AI Tools & Resources for Scientists

A curated list of AI-powered tools to assist with literature review, writing, data analysis, and teaching.

AI Philosophy: Our mission is to understand life and champion open science by sharing that knowledge with the world. We use AI to remove barriers to that mission, using it to code faster, write clearer, and think bigger. Yet, these powerful tools demand equally rigorous oversight. We use AI to expand our minds, not replace them, demanding 100% verification to ensure our work is transparent, reproducible, and stands on a bedrock of accuracy.

Frontier Models (The Engines)

These are not simple chatbots; they are reasoning engines. With the right prompting strategy (giving context, persona, and constraints), they can draft entire manuscripts, synthesize vast literature, and code complex pipelines. If you use them lazily, you get garbage. If you drive them like a Ferrari, you win.

  • ChatGPT (OpenAI): The original heavy hitter. The "o1" model is currently the king of complex reasoning. If you are using the free version (GPT-3.5 or 4o-mini) for science, you are wasting your time. Pay for the real tools.
  • Claude (Anthropic): Currently the best prose writer of the bunch. It sounds less "robotic" than the others and handles massive text inputs (like whole books) beautifully. If you need to draft a paper, start here.
  • Gemini (Google): Fully integrated into the Google ecosystem and has a massive context window. Can be brilliant at multimodal tasks, but can also be confidently wrong. Don't let it do your thinking for you—check my work. Currently this is my go to for many tasks.


    • Thes power of these tools is highly dependent on your prompting. Go here for my guide to prompting. Make sure to review the "mega-prompts" this is how the real power of modern LLMs is unleashed.

Prompt Engineering (Tools to Build Tools)

If you are building complex workflows (Mega-Prompts), you cannot just type into a chat window. You need environments that allow you to test, iterate, and save your "source code."

  • Anthropic Workbench: The absolute best place to build prompts. It has a "Generate a Prompt" feature where you describe a task, and it writes a structured mega-prompt for you. Essential for "System Prompt" testing.
  • OpenAI Playground: Stop using the normal ChatGPT interface for complex tasks. The Playground lets you edit the "System" message separately from the "User" message, which is critical for getting the AI to stay in character.
  • Fabric (GitHub): An open-source project by Daniel Miessler. It is a massive library of "Patterns" (Mega-Prompts) for analyzing life, science, and security. A goldmine for seeing how experts structure their requests.
  • PromptPerfect: A tool that takes your "lazy" prompt and rewrites it into a detailed, optimized version. Good for learning how to be more specific.
  • TypingMind: A much better UI for ChatGPT/Claude. It lets you create a "Prompt Library" where you can save your favorite mega-prompts and call them up with a slash command (e.g., /review).

Literature Search & Discovery

  • Google NotebookLM: An AI research assistant that lets you upload your own PDFs and sources to answer questions and summarize content strictly from your material. Can make podcasts on a topic based on documents that your provide.
  • Elicit: Automates literature reviews by finding relevant papers and summarizing key takeaways in a table format.
  • ResearchRabbit: Visualizes citation networks to help you discover new papers relevant to your seed collection.
  • Consensus: An AI-powered search engine that extracts and aggregates answers to scientific questions directly from peer-reviewed literature.
  • Scite: A smart citation tool that classifies citations to show whether a paper supports, mentions, or contrasts with the cited claim.
  • Google Scholar AI: Think of having a Gemini chat that has access to use google scholar. Great for finding papers that speak to a complex idea or question.
  • Google Scholar PDF Reader: A Chrome extension that adds an AI sidebar to online PDFs to generate outlines and summaries while you read.
  • Connected Papers: Creates a graph of similar papers based on co-citation and bibliographic coupling.
  • Scholarcy: Breaks down complex papers into digestible flashcards, highlighting key findings and methodology.

Writing & Editing

  • Paperpal: AI writing assistant trained on academic manuscripts to check grammar and style against journal standards.
  • Writefull: Provides language feedback using a database of published scientific papers to ensure academic tone.
  • DeepL: Highly accurate AI translation tool useful for clarifying complex phrasing.
  • Grammarly: Standard tool for catching typos, tone issues, and basic grammatical errors.

Data Analysis & Coding

  • GitHub Copilot: AI pair programmer that integrates into code editors (RStudio/VS Code) to autocomplete code.
  • Julius AI: Data analysis assistant that allows you to upload datasets and ask questions in plain English to generate plots.
  • RTutor: Generates R code and plots by asking questions in natural language; great for syntax checks.

Figures & Visualization

  • BioRender: Industry standard for creating professional biological diagrams and pathways.
  • Adobe Firefly: Generative tool integrated into Adobe apps to create vector graphics and illustrations from text.
  • Midjourney / DALL-E: Generative AI tools for conceptual cover art or presentation backgrounds.

Teaching & Presentations

  • Gamma: Generates polished slide decks and presentations from a simple text outline.
  • Curipod: Interactive presentation tool that uses AI to generate polls and questions to engage students.
  • Quizlet: Automatically generates flashcards and practice tests from lecture notes.

Productivity & Lab Management

  • Otter.ai: Meeting assistant that records audio and generates summaries of lab meetings.
  • Notion: Workspace tool with AI to help organize lab wikis and summarize protocols.