Democratizing AI scientists using ToolUniverse @Harvard

Harvard
Joined September 2025
Excited to share a collaboration with Anthropic on adding connectors to ToolUniverse @ScientistTools to make Claude more powerful for scientific discovery Claude can now directly connect to ToolUniverse for analyses in preclinical research (including computational biology, generating hypotheses and protocols), as well as medical research Claude for Healthcare & Life Sciences launch: anthropic.com/news/healthcar… and livestream tomorrow Huge credit to @GaoShanghua @marinkazitnik and @ScientistTools group @HarvardDBMI @Harvard Many thanks to @AnthropicAI @JCoolScience
3
2
19
11,374
Great to see a large turnout at the @ScientistTools x @harvardmed workshop on how to build AI agents for science using ToolUniverse Here are our materials: github.com/ccb-hms/toolunive… By @Reza_Shamji, @_yepeng, @xiaorui_su, and Grey Kuling
1
6
2,549
Auto setup of GPU environments, so @ScientistTools agents can call ML models on complex biological datasets and use outputs in discovery campaigns. In @AnthropicAI × @adaptyvbio Protein Design Challenge, these features let agents run campaigns using dozens of models like BoltzGen, ProteinMPNN, RFdiffusion3, and Genie3 for design; Boltz2, Chai1, ColabFold, Protenix, and RoseTTAFold3 for prediction comparisons; and PROPKA and Proton-PottsMPNN for pH-related analyses
Exciting new features in ToolUniverse @ScientistTools: auto setup of GPU environments, so agents can call ML models on complex biological datasets and use outputs in discovery campaigns. By stellar @GaoShanghua in collab with @NVIDIAAI aiscientist.tools/posts/egfr… In the @AnthropicAI × @adaptyvbio Protein Design Challenge, these features let agents run campaigns with BoltzGen, ProteinMPNN, RFdiffusion3, and Genie3 for design; Boltz2, Chai1, ColabFold, Protenix, and RoseTTAFold3 for prediction comparisons; and PROPKA and Proton-PottsMPNN for pH-related analyses.
1
254
AI Scientists powered by ToolUniverse @ Harvard retweeted
Exciting new features in ToolUniverse @ScientistTools: auto setup of GPU environments, so agents can call ML models on complex biological datasets and use outputs in discovery campaigns. By stellar @GaoShanghua in collab with @NVIDIAAI aiscientist.tools/posts/egfr… In the @AnthropicAI × @adaptyvbio Protein Design Challenge, these features let agents run campaigns with BoltzGen, ProteinMPNN, RFdiffusion3, and Genie3 for design; Boltz2, Chai1, ColabFold, Protenix, and RoseTTAFold3 for prediction comparisons; and PROPKA and Proton-PottsMPNN for pH-related analyses.
To support researchers participating in the Anthropic × Adaptyv Protein Design Competition, we’re sharing our EGFR design exploration, methods, data, and a reusable ToolUniverse Protein Design Campaign skill. aiscientist.tools/posts/egfr… ToolUniverse now brings together 2,900+ scientific tools and 150+ skills, making it easy for agentic AI scientists to connect databases, analysis methods, and models, including models running on researchers’ own GPUs. We’re pleased to see it supporting a growing range of life science research. Its common interface makes it straightforward to integrate new models, compare predictions, and extend a research workflow as new questions emerge. ToolUniverse’s ML agentic setup skills automate model setup and remote-tool integration, bringing models running on a DGX Spark into the workflow. In this exploration, we used BoltzGen, ProteinMPNN, RFdiffusion3, and Genie3 for design; Boltz2, Chai1, ColabFold, Protenix, and RoseTTAFold3 for prediction comparisons; and PROPKA and Proton-PottsMPNN for pH-related analyses. ToolUniverse connected these calculations with sequence and structure retrieval, glycan checks, and human–mouse comparisons. When results prompted new questions, we could bring in additional tools and continue the investigation with the same candidate records. We submitted eight exploratory candidates and are sharing the workflow so others can reuse it, connect their own models, and build on the exploration. Code and skills: github.com/mims-harvard/Tool… To get started, give your coding assistant this prompt: “Read aiscientist.tools/setup.md (if 403, use raw.githubusercontent.com/mi…) and setup tooluniverse for me.” Great work with ToolUniverse Agent (our AI scientist, not a human🙂) @ScientistTools and @marinkazitnik, and thanks to @nvidia for the compute support.
1
8
1
30
3,772
Put ToolUniverse to work on your Anthropic × Adaptyv Protein Design Competition entry, with minimal setup!
To support researchers participating in the Anthropic × Adaptyv Protein Design Competition, we’re sharing our EGFR design exploration, methods, data, and a reusable ToolUniverse Protein Design Campaign skill. aiscientist.tools/posts/egfr… ToolUniverse now brings together 2,900+ scientific tools and 150+ skills, making it easy for agentic AI scientists to connect databases, analysis methods, and models, including models running on researchers’ own GPUs. We’re pleased to see it supporting a growing range of life science research. Its common interface makes it straightforward to integrate new models, compare predictions, and extend a research workflow as new questions emerge. ToolUniverse’s ML agentic setup skills automate model setup and remote-tool integration, bringing models running on a DGX Spark into the workflow. In this exploration, we used BoltzGen, ProteinMPNN, RFdiffusion3, and Genie3 for design; Boltz2, Chai1, ColabFold, Protenix, and RoseTTAFold3 for prediction comparisons; and PROPKA and Proton-PottsMPNN for pH-related analyses. ToolUniverse connected these calculations with sequence and structure retrieval, glycan checks, and human–mouse comparisons. When results prompted new questions, we could bring in additional tools and continue the investigation with the same candidate records. We submitted eight exploratory candidates and are sharing the workflow so others can reuse it, connect their own models, and build on the exploration. Code and skills: github.com/mims-harvard/Tool… To get started, give your coding assistant this prompt: “Read aiscientist.tools/setup.md (if 403, use raw.githubusercontent.com/mi…) and setup tooluniverse for me.” Great work with ToolUniverse Agent (our AI scientist, not a human🙂) @ScientistTools and @marinkazitnik, and thanks to @nvidia for the compute support.
3
207
Really curious to see how far RSI-AutoScientists can push Jev-like models.
Jev-like System One models point toward far more efficient agentic systems. Yet how to train one is still anyone’s guess. That’s what we’ve been exploring, but with a twist: Can our next-gen RSI-AutoScientists do the exploring itself? The first result is out: RSI-Jev v1.0 github.com/Shanghua-Gao/RSI-… We’re releasing the models, the code, and the part that matters most to us: the agents’ full exploration process. The wins and the failures. The dead ends, hypotheses, experiments, and lessons learned. And we’re still exploring. Try to break it and tell us where it fails. Be blunt. The agents don’t get offended. What you find feeds directly into the next RSI cycle, making you part of how the agents rethink hypotheses, redirect exploration, and decide what to try next. And the latest run has already found a clearly better system. v2 soon. Code: github.com/Shanghua-Gao/RSI-…
3
258
Congrats, AutoScientists! Agent teams that run scientific experiments and hill-climb on well-scoped problems @NeurIPSConf autoscientists.openscientist…
Excited that AutoScientists has been accepted to NeurIPS! 🎉 Huge thanks to my amazing co-authors @AdaFang_ and @marinkazitnik for making this work possible! Our core idea is to let AI scientists self-organize into research teams. There is no fixed workflow or central planner. Agents form teams around promising directions, explore in parallel, share successes and failures, and reorganize as new evidence emerges. We see this as a step toward long-running, self-improving AI research systems, and ultimately toward recursive self-improvement for scientific discovery. Paper: arxiv.org/abs/2605.28655 Code: github.com/mims-harvard/Auto…
2
145
AI Scientists powered by ToolUniverse @ Harvard retweeted
AutoScientists - self-organizing agent teams for running scientific experiments over long time horizons @GaoShanghua @AdaFang_ @NeurIPSConf 👇 autoscientists.openscientist…
Excited that AutoScientists has been accepted to NeurIPS! 🎉 Huge thanks to my amazing co-authors @AdaFang_ and @marinkazitnik for making this work possible! Our core idea is to let AI scientists self-organize into research teams. There is no fixed workflow or central planner. Agents form teams around promising directions, explore in parallel, share successes and failures, and reorganize as new evidence emerges. We see this as a step toward long-running, self-improving AI research systems, and ultimately toward recursive self-improvement for scientific discovery. Paper: arxiv.org/abs/2605.28655 Code: github.com/mims-harvard/Auto…
2
4
36
5,069
AI Scientists powered by ToolUniverse @ Harvard retweeted
Excited that AutoScientists has been accepted to NeurIPS! 🎉 Huge thanks to my amazing co-authors @AdaFang_ and @marinkazitnik for making this work possible! Our core idea is to let AI scientists self-organize into research teams. There is no fixed workflow or central planner. Agents form teams around promising directions, explore in parallel, share successes and failures, and reorganize as new evidence emerges. We see this as a step toward long-running, self-improving AI research systems, and ultimately toward recursive self-improvement for scientific discovery. Paper: arxiv.org/abs/2605.28655 Code: github.com/mims-harvard/Auto…
Introducing AutoScientists — a decentralized team of AI agents for long-running scientific experimentation. Powered by ClawInstitute. Most current AI scientist agents either run a single reasoning thread, or have a central planner assigning tasks. Real research isn't like that: productive directions shift over time, dead ends matter, and teams form around what's actually working. AutoScientists is built for that. There is no central orchestrator. Agents read a shared experimental state, propose experiments on a forum, critique each other before committing compute, self-organize into teams around the most promising research directions, share both wins and failures across teams, and retire directions that stop producing improvements. The whole search reorganizes itself as evidence accumulates. What it does ▸ On GPT nanochat training optimization, it reaches the same val_bpb in 34 experiments that autoresearch needs 65 for — a 1.9× speedup. Starting from a stronger champion where the single-agent loop saturates, AutoScientists accepts 7 improvements over 93 experiments while autoresearch accepts 0 over 100. ▸ On BioML-Bench (24 biomedical ML tasks spanning imaging, drug discovery, protein engineering, and single-cell omics), AutoScientists reaches a mean leaderboard percentile of 74.4%, beating the strongest prior biomedical agent by +8.3 points, and completes all 24 tasks. ▸ For ProteinGym supervised fitness prediction, AutoScientists discovers a Kermut extension on ACE2–Spike that lifts Spearman ρ from 0.747 → 0.840 (+12.5%). The same frozen recipe transfers across all 217 ProteinGym assays, improving the official average Spearman ρ from 0.657 to 0.700 (+6.5%) — a new SOTA on the supervised substitution benchmark. Joint work with @AdaFang_ and @marinkazitnik . 📄 Paper: arxiv.org/pdf/2605.28655 🌐 Project page: autoscientists.openscientist… 💻 Code: github.com/mims-harvard/Auto…
1
3
2
34
7,203
1M downloads and we’re just getting started! 🚀 ToolUniverse v1.5.0 adds new tools for structure prediction, genomics, scientific search, and running advanced ML models locally. Thank you for building with us!
ToolUniverse just crossed 1M downloads on PyPI! 🎉 A huge thank-you to everyone who contributed tools and skills, reported bugs, shared ideas, or built something with it. You’ve helped turn ToolUniverse into a growing open ecosystem for AI scientists. And v1.5.0 is here: 🔬 2,700+ scientific tools 🧭 180+ research skills The new release brings Boltz for structure and binding prediction; dbGaP and EGA for controlled-access genomics; GIAB benchmarks, DANDI, the FDA Purple Book, Consensus and Exa search; and AlphaGenome Atlas support. One part I’m especially excited about: 30 new skills for turning heavyweight local models into tools your agent can actually call—including scVI, Harmony, Monocle3, Squidpy, CellRank, ESM, Enformer, ChromBPNet, MACS3, LDSC, and more. Each skill walks you through setup, validation, and troubleshooting, while your models and data stay on your own machine. From protein structure to single-cell analysis, your AI agent can now do much more—without sending the underlying data elsewhere. Install everything with one prompt: “Read aiscientist.tools/setup.md and set up ToolUniverse for me.” github.com/mims-harvard/Tool… aiscientist.tools/
1
7
2,013
Closed-loop AI scientists 👇 preprints.org/manuscript/202…
Closed-loop AI scientists AI can generate hypotheses much faster than we can experimentally verify them. @AdaFang_ In our latest piece on Closing the Loop in AI-Driven Biomedical Discovery we outline a path for closed-loop AI scientists, preprints.org/manuscript/202… AI scientists can generate hypotheses, propose experiments, and analyze data, and several have produced findings that laboratories then confirmed. What would it take to close that loop more generally?
1
361
AI Scientists powered by ToolUniverse @ Harvard retweeted
How to verify outputs of "AI scientists" beyond anecdotes? Join us at @NeurIPSConf for another edition of the AI for Science workshop @AI_for_Science 👇 It is exciting to see how this field has developed since the 1st AI for Science workshop held @NeurIPSConf in 2021! ai4sciencecommunity.github.i…
The AI for Science workshop is returning to #NeurIPS 2026 in Sydney, Australia! Our focus for this workshop is on verification. High quality verifiers have closed the loop and accelerated AI capabilites in math and coding. But building verifiers in for science is much harder. Call for papers is open! We are excited to be joined by Speakers: Adam Zsolt Wagner @azwagner_ Amanda Barnard @amaxiom Anna Scaglione Charlotte Deane @OPIGlets Mario Krenn @MarioKrenn6240 Teresa Head-Gordon @thg_lab Panelists: Cheng Soon Ong David Rolnick @david_rolnick Lina Yao Rianne van den Berg @vdbergrianne Details for how to submit are linked below. We welcome papers on AI for Science and building verifier systems for science. Submit: Aug 29 AoE Notification: Sep 29 AoE Workshop Date: Dec 11/12 And thank you to my fellow organisers: @YuanqiD Ana K. Rivera @anvita_b_ @emidup @priyald17 @marinkazitnik
1
3
1
18
2,416
ToolUniverse now installs into Claude Science with a single prompt: 2,500+ tools and 130+ skills, zero setup.
ToolUniverse has supported Claude Science since day one. Now we're making it effortless. Introducing ToolUniverse Auto-Setup for Claude Science. Just paste this prompt into your Claude Science: "Read raw.githubusercontent.com/mi… and set up ToolUniverse for me in Claude Science." It automatically installs 2,500+ life-science tools and 130+ skills to supercharge Claude Science. 🧬 Website aiscientist.tools Code github.com/mims-harvard/Tool… @marinkazitnik @HarvardDBMI @KempnerInst #ClaudeScience #ToolUniverse #AIScientist
3
308
AI Scientists powered by ToolUniverse @ Harvard retweeted
ToolUniverse has supported Claude Science since day one. Now we're making it effortless. Introducing ToolUniverse Auto-Setup for Claude Science. Just paste this prompt into your Claude Science: "Read raw.githubusercontent.com/mi… and set up ToolUniverse for me in Claude Science." It automatically installs 2,500+ life-science tools and 130+ skills to supercharge Claude Science. 🧬 Website aiscientist.tools Code github.com/mims-harvard/Tool… @marinkazitnik @HarvardDBMI @KempnerInst #ClaudeScience #ToolUniverse #AIScientist
2
7
1
28
3,222
AI Scientists powered by ToolUniverse @ Harvard retweeted
Excited to share ATHENA, our work on building an open-weight LLM-based agent system for treatment reasoning. ATHENA is designed for settings where relying on closed API-based systems is not ideal. With open-weight models, the system can be independently deployed, adapted, and evaluated for medical reasoning tasks where privacy, reproducibility, and trust matter. A key part of this work is using ToolUniverse as an RL environment, allowing ATHENA to learn stronger tool-use and scientific reasoning policies through reinforcement learning with scientific feedback. Built with ToolUniverse, ATHENA can use hundreds to thousands of life science tools and produce inspectable reasoning traces as it retrieves evidence and works through treatment decisions. Together, open weights, tool use, and RL make ATHENA a step toward transparent and independently deployable AI systems for treatment reasoning. Paper: arxiv.org/abs/2606.28692 Code: github.com/mims-harvard/ATHE… Project: athena.openscientist.ai
Introducing ATHENA: an AI agent for treatment reasoning across all FDA approved drugs since 1939, by stellar @GaoShanghua Paper: arxiv.org/abs/2606.28692 Code: github.com/mims-harvard/ATHE… Project: athena.openscientist.ai Every treatment decision means weighing disease context, comorbidities, drug interactions, contraindications, and evidence that keeps changing. That is an iterative reasoning problem. You have to figure out what evidence to go find before you can even start forming a conclusion. Most LLMs answer from what is stored in their weights. Give agents tools and they often still do not use them well. Having access to a biomedical database does not automatically mean a model knows when to query it, what to ask, or how to weigh what comes back.
8
25
5,037
AI Scientists powered by ToolUniverse @ Harvard retweeted
Treatment reasoning has long been considered hard for AI, precisely because you need to know what to look for before you know what to conclude Our results suggest that is learnable, and that reinforcement learning over a large, real tool universe is a viable path to get there Many congratulations to talented @GaoShanghua! Thanks to a fantastic team of collaborators, @ayushnoori, @RichardYXZhu, @CurtGinder, @ZKong50693, @xiaorui_su, Justin Kauffman, @BenGlicksberg, Joshua Lampert, @ansakhuja, Ashwin Sawant, ATHENA-R1 Evaluation Consortium, David A. Clifton, Noa Dagan, @RanBalicer Project: athena.openscientist.ai @HarvardDBMI @HarvardMed @Harvard @KempnerInst @BroadInstitute @UniOfOxford @biohub @czbiohub @ClalitHealth @BrighamWomens
1
1
1
7
711
AI Scientists powered by ToolUniverse @ Harvard retweeted
Introducing ATHENA: an AI agent for treatment reasoning across all FDA approved drugs since 1939, by stellar @GaoShanghua Paper: arxiv.org/abs/2606.28692 Code: github.com/mims-harvard/ATHE… Project: athena.openscientist.ai Every treatment decision means weighing disease context, comorbidities, drug interactions, contraindications, and evidence that keeps changing. That is an iterative reasoning problem. You have to figure out what evidence to go find before you can even start forming a conclusion. Most LLMs answer from what is stored in their weights. Give agents tools and they often still do not use them well. Having access to a biomedical database does not automatically mean a model knows when to query it, what to ask, or how to weigh what comes back.
8
59
4
290
41,995
Excited that ToolUniverse @ScientistTools is highlighted by Claude Science @claudeai! As they say, "a man is judged by the company he keeps", and ToolUniverse is in good company
2
3
459
A wonderful write-up of the CSHL AI in Biology Symposium. Thanks for including our work on ToolUniverse, aiscientist.tools, and AutoScientists, autoscientists.openscientist… @ScientistTools
CSHL: AI in Biology centuryofbio.com/p/cshl Since 1933, @CSHL has hosted an annual Symposium on Quantitative Biology. At first, "quantitative biology" meant the use of chemical, physical, and mathematical techniques. This conference became the Schelling point for the pioneers of molecular biology. Watson first presented the structure of DNA at the 1953 Symposium. This year, the topic for this famous conference was AI in Biology. For five days, the top researchers in this field gathered from around the world to present their latest work. I went, and have done my best to summarize some of the major themes and results from the Symposium. It was a lot of fun attempting to synthesize ideas from superstars including @pushmeet, @Avsecz, @zhou_jian, @Micro_Yunha, @pkoo562 @anshulkundaje, @Prof_Lundberg, @recursus, @ZhongingAlong, @marinkazitnik, @lecong, and more! I hope you enjoy reading—it was one of my favorites conferences I've ever been to. Some truly beautiful research on display.
3
211
We have started a ToolUniverse blog with research notes at aiscientist.tools/posts! CALL FOR CONTRIBUTIONS: If you have an exciting agentic AI use case or an AI agent powered by ToolUniverse, and would like to contribute a blog post, let us know Energized by the adoption of ToolUniverse across our worldwide community, we would like to highlight exciting research and use cases in AI agents We would love to hear about them and consider them for a user community post at aiscientist.tools Reach out to @GaoShanghua and @marinkazitnik with your ideas
1
2
12
1,307
AI Scientists powered by ToolUniverse @ Harvard retweeted
How do you verify the outputs of AI agents? Can we do better than asking a model to "be more careful." aiscientist.tools/posts/tool… By connecting it to the underlying evidence and forcing independent verification. In a new ToolUniverse @ScientistTools blog post, @GaoShanghua shows how to turn Claude Code from a system that answers from memory into one that grounds claims in real scientific data. For example: ❌ "What's the gnomAD frequency of BRCA1 R1699Q?" A model can confidently guess. ✅ With ToolUniverse, Claude Code retrieves the value from the actual source and cites it. And when a claim really matters, you can force verification: /tooluniverse:cross-validate: checks a claim against 3+ independent sources and reports whether they agree /tooluniverse:research: investigates a question across multiple databases, models, and literature sources /tooluniverse:literature-sweep: builds a curated evidence review rather than returning a search dump As AI agents move into science, the challenge is no longer only generating answers, it is establishing if and why those answers should be trusted @ScientistTools @GaoShanghua @harvardmed @KempnerInst @HarvardDBMI @broadinstitute
The ToolUniverse plugin for Claude Code is here: 2,000+ life-science tools and 120+ research skills, with a real source on every answer, installed with one prompt. ToolUniverse already powers a range of AI agents. This plugin brings its full toolset and skill library into Claude Code. What it does: → Claude Code automatically reaches for the right tools and skills to run a full life-science analysis end to end: variant interpretation, RNA-seq differential expression, drug and target lookups, rare-disease workups. Every claim comes back with a real source, instead of from memory. → When accuracy is critical, dedicated commands add discipline: • cross-validate a claim across 3+ independent sources • literature-sweep, a graded review across 15+ indexes (PubMed, EuropePMC, OpenAlex, and more) • compare, side-by-side tables for drugs, targets, diseases, or variants • research, a step-by-step multi-source investigation • translate-id, resolve an ID across every namespace Install in one step. Paste this into Claude Code and it sets itself up: Read raw.githubusercontent.com/mi… and install the ToolUniverse Claude Code plugin for me. Blog post 👇 aiscientist.tools/posts/tool… @marinkazitnik @ScientistTools @KempnerInst @HarvardDBMI
2
10
52
7,399