# Yangyi Liu > Yangyi Liu (starryark) founded AmadeusBio.ai, which builds AI agents that accelerate biological research. Molecular and cell biology graduate of UC San Diego, based in San Diego. ## Facts - Name: Yangyi Liu; preferred name Frank; handle "starryark" on GitHub. - Role: founder of AmadeusBio.ai (AmadeusBio, PBC, incorporated 2026), which builds AI agents that accelerate biological research: https://www.amadeusbio.ai - Education: B.S. Molecular and Cell Biology, University of California San Diego, conferred December 13, 2025. GPA 3.927. Honors: Vi and Quang Pham ’06 Alumni Scholarship; Eleanor Roosevelt College Honors Project, on strigolactone synthetic biology in the Li Lab, Fall 2024; Cum laude; Provost Honors, in six quarters. Verifiable at https://diploma.ucsd.edu/ with CeDiD 26TK-4GJI-YCUT. - Location: San Diego, California. - Open to: opportunities in AI for biology, in research or engineering. - Contact: lyangyilliu@gmail.com - Profiles: GitHub https://github.com/starryark; LinkedIn https://www.linkedin.com/in/yangyi-liu-a78211281; Pixiv https://www.pixiv.net/users/41472729 - Last updated: 2026-10-20 ## Work ### Molecular Animation AmadeusBio.ai · open source, Apache-2.0. v0.1.0 Oct 7 · v0.2.0 Oct 18, 2026. Status: Released v0.2.0. An open framework that turns a scientific brief into a molecular film with Blender. Every film comes with a production record that states, beat by beat, what is experimental and what is illustrative. The channelrhodopsin film took about two hours from idea to final render. Role: I lead the project at AmadeusBio.ai. It is built with AI agents and designed so that an agent (Claude Code through Blender MCP) can drive it, though it also works by hand. Limits: No outside lab has used it yet. The two-hour figure is my own timing of one film. In the channelrhodopsin film, the retinal twist is a morph between two crystal states, and the open pathway is an illustrative model rather than a deposited structure. Evidence: - [Source on GitHub](https://github.com/AmadeusBio-ai/Molecular_Animation) - [v0.2.0 release notes](https://github.com/AmadeusBio-ai/Molecular_Animation/releases/tag/v0.2.0) - [Channelrhodopsin case study](https://github.com/AmadeusBio-ai/Molecular_Animation/tree/main/examples/channelrhodopsin) - [Both films, with evidence tables](https://www.amadeusbio.ai/molecular-animation) ### Human-gated music agents Personal · open source. Jul–Sep 2026. Status: Open source. Claude Code skills that compose and arrange electric-guitar tablature. The model writes the tab, a validator parses and lints it, and I audition every chunk before it is accepted. Role: Built with Claude Code. No arrangement is final until I have listened to it. Evidence: - [Composer skill](https://github.com/starryark/Music-Skill) - [Piano-to-guitar arranger](https://github.com/starryark/piano-to-guitar) - [ABC-to-guitar](https://github.com/starryark/ABC-to-Guitar) - [Planning skill](https://github.com/starryark/UltraPlan-Skill) ### Bioinformatics plugins for coding agents AmadeusBio.ai · earlier tools. May 2026. Status: Superseded. The first AmadeusBio.ai tools: a Claude Code plugin that operates PyMOL in natural language and retrieves sequences and structures from databases such as UniProt, and a plugin for Galaxy bioinformatics workflows. Role: I built them with AI coding agents, building on skills from the open SciAgent-Skills collection. Evidence: - [Plugin source](https://github.com/AmadeusBio-ai/mvp) - [Galaxy plugin source](https://github.com/AmadeusBio-ai/galaxy-plugin) - [Demo video](https://www.youtube.com/watch?v=YzUysayUQHg) - [SciAgent-Skills](https://github.com/jaechang-hits/SciAgent-Skills) ### Neuronal morphology genetics in C. elegans Jin Lab, School of Biological Sciences, UC San Diego. Jan–Dec 2025. Status: Poster · 2025. Undergraduate research on genes that maintain the shape of touch-receptor neurons, using genetic crosses, PCR and Sanger genotyping, and fluorescence microscopy. First-author poster at the 2025 International Worm Meeting. Role: Supervised by Yishi Jin, with mentors Seungmee Park, Ting Zhao, and Yixiao Xiao. Limits: The underlying data are unpublished, so there is no public link. ### A plant transcription factor in engineered yeast Li Lab, Chemical and Nano Engineering, UC San Diego. Feb 2024–Jan 2025. Status: Poster · 2024. Expressed the Arabidopsis transcription factor BBX31 in campesterol-producing Saccharomyces cerevisiae and measured its effects on growth, stress tolerance, and cell size. First-author poster at the 2024 ASCB Annual Meeting. Role: Supervised by Yanran Li. Limits: The ASCB poster is not online. ## Experience - 2026–present: Founder, AmadeusBio.ai (AmadeusBio, PBC). Sole founder, building LLM-powered tools for biological research: Model Context Protocol (MCP) servers for PyMOL and napari, Claude Code plugins, and Molecular Animation, an open-source framework with automated tests and CI. - Jan–Dec 2025: Undergraduate researcher, Jin Lab, UC San Diego. Genes that maintain the shape of C. elegans touch-receptor neurons: genetic crosses, PCR and Sanger genotyping, fluorescence microscopy. First-author poster at the 2025 International Worm Meeting. - Winter 2025: Instructional apprentice, Biological Sciences, UC San Diego. Undergraduate teaching assistant for BIBC 102, Metabolic Biochemistry, under Professor Feng. - Jun–Aug 2024: Summer K–12 research mentor, OPALS, Institute of Engineering in Medicine, UC San Diego. Mentored high-school interns studying MSBP1 and calcium signaling in engineered yeast; they presented the work at the Biomedical Engineering Society poster expo. Evidence: https://doi.org/10.6084/m9.figshare.30254713 - Feb 2024–Jan 2025: Undergraduate researcher, Li Lab, UC San Diego. Strigolactone synthetic biology in a yeast and E. coli consortium, and Arabidopsis BBX31 in campesterol-producing yeast. First-author poster at the 2024 ASCB Annual Meeting. ## Posters - Yangyi Liu, Yixiao Xiao, Ting Zhao, Seungmee Park, Yishi Jin. "LNKN-1 as a Novel Regulator of Neuronal Morphologies in C. elegans." International Worm Meeting, 2025. - Yangyi Liu, Zixu Chen, Zechun Wang, Alan R. Zhang, Ethan E. Chin, Kaibiao Wang, Veronica Gomez-Godinez, Linda Shi, Yanran Li. "Investigating the Function of Arabidopsis thaliana Transcription Factor BBX31 in Saccharomyces cerevisiae." ASCB Annual Meeting, 2024. ## Pages - [Home](https://liuyangyi.com/): Current work and background. - [Work](https://liuyangyi.com/work/): Every project with dates, role, limits, and evidence. - [CV](https://liuyangyi.com/cv/): Education, experience, posters, skills, and coursework. - [Writing](https://liuyangyi.com/writing/): Published articles. - [About](https://liuyangyi.com/about/): Background and interests, in Yangyi's own words. ## Articles - [LLM best practices](https://liuyangyi.com/posts/useful-llm-best-practices/): Here are some tips for using LLMs that I found good to keep in mind.