ToolUniverse is a collection of 211 biomedical tools designed for Agentic AI, providing access to biomedical knowledge for solving therapeutic reasoning tasks. The tools cover various aspects of drugs and diseases, linked to trusted sources like US FDA-approved drugs since 1939, Open Targets, and Monarch Initiative.

Presenton is an open-source AI presentation generator and API that allows users to create professional presentations locally on their devices. It offers complete control over the presentation workflow, including custom templates, AI template generation, flexible generation options, and export capabilities. Users can use their own API keys for various models, integrate with Ollama for local model running, and connect to OpenAI-compatible endpoints. The tool supports multiple providers for text and image generation, runs locally without cloud dependencies, and can be deployed as a Docker container with GPU support.

AutoAgents is a cutting-edge multi-agent framework built in Rust that enables the creation of intelligent, autonomous agents powered by Large Language Models (LLMs) and Ractor. Designed for performance, safety, and scalability. AutoAgents provides a robust foundation for building complex AI systems that can reason, act, and collaborate. With AutoAgents you can create Cloud Native Agents, Edge Native Agents and Hybrid Models as well. It is so extensible that other ML Models can be used to create complex pipelines using Actor Framework.

AGiXT is a dynamic Artificial Intelligence Automation Platform engineered to orchestrate efficient AI instruction management and task execution across a multitude of providers. Our solution infuses adaptive memory handling with a broad spectrum of commands to enhance AI's understanding and responsiveness, leading to improved task completion. The platform's smart features, like Smart Instruct and Smart Chat, seamlessly integrate web search, planning strategies, and conversation continuity, transforming the interaction between users and AI. By leveraging a powerful plugin system that includes web browsing and command execution, AGiXT stands as a versatile bridge between AI models and users. With an expanding roster of AI providers, code evaluation capabilities, comprehensive chain management, and platform interoperability, AGiXT is consistently evolving to drive a multitude of applications, affirming its place at the forefront of AI technology.

The MCP Memory Service is a universal memory service designed for AI assistants, providing semantic memory search and persistent storage. It works with various AI applications and offers fast local search using SQLite-vec and global distribution through Cloudflare. The service supports intelligent memory management, universal compatibility with AI tools, flexible storage options, and is production-ready with cross-platform support and secure connections. Users can store and recall memories, search by tags, check system health, and configure the service for Claude Desktop integration and environment variables.

LlamaFarm is a comprehensive AI framework that empowers users to build powerful AI applications locally, with full control over costs and deployment options. It provides modular components for RAG systems, vector databases, model management, prompt engineering, and fine-tuning. Users can create differentiated AI products without needing extensive ML expertise, using simple CLI commands and YAML configs. The framework supports local-first development, production-ready components, strategy-based configuration, and deployment anywhere from laptops to the cloud.

J.A.R.V.I.S. 2.0 is an AI-powered assistant designed for voice commands, capable of tasks like providing weather reports, summarizing news, sending emails, and more. It features voice activation, speech recognition, AI responses, and handles multiple tasks including email sending, weather reports, news reading, image generation, database functions, phone call automation, AI-based task execution, website & application automation, and knowledge-based interactions. The assistant also includes timeout handling, automatic input processing, and the ability to call multiple functions simultaneously. It requires Python 3.9 or later and specific API keys for weather, news, email, and AI access. The tool integrates Gemini AI for function execution and Ollama as a fallback mechanism. It utilizes a RAG-based knowledge system and ADB integration for phone automation. Future enhancements include deeper mobile integration, advanced AI-driven automation, improved NLP-based command execution, and multi-modal interactions.

Claude Code Agents is an open-source AI agent system designed to enhance development workflows by providing specialized AI agents for orchestration, resilience engineering, and organizational memory. These agents offer specialized expertise across technologies, AI system with organizational memory, and an agent orchestration system. The system includes features such as engineering excellence by design, advanced orchestration system, Task Master integration, live MCP integrations, professional-grade workflows, and organizational intelligence. It is suitable for solo developers, small teams, enterprise teams, and open-source projects. The system requires a one-time bootstrap setup for each project to analyze the tech stack, select optimal agents, create configuration files, set up Task Master integration, and validate system readiness.

Persistent AI Memory System is a comprehensive tool that offers persistent, searchable storage for AI assistants. It includes features like conversation tracking, MCP tool call logging, and intelligent scheduling. The system supports multiple databases, provides enhanced memory management, and offers various tools for memory operations, schedule management, and system health checks. It also integrates with various platforms like LM Studio, VS Code, Koboldcpp, Ollama, and more. The system is designed to be modular, platform-agnostic, and scalable, allowing users to handle large conversation histories efficiently.

Aegra is a self-hosted AI agent backend platform that provides LangGraph power without vendor lock-in. Built with FastAPI + PostgreSQL, it offers complete control over agent orchestration for teams looking to escape vendor lock-in, meet data sovereignty requirements, enable custom deployments, and optimize costs. Aegra is Agent Protocol compliant and perfect for teams seeking a free, self-hosted alternative to LangGraph Platform with zero lock-in, full control, and compatibility with existing LangGraph Client SDK.

evi-run is a powerful, production-ready multi-agent AI system built on Python using the OpenAI Agents SDK. It offers instant deployment, ultimate flexibility, built-in analytics, Telegram integration, and scalable architecture. The system features memory management, knowledge integration, task scheduling, multi-agent orchestration, custom agent creation, deep research, web intelligence, document processing, image generation, DEX analytics, and Solana token swap. It supports flexible usage modes like private, free, and pay mode, with upcoming features including NSFW mode, task scheduler, and automatic limit orders. The technology stack includes Python 3.11, OpenAI Agents SDK, Telegram Bot API, PostgreSQL, Redis, and Docker & Docker Compose for deployment.

Claude-Flow is a workflow automation tool designed to streamline and optimize business processes. It provides a user-friendly interface for creating and managing workflows, allowing users to automate repetitive tasks and improve efficiency. With features such as drag-and-drop workflow builder, customizable templates, and integration with popular business tools, Claude-Flow empowers users to automate their workflows without the need for extensive coding knowledge. Whether you are a small business owner looking to streamline your operations or a project manager seeking to automate task assignments, Claude-Flow offers a flexible and scalable solution to meet your workflow automation needs.

A comprehensive web application for auto-subtitling videos and audio, translating SRT files, generating AI narration with voice cloning, creating background images, and rendering professional subtitled videos. Designed for content creators, educators, and general users who need high-quality subtitle generation and video production capabilities.

Zettelgarden is a human-centric, open-source personal knowledge management system that helps users develop and maintain their understanding of the world. It focuses on creating and connecting atomic notes, thoughtful AI integration, and scalability from personal notes to company knowledge bases. The project is actively evolving, with features subject to change based on community feedback and development priorities.

Model Context Protocol (MCP) is an open protocol that standardizes how applications provide context to large language models (LLMs). It allows AI applications to connect with various data sources and tools in a consistent manner, enhancing their capabilities and flexibility. This repository contains core libraries, test frameworks, engineering systems, pipelines, and tooling for Microsoft MCP Server contributors to unify engineering investments and reduce duplication and divergence. For more details, visit the official MCP website.

FiniteMonkey is an advanced vulnerability mining engine powered purely by GPT, requiring no prior knowledge base or fine-tuning. Its effectiveness significantly surpasses most current related research approaches. The tool is task-driven, prompt-driven, and focuses on prompt design, leveraging 'deception' and hallucination as key mechanics. It has helped identify vulnerabilities worth over $60,000 in bounties. The tool requires PostgreSQL database, OpenAI API access, and Python environment for setup. It supports various languages like Solidity, Rust, Python, Move, Cairo, Tact, Func, Java, and Fake Solidity for scanning. FiniteMonkey is best suited for logic vulnerability mining in real projects, not recommended for academic vulnerability testing. GPT-4-turbo is recommended for optimal results with an average scan time of 2-3 hours for medium projects. The tool provides detailed scanning results guide and implementation tips for users.

PINNACLE is a flexible geometric deep learning approach that trains on contextualized protein interaction networks to generate context-aware protein representations. It provides protein representations split across various cell-type contexts from different tissues and organs. The tool can be fine-tuned to study the genomic effects of drugs and nominate promising protein targets and cell-type contexts for further investigation. PINNACLE exemplifies the paradigm of incorporating context-specific effects for studying biological systems, especially the impact of disease and therapeutics.

ToolUniverse is a collection of 211 biomedical tools designed for Agentic AI, providing access to biomedical knowledge for solving therapeutic reasoning tasks. The tools cover various aspects of drugs and diseases, linked to trusted sources like US FDA-approved drugs since 1939, Open Targets, and Monarch Initiative.

KG-RAG (Knowledge Graph-based Retrieval Augmented Generation) is a task agnostic framework that combines the explicit knowledge of a Knowledge Graph (KG) with the implicit knowledge of a Large Language Model (LLM). KG-RAG extracts "prompt-aware context" from a KG, which is defined as the minimal context sufficient enough to respond to the user prompt. This framework empowers a general-purpose LLM by incorporating an optimized domain-specific 'prompt-aware context' from a biomedical KG. KG-RAG is specifically designed for running prompts related to Diseases.

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.

Generative AI models have shown tremendous usefulness in increasing accessibility and automation of a wide range of tasks. This repository contains the `biochatter` Python package, a generic backend library for the connection of biomedical applications to conversational AI. It aims to provide a common framework for deploying, testing, and evaluating diverse models and auxiliary technologies in the biomedical domain. BioChatter is part of the BioCypher ecosystem, connecting natively to BioCypher knowledge graphs.

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.

AICSImageIO is a Python tool for Image Reading, Metadata Conversion, and Image Writing for Microscopy Images. It supports various file formats like OME-TIFF, TIFF, ND2, DV, CZI, LIF, PNG, GIF, and Bio-Formats. Users can read and write metadata and imaging data, work with different file systems like local paths, HTTP URLs, s3fs, and gcsfs. The tool provides functionalities for full image reading, delayed image reading, mosaic image reading, metadata reading, xarray coordinate plane attachment, cloud IO support, and saving to OME-TIFF. It also offers benchmarking and developer resources.

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.

PINNACLE is a flexible geometric deep learning approach that trains on contextualized protein interaction networks to generate context-aware protein representations. It provides protein representations split across various cell-type contexts from different tissues and organs. The tool can be fine-tuned to study the genomic effects of drugs and nominate promising protein targets and cell-type contexts for further investigation. PINNACLE exemplifies the paradigm of incorporating context-specific effects for studying biological systems, especially the impact of disease and therapeutics.

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.