C. elegans DevoLearn

Web App to support the C. elegans part of the Devolearn library.

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What is it?

This is a web app implementation of C.elegans part of the Devolearn library. For the researchers out there who are not very familiar with programing but are in need to use Machine lerning and Neural networks to accelerate their research can use this tool.

It is a highly interactive and user friendly tool to get quick results, with all the information of C.elegans Embrogenesis process.

Repository Tree

Below is the repository tree to indicate where which files are being located.

│   app.py
│   Aptfile
│   Procfile
│   requirements.txt
│   runtime.txt
│
├───static
│   │   devoworm-logo.png
│   │   google_summer_of_code.png
│   │   incf.png
│   │   openworm.jpeg
│   │
│   ├───css
│   │   │   css-main.css
│   │   │   css-noscript.css
│   │   │
│   │   └───styles
│   │           bootstrap_min.css
│   │           font_awesome_min.css
│   │           min.css
│   │
│   ├───images
│   │       22.gif
│   │       3d_segmentation_preds.gif
│   │       DevoLearn.gif
│   │       generated_embryos_3.gif
│   │       images-bg.jpg
│   │       images-overlay.png
│   │       images-pic01.jpg
│   │       images-pic02.jpg
│   │       images-pic03.jpg
│   │       resnet_preds_with_input.gif
│   │       worm_stages.jpg
│   │
│   ├───js
│   │       js-jquery.min.js
│   │       js-main.js
│   │       js-skel.min.js
│   │       js-util.js
│   │
│   └───styles
│           bootstrap_min.css
│           font_awesome_min.css
│           min.css
│
├───templates
│       index.html
│       result.html
│
└───__pycache__
        app.cpython-38.pyc

How to use it?

This tool is part of DevoWormAI. More over, this tool also provides reseachers all necessary code by the means of Google Colab notebooks which can be found in this directory. This notebook is for those who have understanding of Machine learning and neural networks and they can tweak the params according to their need for the best results.

Online Resource

If you want to try out our online tool, please visit - OpenDevoCell For more of our research and tools, please visit our Home Page - DevoWormAI

Can I use it on my local machine?

Yes, it is a web app that you can easily install and run on your device. Please Follow the below instructions to proceed.

Step 1- Clone this repo in your Computer. Step 2- Unzip the contents into desired folder. Step 3- Go to your Terminal/Command Prompt(CMD) and navigate to the folder where you have extracted files. Step 4- Create a Virtual Environment by using the below command.

• For macOS and Linux use

python3 -m pip install --user <your_virtual_env_name>

• For Windows use

py -m pip install --user <your_virtual_env_name>

Step 5- After creating virtual environment, enter in it using command.

source <your_virtual_env_name>/bin/activate

Step 6- Now, install all the required packages using requirements.txt using command.

pip install -r requirements.txt

Step 7- Now, all the installation process is done, and is done correctly, app is ready to run. To run the app, use command.

python3 -m flask run

Version

Version Info: V-0.0.1

Contact us

Authors/maintainers:

• Ujjwal Singh
• Mayukh Deb
• Dr. Bradly Alicea

Feel free to join our slack!