vbookshelf/Bioinformatics-Toolkit-HYA

Bioinformatics Toolkit v1.0

Bioinformatics is plagued by software dependency drama. The Bioinformatics Toolkit makes it easy to set up a computational software environment. This allows researchers and students to focus on science rather than software troubleshooting.

It's a pre-built bioinformatics env for macOS that bundles the Python 3.12 interpreter and the uv binary. Packages are auto downloaded during the first run. The app is launched with a double-click.

This is a Hybrid App (HYA). The first install requires an internet connection. After that it can run offline.

• A portable folder-based app.
• No system-wide installation required.
• The Python 3.12 interpreter is included.
• The uv binary is also included.
• The list of included packages can be easily modified.
• uv automatically resolves all dependencies to prevent clashes.
• Internet access can be toggled off after the initial install. This ensures the environment is frozen and work is reproducible.
• Double-click to launch.

Who is this for?

• Educators and Students
• Researchers who are transitioning into computational biology
• Anyone who wants to explore and experiment with Bioinformatics tools and techniques

What packages are included?

pandas==3.0.1
numpy==2.4.3
scipy==1.17.1
scikit-learn==1.8.0
xgboost==3.2.0
lightgbm==4.6.0
catboost==1.2.10
tqdm==4.67.3
biopython==1.86
scanpy==1.12
pysam==0.23.3
scikit-bio==0.7.2
pyucell==0.5.0
matplotlib==3.10.8
seaborn==0.13.2
plotly==6.6.0
nglview==4.0.1
jupyter==1.1.1
jupyterlab==4.5.6

How to Use

System Requirements:

• Operating System: MacOS
• Computer: Apple Silicon Mac (M1, M2, M3, etc.)
• RAM: 8 GB
• Free disk Space: 1.1 GB

1. Download the Bioinformatics-Toolkit-v1.0-HYA.zip folder and unzip.

2. Right click on the Bioinformatics-Toolkit-v1.0-HYA folder and select: New Terminal at Folder

3. MacOS often quarantines downloaded files. To make the launch script executable, paste this command into the terminal and press Enter:

cat start-mac-app.command > temp && mv temp start-mac-app.command && chmod +x start-mac-app.command

You only need to do this once, during the setup.

4. Open the Bioinformatics-Toolkit-v1.0-HYA folder and double-click this file: start-mac-app.command
   If a MacOS security popup appears, click: "Allow"

5. The packages will be downloaded.

6. JupyterLab will then open. This may take a few seconds. Please be patient if you don't see anything happening. During normal use the app will open much faster.

One Command. Complete Control.

You would have noticed that, to make this app executable, this command needed to be typed in the terminal:

cat start-mac-app.command > temp && mv temp start-mac-app.command && chmod +x start-mac-app.command

To remove this requirement the start-mac-app.command file would need to be code signed. Most macOS apps distributed outside the App Store are code signed using an Apple Developer ID certificate. Code signing requires an active Apple Developer Program membership.

This project does not use code signing because it introduces a point of failure. If the Apple membership lapses, or if Apple revokes the certificate for any reason, signed apps will stop launching cleanly for new users. This risk is unacceptable.

In exchange for the minor inconvenience of typing one command into the terminal during setup, you get a reliable app that has no dependency on any third party. You have complete control.

How to add or remove packages

First, install uv (system-wide)

Paste this command into the terminal and press Enter:

wget -qO- https://astral.sh/uv/install.sh | sh

There are two ways to add new python packages.

You won’t need to worry about clashes - uv will automatically resolve all dependencies.

Option 1:

Right click on the app sub folder and select: New Terminal at Folder
Type this into the terminal and press Enter:

uv add <package-name>

e.g. uv add pyserial

The package will be downloaded and the pyproject.toml file will be automatically updated to include the new package name.

Option 2:

Open the pyproject.toml file in a text editor. Add the new package name/s to the list.
Right click on the app sub folder and select: New Terminal at Folder
Type this into the terminal and press Enter:

uv sync

The packages will be downloaded.

To ensure that your work is reproducible, please pin all dependencies to exact versions in pyproject.toml.
Do: pandas==3.0.1
Avoid: pandas>=3.0.1
This prevents 'dependency drift' and ensures everyone on your team is running the same code.

References

• Offline Data Lab
  https://huggingface.co/datasets/vbookshelf/Offline-Data-Lab-TDA

• Data Science Toolkit
  https://huggingface.co/datasets/vbookshelf/Data-Science-Toolkit-HYA

Revision History

Version 1.0
22-March-2026
Prototype. Released for testing.