C. elegans Protein Extraction Pipeline 🪱

A DevoWorm / OpenWorm Studentship Project

📖 About This Project

This repository provides an automated, open-source pipeline to extract and analyze protein sequence data specific to the nematode Caenorhabditis elegans.

Computational models of C. elegans embryogenesis, such as those exploring invariant cell lineages and differentiation waves (e.g., Alicea et al., 2024), must be grounded in underlying molecular biology. This tool uses Biopython and the NCBI API to automate BLAST searches against the non-redundant database, strictly filtering for the C. elegans proteome.

It allows researchers to rapidly pull homolog data, sequence alignments, and e-values for key developmental drivers without manual web scraping. Target proteins include:

• Wnt Signaling Pathway: APC, AXIN, and β-catenin, which help dictate cell fate and polarity.
• Cell Cycle Regulators: CDK-1 and Cyclin D, which drive the timing of lineage divisions.
• Kinase Cascades: MAPK and JNK, which transduce developmental signals.

🗂️ Repository Contents

• DevoWorm_Protein_Pipeline.ipynb: The main Jupyter Notebook containing the automated extraction pipeline.
• requirements.txt: The Python dependencies required to run the code.
• Alicea et al.pdf: Reference literature detailing the differentiation wave models this pipeline supports.

⚙️ How to Use This Pipeline

1. Clone the Repository

Clone this repository to your local machine using your terminal:

git clone https://github.com/bastanisl/owproject.git
cd owproject

2. Install Dependencies

Ensure you have Jupyter installed, then install the required Python libraries:

pip install -r requirements.txt

3. Run the Notebook

Launch Jupyter:

jupyter lab

Open DevoWorm_Protein_Pipeline.ipynb and run the cells sequentially. The notebook includes Markdown explanations describing how to modify the protein targets and parse the resulting JSON data.

📊 What the Data Shows

The pipeline outputs structured JSON files containing BlastOutput2 objects. These files contain:

• Confirmed C. elegans homolog accession IDs.
• E-values indicating the statistical significance of each match.
• Sequence identity and alignment lengths.

This data can be directly integrated into downstream systems biology models to bridge theoretical lineage waves with actual genomic sequence data.

👨‍🔬 Author

Soroush Bastani
Developed as part of the OpenWorm Foundation Studentship.