one of the options are selected, it navigates the users to a page that describes the function of the tool and allows the users to run each tools individually and separately from the pipeline.
      - Contact Us: Navigates the users to the contact page. Users can contact the developers using this function.
    - Header: This has a basic description of the website also giving the user the option to know more about the website by referring them to a link that has a more indepth description of the project.
    - Choose your Pipeline: This section gives access to the tools from the very beginning. Pipeline 1, 2, 3, and 4 are buttons that navigate the users to the respective page that allows users to input their sample reads to run the set of tools that are needed to execute each of the pipeline.
  - Second Page of home page:
    - Scroll down to the second page of the home page, and we will see the flow diagram of the tools:
  - Third Page of home page:
    - Scroll down to the third page of the home page, and we will see the Applications that are included in the website:
      - Each tools shown are buttons that takes users to the page that describes and run each tool.
When the user clicks on any of the Application tools, the user will see the following form:
- - After a brief explanation of the tool, there is a form that allows users to run the tools individually from the pipeline.
  - User email is required since the tool is ran independently of local computer. Inputting email allows the users to navigate away from the web page and still receive the results via email.
  - Once the user submits the sample input and email address and the results are processed, the user will receive an email with a link to the results page with the visualization of the output and text files that contains the output:
Results Page:
- The visualization is still in development
Contact Us page:
- - Asks for user's Name, email address and Reason of Contact
  - When the email is sent to the user, the developers will receive an email of this form