kyegomez / GeneSplice

An Model for Ultra Long Gene Expression sequences

GeneSplice 🧬

"Nature uses only the longest threads to weave her patterns, so each small piece of her fabric reveals the organization of the entire tapestry." - Richard Feynman

What is Geneplice?

Leveraging advanced machine learning techniques, particularly transformer-based models, in the realm of gene editing could revolutionize the treatment of genetic disorders and disease. GeneSplice aims to harness the capabilities of transformer models to expedite and streamline the creation of plasmid DNA sequences for CRISPR gene editing.

Objective

The primary objective of GeneSplice is to provide an end-to-end solution for gene sequencing and editing:

1. Obtain a DNA sample from a patient (for instance, via saliva).
2. The DNA is sequenced and the data is processed by GeneSplice.
3. GeneSplice identifies potentially harmful mutations and devises a new plasmid DNA sequence that can be used for CRISPR gene editing.
4. The new DNA sequence is then inserted back into the patient to counteract the disorder.

Model Architecture

The GeneSplice model is predicated on the transformer architecture, which is renowned for its proficiency in handling large datasets and its scalability, making it an ideal choice for genomic data processing.

The transformer model in GeneSplice utilizes four distinct tokens: G, T, A, C, which correspond to the four nucleobases in DNA. The model will be trained to comprehend different DNA sequences and their possible implications, and identify patterns associated with various health conditions.

Getting Started

Embark on your journey with Geneplice by ensuring you have Python 3.8 or newer installed on your system. Use the following command to clone the repository:

git clone https://github.com/geneplice/geneplice.git
cd geneplice

Next, install the necessary dependencies:

pip install -r requirements.txt

Now, you're all set to launch Geneplice:

python main.py

Contributions

As explorers on this frontier, your contributions are invaluable! Should you discover a bug or wish to propose a feature, please open an issue. Those of you eager to contribute code, kindly fork the repository and make a pull request. For a more detailed guide, please consult our Contributing Guide.

License

Geneplice is licensed under the MIT license. For further information, kindly refer to LICENSE.

A Feynman-esque Thought for the Road

As Feynman famously said, "What I cannot create, I do not understand." Geneplice serves not only to enhance understanding but also to empower creation. We hope this tool enables you to weave your own threads into the tapestry of life's codes and patterns, extending the reach of our collective knowledge.

Happy journeying!