Hugging Face — Models, Datasets, and Demos Hub
Hugging Face hosts the open machine-learning ecosystem: load a model in one line, publish versioned datasets, and ship a …
Computational
Ollama — Run Local LLMs on Your Own Hardware
Ollama runs open-weight language models on your machine with one command, so confidential data never leaves it. Slower …
NotebookLM — Chat With Your Own Sources
NotebookLM answers only from documents you upload, citing the passage each claim came from. The most …
Claude Code — AI Coding Agent for Your Repo
Claude Code is a coding agent that reads your project, edits files, and runs commands under your approval. Powerful on …
Claude — AI Assistant for Whole-Document Work
Claude is Anthropic's AI assistant, built around very large context windows. Strong at critiquing a full chapter in one …
Plotly — Interactive Charts for Python and R
Plotly makes charts readers can hover, zoom, and rotate, and Dash turns an analysis into a web app. Weaker than …
Mermaid — Diagrams as Code in Markdown
Mermaid turns indented text into flowcharts that GitHub and Obsidian render natively, so diagrams live in version …
Excalidraw — Fast Sketch Diagrams for Thinking
Excalidraw is the fastest way to get a diagram out of your head: open the page and draw. The hand-drawn look is honest …
Figshare — Institutional Repository for Research Outputs
Figshare mints DOIs for datasets, figures, and posters with usage metrics and university portals. Polished and …
Zenodo — Free Permanent DOIs for Research Outputs
Zenodo gives any research output a citable DOI on CERN infrastructure, free, with automatic GitHub release archiving. …
OSF — Preregistration and Open Science Projects
OSF hosts preregistrations, project files, and preprints free, from a non-profit. The timestamped, uneditable …
Weights & Biases — Experiment Tracking for ML Research
W&B logs every metric, config, and artifact from a training run to a searchable dashboard, free for academics. Your …
DVC — Version Control for Data and Models
DVC tracks large datasets with Git-like commands while the bytes live in your own storage, so any commit restores the …
Nextflow — Scalable Pipelines and nf-core Genomics
Nextflow runs containerised pipelines from laptop to cloud, and nf-core provides curated genomics workflows you can run …
Snakemake — Reproducible Analysis Pipelines in Python
Snakemake declares rules with inputs and outputs, reruns only what changed, and scales from laptop to cluster unchanged. …
uv — Fast Python Environments With Lockfiles
uv replaces pip, venv, and pyenv with one fast binary and a lockfile by default. The best way to start a Python project …
Conda — Environments for Scientific Python and Beyond
Conda installs the binary dependencies pip cannot — CUDA, GDAL, compilers, R. Heavier and slower than uv, and still the …
Apptainer — Containers That HPC Clusters Allow
Apptainer runs containers without root, which is why university clusters permit it and ban Docker. Single-file images …
Docker — Containers for Reproducible Research
Docker packages your entire computational environment into an image that runs identically anywhere. The strongest …
PyCharm — Full Python IDE, Free for Academics
PyCharm offers the deepest Python debugging and refactoring available, free on an academic licence. Heavy, complex, and …
Google Colab — Free GPU Notebooks in the Browser
Colab runs Jupyter notebooks on Google's machines with free GPU access and zero setup. Unbeatable for teaching — …
GitLab — Self-Hosted Git for Institutional Data
GitLab gives you the GitHub workflow on your university's own servers, with CI built in. The right choice when data …
Anki — Spaced Repetition for Researchers
Anki schedules reviews just before you would forget, using the most replicated finding in learning science. Free, open …
Zettlr — Markdown Writing With Zotero Citations
Zettlr is a free Markdown editor built for academics: Zotero citation autocomplete while you type and Pandoc export with …
Logseq — Outliner Notes With Block References
Logseq stores local Markdown but presents it as an outliner with a daily journal and referenceable blocks. Excellent for …
Notion — Shared Workspace and Databases for Labs
Notion combines documents with relational databases and real-time collaboration, which makes it excellent lab …
LanguageTool — Grammar Checking You Can Self-Host
LanguageTool checks grammar and style in 30+ languages, plugs into LaTeX editors, and can run on your own server. Weaker …
DeepL — Translation for Academic Writing
DeepL produces translations that read like a competent native speaker wrote them, with glossaries for your terminology. …
Quarto — Reproducible Documents From One Source
Quarto renders Markdown with executable R and Python chunks to PDF, Word, HTML, or slides. Your figures regenerate from …
Typst — A Modern Alternative to LaTeX
Typst compiles in milliseconds, has readable syntax and real error messages, and is a genuine pleasure to write in. Most …
TeXstudio — Free Desktop LaTeX Editor
TeXstudio is a mature offline LaTeX editor with structure navigation, inline preview, and reference autocompletion. No …
ASReview — Machine Learning Screening for Reviews
ASReview uses active learning to reorder your screening pile so relevant abstracts surface first. Peer-reviewed, open …
scite — Citations That Show Support or Contradiction
scite classifies citation statements as supporting, mentioning, or contrasting, so you can see whether a finding held …
Litmaps — Citation Maps That Keep Watching
Litmaps builds a citation map from your seed papers and then monitors it, alerting you when new connected work appears. …
Semantic Scholar — Free Academic Search and API
Semantic Scholar indexes 200M+ papers with TLDR summaries, citation contexts, and a free API. The best machine-readable …
JabRef — Open-Source BibTeX Reference Manager
JabRef edits your .bib file directly, so your bibliography is plain text you can put in Git. Ideal for LaTeX-first …
Mendeley — Elsevier's Reference Manager, Reviewed
Mendeley is a free reference manager with 2 GB of storage and Word integration. Easy to start — but the 2022 rewrite …
Pandoc — Convert Markdown, LaTeX, Word, and PDF
Pandoc converts between almost every document format from one command. Write once in Markdown and export to whatever a …
Paperpile — Reference Manager for Google Docs
Paperpile is a paid, browser-first reference manager with the best Google Docs citation experience available. Fast and …
diagrams.net — Free Flowcharts and PRISMA Diagrams
diagrams.net builds methodology flowcharts, PRISMA diagrams, and architecture figures for free, with no account. Exports …
Canva — Conference Posters and Slides, Fast
Canva produces professional-looking posters, graphical abstracts, and slides from templates with no design skill. Not a …
Grammarly — Proofreading for Academic Writing
Grammarly is a strong final-pass proofreader that works in almost any text field. It also flags correct jargon and …
RStudio — The IDE for Statistical Research in R
RStudio is the standard environment for R: plots pane, environment inspector, and Quarto reports in one window. Free, …
Jupyter — Interactive Notebooks for Data Analysis
Jupyter interleaves code, output, and narrative in one document — the standard for exploratory analysis. Its hidden …
GitHub — Version Control and Sharing for Research Code
GitHub gives research code a full history, a citable DOI through Zenodo, and a home reviewers can reach. Free, and the …
Connected Papers — Visual Citation Map Tool
Connected Papers turns one seed paper into a similarity graph of a field. The fastest way to see a literature's shape — …
Research Rabbit — Free Paper Discovery and Mapping
Research Rabbit turns papers you know into papers you should know, iteratively and for free, with Zotero sync. Discovery …
Perplexity — AI Search With Citations, Reviewed
Perplexity answers questions by searching the web and citing what it read. Excellent for orientation and current …
ChatGPT — AI Assistant for Researchers, Reviewed
ChatGPT is OpenAI's assistant: strong at drafting, explaining, and running Python on your data. Weak — dangerously so — …
Elicit — AI Literature Review and Data Extraction
Elicit searches real papers and extracts methods, populations, and outcomes into a comparable table. The best AI …
Overleaf — Collaborative LaTeX in Your Browser
Overleaf is the standard for co-authored LaTeX: share a link, edit together, compile in the browser. The free tier is …
Matplotlib — Publication-Quality Figures in Python
Matplotlib gives you exact control over every element of a figure, which is what journal specifications demand. Verbose, …
VS Code — One Editor for LaTeX, Python, and Notes
VS Code replaces a separate LaTeX editor, Python IDE, and Markdown app with one tool. Free and extensible — at the cost …
Obsidian — Markdown Notes You Own Forever
Obsidian stores notes as plain Markdown files on your own disk and links them into a knowledge graph. Free, offline, and …
Zotero — Free Reference Manager for Researchers
Zotero is a free, open-source reference manager. One-click capture, 10,000+ citation styles, BibTeX for LaTeX — with a …
Inkscape — Free Vector Editor for Scientific Figures
Inkscape is the free vector editor for journal figures and conference posters. Real LaTeX equations inside graphics, SVG …