Best AI tools for< Gene Therapy >

Deep Genomics is a company that uses artificial intelligence (AI) to develop RNA therapies for genetic diseases. The company's AI platform is designed to identify novel targets and evaluate thousands of possibilities to identify the best therapeutic candidates. Deep Genomics is currently developing BigRNA+, which will expand the number of mechanisms and genetic variants the company can pursue.

OpenCRISPR is a set of free and open gene editing systems designed by Profluent Bio. The OpenCRISPR-1 protein maintains the prototypical architecture of a Type II Cas9 nuclease but is hundreds of mutations away from SpCas9 or any other known natural CRISPR-associated protein. You can view OpenCRISPR-1 as a drop-in replacement for many protocols that need a cas9-like protein with an NGG PAM and you can even use it with canonical SpCas9 gRNAs. OpenCRISPR-1 can be fused in a deactivated or nickase format for next generation gene editing techniques like base, prime, or epigenome editing.

A repository that lists papers related to Large Language Model (LLM) based agents. The repository covers various topics including survey, planning, feedback & reflection, memory mechanism, role playing, game playing, tool usage & human-agent interaction, benchmark & evaluation, environment & platform, agent framework, multi-agent system, and agent fine-tuning. It provides a comprehensive collection of research papers on LLM-based agents, exploring different aspects of AI agent architectures and applications.

Taiyi (太一) is a bilingual large language model fine-tuned for diverse biomedical tasks. It aims to facilitate communication between healthcare professionals and patients, provide medical information, and assist in diagnosis, biomedical knowledge discovery, drug development, and personalized healthcare solutions. The model is based on the Qwen-7B-base model and has been fine-tuned using rich bilingual instruction data. It covers tasks such as question answering, biomedical dialogue, medical report generation, biomedical information extraction, machine translation, title generation, text classification, and text semantic similarity. The project also provides standardized data formats, model training details, model inference guidelines, and overall performance metrics across various BioNLP tasks.

SurveyX is an advanced academic survey automation system that leverages Large Language Models (LLMs) to generate high-quality, domain-specific academic papers and surveys. Users can request comprehensive academic papers or surveys tailored to specific topics by providing a paper title and keywords for literature retrieval. The system streamlines academic research by automating paper creation, saving users time and effort in compiling research content.

OntoGPT is a Python package for extracting structured information from text using large language models, instruction prompts, and ontology-based grounding. It provides a command line interface and a minimal web app for easy usage. The tool has been evaluated on test data and is used in related projects like TALISMAN for gene set analysis. OntoGPT enables users to extract information from text by specifying relevant terms and provides the extracted objects as output.

Trinity is an Explainable AI (XAI) Analysis and Visualization tool designed for Deep Learning systems or other models performing complex classification or decoding. It provides performance analysis through interactive 3D projections that are hyper-dimensional aware, allowing users to explore hyperspace, hypersurface, projections, and manifolds. Trinity primarily works with JSON data formats and supports the visualization of FeatureVector objects. Users can analyze and visualize data points, correlate inputs with classification results, and create custom color maps for better data interpretation. Trinity has been successfully applied to various use cases including Deep Learning Object detection models, COVID gene/tissue classification, Brain Computer Interface decoders, and Large Language Model (ChatGPT) Embeddings Analysis.

NoLabs is an open-source biolab that provides easy access to state-of-the-art models for bio research. It supports various tasks, including drug discovery, protein analysis, and small molecule design. NoLabs aims to accelerate bio research by making inference models accessible to everyone.

ceLLama is a streamlined automation pipeline for cell type annotations using large-language models (LLMs). It operates locally to ensure privacy, provides comprehensive analysis by considering negative genes, offers efficient processing speed, and generates customized reports. Ideal for quick and preliminary cell type checks.

Scientific Large Language Models (Sci-LLMs) is a repository that collects papers on scientific large language models, focusing on biology and chemistry domains. It includes textual, molecular, protein, and genomic languages, as well as multimodal language. The repository covers various large language models for tasks such as molecule property prediction, interaction prediction, protein sequence representation, protein sequence generation/design, DNA-protein interaction prediction, and RNA prediction. It also provides datasets and benchmarks for evaluating these models. The repository aims to facilitate research and development in the field of scientific language modeling.

DNAnalyzer is a nonprofit organization dedicated to revolutionizing DNA analysis through AI-powered tools. It aims to democratize access to DNA analysis for a deeper understanding of human health and disease. The tool provides innovative AI-powered analysis and interpretive tools to empower geneticists, physicians, and researchers to gain deep insights into DNA sequences, revolutionizing how we understand human health and disease.

AiTreasureBox is a versatile AI tool that provides a collection of pre-trained models and algorithms for various machine learning tasks. It simplifies the process of implementing AI solutions by offering ready-to-use components that can be easily integrated into projects. With AiTreasureBox, users can quickly prototype and deploy AI applications without the need for extensive knowledge in machine learning or deep learning. The tool covers a wide range of tasks such as image classification, text generation, sentiment analysis, object detection, and more. It is designed to be user-friendly and accessible to both beginners and experienced developers, making AI development more efficient and accessible to a wider audience.

This repository serves as a practical guide for Medical Large Language Models (Medical LLMs) and provides resources, surveys, and tools for building, fine-tuning, and utilizing LLMs in the medical domain. It covers a wide range of topics including pre-training, fine-tuning, downstream biomedical tasks, clinical applications, challenges, future directions, and more. The repository aims to provide insights into the opportunities and challenges of LLMs in medicine and serve as a practical resource for constructing effective medical LLMs.

cellseg-models.pytorch is a Python library built upon PyTorch for 2D cell/nuclei instance segmentation models. It provides multi-task encoder-decoder architectures and post-processing methods for segmenting cell/nuclei instances. The library offers high-level API to define segmentation models, open-source datasets for training, flexibility to modify model components, sliding window inference, multi-GPU inference, benchmarking utilities, regularization techniques, and example notebooks for training and finetuning models with different backbones.

Phi-3-MLX is a versatile AI framework that leverages both the Phi-3-Vision multimodal model and the Phi-3-Mini-128K language model optimized for Apple Silicon using the MLX framework. It provides an easy-to-use interface for a wide range of AI tasks, from advanced text generation to visual question answering and code execution. The project features support for batched generation, flexible agent system, custom toolchains, model quantization, LoRA fine-tuning capabilities, and API integration for extended functionality.

AI-resources is a repository containing links to various resources for learning Artificial Intelligence. It includes video lectures, courses, tutorials, and open-source libraries related to deep learning, reinforcement learning, machine learning, and more. The repository categorizes resources for beginners, average users, and advanced users/researchers, providing a comprehensive collection of materials to enhance knowledge and skills in AI.

The lil brother of CF+ altering genomes without a license (not for the faint of heart)

In-depth CRISPR research and analysis expert, ensuring comprehensive and step-by-step coverage of topics.

Friendly and professional cannabis genetics AI.

Expert in guiding genetic modification processes with scientific accuracy.

I assist with gene data queries and enable file downloads.

CRISPR GPT Tutor by Ascendance.dev

Assists with biological image processing tools.