Best AI tools for< Bioinformatics Researcher >

VantAI is an AI application focused on generative AI-enabled drug discovery. Their mission is to unlock a new chapter in medicine by making protein interactions programmable. They have an integrated discovery platform with phase-shifting technologies designed to unlock the full potential of the proximity modulator modality. VantAI collaborates with industry leaders to build the future of therapeutic design. The company has launched Neo-1, the first AI model to rewire molecular interactions by unifying structure prediction and generation.

HUAWEI Cloud Pangu is an AI tool designed for accelerating drug discovery by optimizing drug molecules. It offers features such as Molecule Search, Molecule Optimizer, and Pocket Molecule Design. Users can submit molecules for optimization and view historical optimization results. The tool is based on the MindSpore framework and has been visited over 300,000 times since August 23, 2021.

Bionl is a no-code bioinformatics platform designed to streamline biomedical research for researchers and scientists. It offers a full workspace with features such as bioinformatics pipelines customization, GenAI for data analysis, AI-powered literature search, PDF analysis, and access to public datasets. Bionl aims to automate cloud, file system, data, and workflow management for efficient and precise analyses. The platform caters to Pharma and Biotech companies, academic researchers, and bioinformatics CROs, providing powerful tools for genetic analysis and speeding up research processes.

Ignota Labs is a technology company focused on rescuing failing drugs and bringing new life to abandoned projects, ultimately providing hope to patients. The company utilizes a proprietary AI model, SAFEPATH, which applies deep learning to bioinformatics and cheminformatics datasets to solve drug safety issues. Ignota Labs aims to identify promising drug targets, address safety problems in clinical trials, and accelerate the delivery of therapeutically effective drugs to patients.

Genie TechBio is the world's first AI bioinformatician, offering an LLM-powered omics analysis software that operates entirely in natural language, eliminating the need for coding. Researchers can effortlessly analyze extensive datasets by engaging in a conversation with Genie, receiving recommendations for analysis pipelines, and obtaining results. The tool aims to accelerate biomedical research and empower scientists with newfound data analysis capabilities.

Synthace is a software and expertise platform designed for Discovery Biology Teams to streamline and optimize their experiments in assay development, media optimization, and purification process development. The platform offers software solutions, training, and on-site support from specialists to help scientists conduct experiments more efficiently and effectively. By leveraging multifactorial methods and automation, Synthace aims to accelerate drug discovery processes and deliver faster, definitive results.

Insitro is a drug discovery and development company that uses machine learning and data to identify and develop new medicines. The company's platform integrates in vitro cellular data produced in its labs with human clinical data to help redefine disease. Insitro's pipeline includes wholly-owned and partnered therapeutic programs in metabolism, oncology, and neuroscience.

Recursion is a techbio company that uses artificial intelligence to accelerate drug discovery. The company's platform combines hardware, software, and data to create a more efficient and effective drug discovery process. Recursion has a broad pipeline of drug candidates in development, and it has partnered with several leading pharmaceutical companies. The company is headquartered in Salt Lake City, Utah.

Cradle is a protein engineering platform that uses machine learning to design improved protein sequences. It allows users to import assay data, generate new sequences, test them in the lab, and import the results to improve the model. Cradle can be used to optimize multiple properties of a protein simultaneously, and it has been used by leading biotech teams to accelerate new and ongoing projects.

AI2BMD is a program for efficiently simulating protein molecular dynamics with ab initio accuracy. The repository contains datasets, simulation programs, and public materials related to AI2BMD. It provides a Docker image for easy deployment and a standalone launcher program. Users can run simulations by downloading the launcher script and specifying simulation parameters. The repository also includes ready-to-use protein structures for testing. AI2BMD is designed for x86-64 GNU/Linux systems with recommended hardware specifications. The related research includes model architectures like ViSNet, Geoformer, and fine-grained force metrics for MLFF. Citation information and contact details for the AI2BMD Team are provided.

ProLLM is a framework that leverages Large Language Models to interpret and analyze protein sequences and interactions through natural language processing. It introduces the Protein Chain of Thought (ProCoT) method to transform complex protein interaction data into intuitive prompts, enhancing predictive accuracy by incorporating protein-specific embeddings and fine-tuning on domain-specific datasets.

Generative-AI-Drug-Discovery is a public repository on GitHub focused on using tensor network machine learning approaches to accelerate GenAI for drug discovery. The repository aims to implement effective architectures and methodologies into Large Language Models (LLMs) to enhance Drug Discovery Generative AI performance.

mercure DICOM Orchestrator is a flexible solution for routing and processing DICOM files. It offers a user-friendly web interface and extensive monitoring functions. Custom processing modules can be implemented as Docker containers. Written in Python, it uses the DCMTK toolkit for DICOM communication. It can be deployed as a single-server installation using Docker Compose or as a scalable cluster installation using Nomad. mercure consists of service modules for receiving, routing, processing, dispatching, cleaning, web interface, and central monitoring.

Slideflow is a deep learning library for digital pathology, offering a user-friendly interface for model development. It is designed for medical researchers and AI enthusiasts, providing an accessible platform for developing state-of-the-art pathology models. Slideflow offers customizable training pipelines, robust slide processing and stain normalization toolkit, support for weakly-supervised or strongly-supervised labels, built-in foundation models, multiple-instance learning, self-supervised learning, generative adversarial networks, explainability tools, layer activation analysis tools, uncertainty quantification, interactive user interface for model deployment, and more. It supports both PyTorch and Tensorflow, with optional support for Libvips for slide reading. Slideflow can be installed via pip, Docker container, or from source, and includes non-commercial add-ons for additional tools and pretrained models. It allows users to create projects, extract tiles from slides, train models, and provides evaluation tools like heatmaps and mosaic maps.

The 'awesome-AI4MolConformation-MD' repository focuses on protein conformations and molecular dynamics using generative artificial intelligence and deep learning. It provides resources, reviews, datasets, packages, and tools related to AI-driven molecular dynamics simulations. The repository covers a wide range of topics such as neural networks potentials, force fields, AI engines/frameworks, trajectory analysis, visualization tools, and various AI-based models for protein conformational sampling. It serves as a comprehensive guide for researchers and practitioners interested in leveraging AI for studying molecular structures and dynamics.

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.

The 'machine-learning-research' repository is a comprehensive collection of resources related to mathematics, machine learning, deep learning, artificial intelligence, data science, and various scientific fields. It includes materials such as courses, tutorials, books, podcasts, communities, online courses, papers, and dissertations. The repository covers topics ranging from fundamental math skills to advanced machine learning concepts, with a focus on applications in healthcare, genetics, computational biology, precision health, and AI in science. It serves as a valuable resource for individuals interested in learning and researching in the fields of machine learning and related disciplines.

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.

ADMET-AI is a platform for ADMET prediction using Chemprop-RDKit models trained on ADMET datasets from the Therapeutics Data Commons. It offers command line, Python API, and web server interfaces for making ADMET predictions on new molecules. The platform can be easily installed using pip and supports GPU acceleration. It also provides options for processing TDC data, plotting results, and hosting a web server. ADMET-AI is a machine learning platform for evaluating large-scale chemical libraries.

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.

This repository focuses on exploring tools that enhance the performance of language models for various tasks. It provides a structured list of literature relevant to tool-augmented language models, covering topics such as tool basics, tool use paradigm, scenarios, advanced methods, and evaluation. The repository includes papers, preprints, and books that discuss the use of tools in conjunction with language models for tasks like reasoning, question answering, mathematical calculations, accessing knowledge, interacting with the world, and handling non-textual modalities.

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.

GROMACS Copilot is an agent designed to automate molecular dynamics simulations for proteins in water using GROMACS. It handles system setup, simulation execution, and result analysis automatically, providing outputs such as RMSD, RMSF, Rg, and H-bonds. Users can interact with the agent through prompts and API keys from DeepSeek and OpenAI. The tool aims to simplify the process of running MD simulations, allowing users to focus on other tasks while it handles the technical aspects of the simulations.

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.

New AI Drug Discovery is a repository focused on the applications of Large Language Models (LLM) in drug discovery. It provides resources, tools, and examples for leveraging LLM technology in the pharmaceutical industry. The repository aims to showcase the potential of using AI-driven approaches to accelerate the drug discovery process, improve target identification, and optimize molecular design. By exploring the intersection of artificial intelligence and drug development, this repository offers insights into the latest advancements in computational biology and cheminformatics.

Unlock the secrets of DNA with 🧬GenoCode Wizard🔬! Dive into genetic analysis, decode sequences, and explore bioinformatics with ease. Perfect for researchers and students!

R programming whiz for microbiome analysis

I assist with gene data queries and enable file downloads.

Skilled in Python, Linux, R, and more.

Compile instructions from the web and github for bioinformatics applications. Receive line-by-line instructions and commands to get started

生成操作流程的生物信息学 GPT

Assists in evaluating protein engineering tools.

Especialista em Biotecnologia e Análise de Dados Acadêmicos

A guide for ML & LLM bootcamp with a bioengineering background.

Academic-level genomics expertise.

Expert in microsporidia and omics, tailors responses to student or expert background

Advises on Bioconda recipes, following community guidelines

Especialista em dados de pós-graduação em Fisiologia

Echoes Watson & Crick, educates on DNA with depth.

Aids in biological science writing with concise, professional advice.

An expert in bioengineering, skilled in logical problem-solving

AI protein design assistant