# Awesome Scientific AI Tools [![Awesome](https://awesome.re/badge.svg)](https://awesome.re) AI-powered tools, MCP servers, and agent skills for the day-to-day workflow of scientific research — from literature search to manuscript submission. [English](README.md) | [中文](README-zh.md) | [日本語](README-ja.md) | [Español](README-es.md) | [Deutsch](README-de.md)
--- This list focuses on tools researchers use *in their workflow* — searching literature, reading papers, writing manuscripts, analyzing data, generating figures, submitting to journals, applying for grants. Each entry must be a tool, server, or agent skill (not a paper, dataset, or foundation-model checkpoint), must be actively maintained, and must offer a free tier or be in widespread academic use. Two sections are unique to this list: **MCP Servers for Research** (Model Context Protocol bridges to scientific databases) and **AI Agent Skills & Plugins** (skills for Claude Code, Cursor, and other coding agents). Sections are ordered to follow a typical research project: discover → read → write → analyze → compute → automate → publish → fund → collaborate. ## Contents - [MCP Servers for Research](#mcp-servers-for-research) - [AI Agent Skills & Plugins](#ai-agent-skills--plugins) - [Literature Search & Discovery](#literature-search--discovery) - [Citation Management](#citation-management) - [Research Reading & Comprehension](#research-reading--comprehension) - [Writing & Editing](#writing--editing) - [Data Analysis & Visualization](#data-analysis--visualization) - [Scientific Computing](#scientific-computing) - [Figure & Diagram Generation](#figure--diagram-generation) - [Experiment & Lab Tools](#experiment--lab-tools) - [Drug Discovery & Chemistry](#drug-discovery--chemistry) - [Bioinformatics & Genomics](#bioinformatics--genomics) - [Clinical Trials & Medical](#clinical-trials--medical) - [Research Workflow Automation](#research-workflow-automation) - [Preprint & Publication Tools](#preprint--publication-tools) - [Grant Writing & Funding](#grant-writing--funding) - [Collaboration & Project Management](#collaboration--project-management) --- ## MCP Servers for Research MCP (Model Context Protocol) servers extend AI agents with real-time access to scientific databases. - [PubMed MCP](https://github.com/cyanheads/pubmed-mcp-server) - Search PubMed and the NCBI E-utilities API for biomedical literature, with article metadata, full text, citations, and MeSH terms. - [arXiv MCP](https://github.com/blazickjp/arxiv-mcp-server) - Search and fetch arXiv preprints across physics, math, computer science, and biology, with PDF-to-Markdown conversion. - [Semantic Scholar MCP](https://github.com/JackKuo666/semanticscholar-MCP-Server) - Access the Semantic Scholar API for paper search, author details, citations, and references. - [ChEMBL MCP](https://github.com/Augmented-Nature/ChEMBL-MCP-Server) - Query bioactivity data, compound information, target interactions, and mechanisms of action from ChEMBL. - [ClinicalTrials MCP](https://github.com/cyanheads/clinicaltrialsgov-mcp-server) - Search the ClinicalTrials.gov v2 API for trials, study details, results, and patient eligibility matching. - [bioRxiv MCP](https://github.com/JackKuo666/bioRxiv-MCP-Server) - Search and access bioRxiv preprints for biology research. - [CrossRef MCP](https://github.com/JackKuo666/Crossref-MCP-Server) - Metadata lookup for DOIs, citations, journals, and funder information through the Crossref API. - [Google Scholar MCP](https://github.com/JackKuo666/Google-Scholar-MCP-Server) - Search Google Scholar for academic papers, citations, and author profiles. ## AI Agent Skills & Plugins Skills and plugins that extend AI coding agents (Claude Code, Cursor, Codex) for research workflows. - [Professional Word Document Generator](https://github.com/Harsh9005/professional-word-document-generator) - Generate publication-ready .docx from JSON. LaTeX equations, 200+ scientific symbols, auto-citations. - [Multi-Agent Orchestrator](https://github.com/Harsh9005/multi-agent-orchestrator) - 6-phase pipeline with adaptive complexity, parallel agents, and quality gates. - [AI Session Logger](https://github.com/Harsh9005/ai-session-logger) - Persistent session memory — track files, decisions, and progress across conversations. - [Scientific Agent Skills](https://github.com/K-Dense-AI/scientific-agent-skills) - Open collection of scientific skills for Claude Code and other AI coding agents across multiple research domains. - [Awesome Claude Code](https://github.com/hesreallyhim/awesome-claude-code) - Curated list of Claude Code extensions, skills, and resources. ## Literature Search & Discovery - [Consensus](https://consensus.app/) - AI-powered academic search engine that extracts findings from peer-reviewed papers. Uses LLMs to synthesize yes/no answers from scientific literature. - [Semantic Scholar](https://www.semanticscholar.org/) - Free AI-powered research tool by Allen Institute. Covers 200M+ papers with citation context, TLDR summaries, and influence scores. - [Elicit](https://elicit.com/) - AI research assistant that finds relevant papers, extracts key claims, and synthesizes findings across studies. - [Connected Papers](https://www.connectedpapers.com/) - Visual tool for exploring academic paper connections. Builds a graph of related papers from any seed paper. - [Research Rabbit](https://www.researchrabbit.ai/) - Free tool for discovering and visualizing research paper networks. Monitors collections for new related papers. - [Scite.ai](https://scite.ai/) - Smart citation analysis showing how papers have been cited — supporting, contrasting, or mentioning. - [Litmaps](https://www.litmaps.com/) - Dynamic citation maps for literature discovery. Tracks research lineages and finds gaps. - [OpenAlex](https://openalex.org/) - Free, open catalog of the global research system. 250M+ works with rich metadata and API access. - [Inciteful](https://inciteful.xyz/) - Free tool to build a network of academic papers and analyze citation patterns. ## Citation Management - [Zotero](https://www.zotero.org/) - Free, open-source reference manager with browser integration, PDF management, and Word/Google Docs plugins. - [Paperpile](https://paperpile.com/) - Modern reference manager with Google Docs/Word integration and AI-powered metadata extraction. - [Mendeley](https://www.mendeley.com/) - Reference manager with social networking features, PDF annotation, and collaboration tools. - [EndNote](https://endnote.com/) - Industry-standard reference manager with journal style databases and Cite While You Write for Word. - [ReadCube Papers](https://www.papersapp.com/) - AI-enhanced reference manager with smart recommendations and enhanced PDF reader. ## Research Reading & Comprehension - [SciSpace](https://typeset.io/) - AI copilot for reading papers. Explains text, math, and tables in plain language. - [Explainpaper](https://www.explainpaper.com/) - Upload a paper, highlight confusing text, get AI explanations. - [ChatPDF](https://www.chatpdf.com/) - Chat with any PDF document. Particularly useful for long research papers and reports. - [Scholarcy](https://www.scholarcy.com/) - AI summarizer that creates flashcards of key findings, methods, and contributions. - [Unriddle](https://www.unriddle.ai/) - AI assistant for understanding complex documents. Generates knowledge graphs from papers. ## Writing & Editing - [Jenni AI](https://jenni.ai/) - AI writing assistant specifically for academic writing with citation support and paraphrasing. - [Paperpal](https://paperpal.com/) - AI grammar and language checker trained on millions of published papers. By Cactus Communications. - [Writefull](https://www.writefull.com/) - AI writing tool trained on published journal articles. Integrated into Overleaf. - [Trinka](https://www.trinka.ai/) - AI grammar checker for academic and technical writing with style and tone suggestions. - [QuillBot](https://quillbot.com/) - AI paraphrasing and summarizing tool with grammar checker and citation generator. - [Overleaf](https://www.overleaf.com/) - Online LaTeX editor with real-time collaboration, templates, and Writefull AI integration. - [Typst](https://typst.app/) - Modern markup-based typesetting system. Faster compilation than LaTeX with better error messages. ## Data Analysis & Visualization - [Julius AI](https://julius.ai/) - AI data analyst that interprets data, creates visualizations, and runs statistical tests from natural language. - [Hal9](https://hal9.com/) - AI-powered data analysis and dashboard creation from natural language queries. - [Obviously AI](https://www.obviously.ai/) - No-code ML platform for prediction, classification, and time-series analysis. - [JASP](https://jasp-stats.org/) - Free, open-source statistical software with both frequentist and Bayesian analysis. UI alternative to R/SPSS. - [Datawrapper](https://www.datawrapper.de/) - Create publication-ready charts, maps, and tables without coding. - [Plotly](https://plotly.com/) - Interactive graphing library for Python, R, and JavaScript with Dash framework for dashboards. - [Observable](https://observablehq.com/) - Collaborative data visualization platform with reactive notebooks and D3.js integration. ## Scientific Computing - [Wolfram Alpha](https://www.wolframalpha.com/) - Computational knowledge engine for math, physics, chemistry, and engineering calculations. - [COMSOL](https://www.comsol.com/) - Multiphysics simulation with AI-enhanced meshing and solver selection. - [MATLAB](https://www.mathworks.com/products/matlab.html) - Numerical computing environment with AI/ML toolboxes, Simulink, and domain-specific packages. - [Google Colab](https://colab.research.google.com/) - Free Jupyter notebook environment with GPU/TPU access for ML and scientific computing. - [Weights & Biases](https://wandb.ai/) - ML experiment tracking, hyperparameter tuning, and model versioning. - [DVC](https://dvc.org/) - Open-source version control for ML projects. Tracks data, models, and experiments alongside code. ## Figure & Diagram Generation - [BioRender](https://www.biorender.com/) - Scientific illustration tool with 50K+ icons for biology, chemistry, and medical figures. - [Mermaid](https://mermaid.js.org/) - Text-based diagramming in Markdown. Flowcharts, sequence diagrams, Gantt charts — all from code. - [draw.io / diagrams.net](https://www.diagrams.net/) - Free, open-source diagramming tool with scientific shape libraries. - [Inkscape](https://inkscape.org/) - Free, open-source vector graphics editor. Publication-quality SVG figures. - [Matplotlib](https://matplotlib.org/) - Python 2D plotting library producing publication-quality figures. The foundation of scientific visualization in Python. - [Seaborn](https://seaborn.pydata.org/) - Statistical visualization library built on Matplotlib. Beautiful defaults for publication figures. - [PlotNeuralNet](https://github.com/HarisIqbal88/PlotNeuralNet) - LaTeX code for drawing neural network architecture diagrams. - [Excalidraw](https://excalidraw.com/) - Hand-drawn style whiteboarding tool. Great for conceptual diagrams and brainstorming. ## Experiment & Lab Tools - [Benchling](https://www.benchling.com/) - Cloud platform for life sciences R&D — molecular biology, CRISPR design, inventory management. - [LabArchives](https://www.labarchives.com/) - Electronic lab notebook with version control, collaboration, and institutional compliance. - [Protocols.io](https://www.protocols.io/) - Open-access platform for sharing reproducible research protocols with version tracking. - [Hive Benchmarks](https://hivebenchmark.com/) - AI-powered lab workflow optimization and equipment benchmarking. ## Drug Discovery & Chemistry - [AlphaFold](https://alphafold.ebi.ac.uk/) - DeepMind's protein structure prediction. 200M+ predicted structures in the database. - [AlphaFold Server](https://alphafoldserver.com/) - Web server to run AlphaFold 3 predictions for proteins, DNA, RNA, ligands, and their interactions. Free for non-commercial use. - [RDKit](https://www.rdkit.org/) - Open-source cheminformatics toolkit for molecular analysis, fingerprinting, and descriptor calculation. - [DeepChem](https://deepchem.io/) - Open-source library for drug discovery, materials science, and quantum chemistry with deep learning. - [ChEMBL](https://www.ebi.ac.uk/chembl/) - Open large-scale bioactivity database with 2M+ compounds and 20M+ activity measurements. - [ZINC](https://zinc.docking.org/) - Free database of commercially available compounds for virtual screening. 230M+ molecules. - [Schrödinger](https://www.schrodinger.com/) - Physics-based computational platform for drug discovery and materials science. - [Open Babel](https://openbabel.org/) - Open-source chemical toolbox for molecular file format conversion and fingerprinting. - [PubChem](https://pubchem.ncbi.nlm.nih.gov/) - Open chemistry database with 100M+ compounds, bioassays, and literature references. ## Bioinformatics & Genomics - [Galaxy](https://galaxyproject.org/) - Open-source web platform for accessible, reproducible bioinformatics analysis. - [Biopython](https://biopython.org/) - Python tools for computational molecular biology — sequence analysis, structure, phylogenetics. - [BLAST](https://blast.ncbi.nlm.nih.gov/) - Basic Local Alignment Search Tool for comparing nucleotide or protein sequences. - [Nextflow](https://www.nextflow.io/) - Workflow engine for scalable, reproducible bioinformatics pipelines across computing environments. - [DESeq2](https://bioconductor.org/packages/DESeq2/) - R package for differential gene expression analysis from RNA-seq count data. - [Scanpy](https://scanpy.readthedocs.io/) - Python toolkit for single-cell gene expression analysis with scalable performance. - [IGV](https://igv.org/) - Integrative Genomics Viewer for interactive visualization of genomic data. ## Clinical Trials & Medical - [ClinicalTrials.gov](https://clinicaltrials.gov/) - US registry of clinical studies. 500K+ studies, searchable by condition, intervention, and sponsor. - [PubMed](https://pubmed.ncbi.nlm.nih.gov/) - Free search engine for biomedical literature. 36M+ citations from MEDLINE and life science journals. - [Europe PMC](https://europepmc.org/) - Open-access biomedical literature with full-text search, citation networks, and API access. - [Cochrane Library](https://www.cochranelibrary.com/) - Gold-standard systematic reviews and meta-analyses for evidence-based medicine. - [OHDSI / OMOP](https://www.ohdsi.org/) - Open-source tools for observational health data analysis with a common data model. ## Research Workflow Automation - [Snakemake](https://snakemake.readthedocs.io/) - Python-based workflow management for reproducible and scalable data analysis. - [Apache Airflow](https://airflow.apache.org/) - Platform to programmatically author, schedule, and monitor data workflows. - [Prefect](https://www.prefect.io/) - Modern workflow orchestration for data engineering and ML pipelines. - [Kedro](https://kedro.org/) - Open-source Python framework for creating reproducible, maintainable, and modular data science code. - [CWL](https://www.commonwl.org/) - Common Workflow Language for describing analysis tools and workflows portably. - [Papermill](https://papermill.readthedocs.io/) - Parameterize and execute Jupyter Notebooks as workflows. ## Preprint & Publication Tools - [arXiv](https://arxiv.org/) - Open-access preprint server for physics, math, CS, biology, and more. 2M+ papers. - [bioRxiv](https://www.biorxiv.org/) - Preprint server for biology. Fast publication, free access. - [medRxiv](https://www.medrxiv.org/) - Preprint server for health sciences. - [ChemRxiv](https://chemrxiv.org/) - Preprint server for chemistry. - [Authorea](https://www.authorea.com/) - Collaborative writing platform with built-in data visualization and journal submission. - [Curvenote](https://curvenote.com/) - Scientific writing platform with Jupyter integration and interactive figures. ## Grant Writing & Funding - [Granted.ai](https://granted.ai/) - AI-powered grant writing assistant with proposal optimization. - [GrantForward](https://www.grantforward.com/) - Funding opportunity search engine covering 14K+ sponsors. - [Pivot-RP](https://pivot.proquest.com/) - Comprehensive funding discovery tool with researcher profiles and collaboration matching. - [Dimensions](https://www.dimensions.ai/) - Linked research data platform connecting grants, publications, patents, and clinical trials. - [NIH Reporter](https://reporter.nih.gov/) - Search NIH-funded research projects, publications, and patents. ## Collaboration & Project Management - [Obsidian](https://obsidian.md/) - Markdown-based knowledge management with graph view, plugins, and local-first storage. - [Logseq](https://logseq.com/) - Open-source, privacy-first knowledge management and note-taking tool. - [OSF](https://osf.io/) - Open Science Framework — free platform for research project management, preregistration, and data sharing. ## Footnotes Your contributions are welcome! Please read the [contributing guidelines](CONTRIBUTING.md) before submitting a pull request.