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AutoBA is a singleagent system designed to perform fully automated [[domain:multiomics]] analyses. By leveraging large language models, the agent minimizes user input requirements while generating detailed, step-by-step analytical plans. Its architecture allows for the self-design of processes based on input data…
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AILA is a multiagent framework designed to automate atomic force microscopy experiments within self-driving laboratories. By leveraging large language models, the system aims to replicate the adaptive decision-making and experimental intuition required for complex tasks such as calibration, feature detection, and…
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AutoResearchClaw is a multi-agent, self-evolving system built by [[org:aiming-lab]] to facilitate autonomous research. Designed to support both fully autonomous workflows and human-in-the-loop collaboration, the system enables users to generate research papers by providing a topic or idea. It is evaluated on…
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AutoScientists is a multi-agent system built by [[org:harvard-medical-school]] designed for long-running computational scientific experimentation. The system utilizes a decentralized architecture where AI agents self-organize into teams to evaluate hypotheses, critique proposals, and share findings to optimize…
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Aviary is a multiagent gymnasium built by [[org:future-house]] for defining custom language agent reinforcement learning environments. The system provides a library and notebook interface to facilitate the development and testing of agents across various scientific and technical domains.
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BIA (BioInformatics Agent) is a system designed to leverage large language models to optimize and reshape bioinformatics workflows. It aims to streamline complex computational biology tasks by integrating advanced language processing capabilities into the research pipeline.
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BioAgents is a multi-agent system designed to streamline complex bioinformatics workflows through a combination of small language models and retrieval augmented generation. Built by [[org:bio-xyz]], the system is optimized for local operation and personalization using proprietary data, providing nuanced guidance for…
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BioDiscoveryAgent is a multiagent system built by [[org:stanford-university]] designed to automate the closed-loop design of genetic [[domain:perturbation]] experiments. By leveraging large language models and a suite of integrated tools—including literature search, gene search, and AI-driven critique—the agent…
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BioInformatics Agent (BIA) is an intelligent system built by [[org:vin-bio]] designed to facilitate autonomous bioinformatics analysis through natural language. Utilizing a multiagent architecture and a toolregistry, the system automates data extraction, workflow design, code generation, and report delivery. It is…
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BioMaster is a multi-agent system designed to automate complex bioinformatics workflows through specialized, role-based agents. By utilizing a multiagent architecture combined with rag, the system dynamically retrieves domain-specific knowledge to improve adaptability and task execution. It is distributed as a library…
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Biomni is a general-purpose biomedical AI agent built by [[org:stanford-university]] to autonomously execute complex research workflows. Utilizing a singleagent architecture powered by rag and code-based execution, the system dynamically composes tasks without relying on predefined templates. It is accessible via a…
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BioReason is a multimodal biomedical LLM-agent system developed by [[org:bowang-lab]]. Utilizing a multiagent architecture, the system integrates DNA foundation models with large language models to facilitate complex biological reasoning and generate interpretable, step-by-step mechanistic insights from genomic data.
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BioScientist Agent is an end-to-end framework designed to address the inefficiencies of traditional [[domain:drugdiscovery]]. By integrating a billion-fact biomedical knowledge graph with a multi-agent LLM architecture, the system facilitates systematic drug repurposing and the elucidation of mechanisms of action.
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BORA is a Language-Based Bayesian Optimization Research Assistant designed to address high-dimensional, non-convex optimization challenges. Built by [[org:weixiang-sun]], the system utilizes a singleagent architecture to integrate Large Language Models with Bayesian optimization, providing real-time commentary and…
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Camyla is a multiagent system built by [[org:yifangao112]] designed to automate the end-to-end research process for [[domain:medicalimaging]]. By taking a dataset as input, the system autonomously generates research hypotheses, executes deep-learning experiments, and produces publication-ready manuscripts. It is…
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CASSIA is a multi-agent large language model designed to automate the annotation of [[domain:singlecell]] RNA-sequencing data. By integrating reasoning and quality assessment, the system aims to improve annotation accuracy while addressing common challenges such as hyperconfidence and hallucinations in existing…
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CellAgent is an autonomous, LLM-driven framework designed to streamline the analysis of [[domain:singlecell]] and [[domain:spatial]] transcriptomics data. By utilizing a multi-agent hierarchical decision-making architecture, the system translates natural language interactions into end-to-end analytical workflows…
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CellVoyager is a singleagent system designed to autonomously explore [[domain:singlecell]] datasets. By ingesting both raw data and records of prior research, the agent generates and tests new insights within a notebook environment, facilitating advanced [[domain:hypothesisgen]].
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CellWhisperer is a multimodal AI model developed by [[org:epigen]] that integrates transcriptomics with natural language to facilitate intuitive interaction with [[domain:singlecell]] datasets. Published in Nature Biotechnology in 2025, the system enables users to analyze scRNA-seq data through a single-agent…
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ChatMol Copilot is a singleagent system designed to facilitate molecular modeling and computational tasks. By leveraging large language models, it assists users in navigating complex biochemical workflows and data analysis.
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ChatNT is a singleagent multimodal conversational system built by [[org:ruisiang]] to bridge the gap between foundation models and biological sequence analysis. It provides an accessible webui for users to perform tasks involving DNA, RNA, and protein sequences without requiring coding expertise.
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ChatSpatial is a specialized MCP server designed to facilitate [[domain:spatial]] transcriptomics analysis through natural language. Built by [[org:cafferychen777]], the system utilizes a toolregistry architecture to provide schema-enforced orchestration, replacing ad-hoc code generation with a stable interface for…
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ChemMiner is a multiagent system designed to extract high-fidelity chemical data from scientific [[domain:literature]]. Built by [[org:nikki0526]], the framework utilizes specialized agents to perform coreference mapping, multimodal information extraction, and synthesis analysis, enabling the conversion of…
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ClinicalAgent is an autonomous multi-agent system designed to support [[domain:clinicalqa]] and decision-making tasks. Built by [[org:jithubaiju55]], the system utilizes a multiagent architecture powered by LangGraph and Llama 3.3 70B to perform complex reasoning, evidence retrieval, and clinical analysis.