Project Tolera — Work Archive
A browsable record of a week-long computational campaign to identify novel therapeutic targets and design protein therapeutics for eosinophilic esophagitis (EoE) and related conditions. Every working session is summarized below and linked to the files it produced, so reviewers can check the work and reuse it for further tool development and programs.
Develop a comprehensive project plan for Phase 1 that includes extensive and exhaustive analysis of all existing datasets, defining scope, methodology, and analysis objectives.
The session set out to develop a comprehensive Phase 1 project plan — including exhaustive analysis of existing datasets, defined scope, methodology, and analysis objectives — for a protein-therapeutics target-discovery effort in eosinophilic esophagitis (EoE) and related conditions.
Publish the omics-target-mining skill using the SKILL.md documentation and kernel.py implementation artifacts. This involves finalizing and releasing the skill package for use.
Publish the omics-target-mining skill (SKILL.md and kernel.py implementation) as a public, reusable package for other researchers.
Develop a comprehensive methods manuscript detailing the integrated computational and literature-mining approaches used to generate novel therapeutic hypotheses and identify tractable pMHC therapeutic targets for EoE.
This session aimed to develop a comprehensive methods manuscript documenting the integrated computational and literature-mining pipeline used to generate novel therapeutic hypotheses and identify tractable pMHC therapeutic targets for eosinophilic esophagitis (EoE).
Adapt and apply our EoE research framework and methodologies to celiac disease, leveraging existing skills, manuscripts, and learnings from the EoE project to model food-antigen-mediated immune responses in celiac disease.
This session aimed to adapt the team's existing EoE research framework and methodologies to celiac disease, applying prior skills, manuscripts, and learnings to model food-antigen-mediated immune responses in celiac disease.
Audit all stalled and postponed tasks requiring GPU access across the project. Compile exhaustive list with estimated computational costs and resource requirements to inform GPU infrastructure investment decision.
Audit all stalled and postponed tasks across the EoE protein-therapeutics project that require GPU access, compiling an exhaustive list with estimated computational costs and resource requirements to inform a GPU infrastructure investment decision.
Record a two-minute podcast discussing progress made through day 2 of the hackathon and outlining plans for the remaining 5 days of work.
The session set out to produce a two-minute podcast recapping progress from the first two days of the EoE protein-therapeutics hackathon and outlining plans for the remaining five days.
Develop a skill that guides users through preparing a professional scientific poster for conference presentations or virtual Zoom presentations, including layout design, content organization, and visual best practices.
This session aimed to build a reusable skill for guiding users through creating professional scientific posters (for conference or virtual Zoom presentation), covering layout design, content organization, and visual best practices.
Identify and plan strategic uses for $200 in API credits across Claude Science and Claude Code during the hackathon. Evaluate potential applications such as large-scale data processing, model training, or advanced analysis tasks that could accelerate project goals.
This session was intended to identify and plan strategic uses for $200 in API credits across Claude Science and Claude Code during a hackathon, evaluating applications like large-scale data processing, model training, or advanced analysis to accelerate project goals.
Design peptide-MHC (pMHC) therapeutic candidates targeting wheat, dairy, and soy allergens for eosinophilic esophagitis (EoE) treatment using GPU-accelerated molecular design.
This session aimed to design peptide-MHC (pMHC) therapeutic candidates targeting wheat, dairy, and soy allergens as a treatment approach for eosinophilic esophagitis (EoE), using GPU-accelerated molecular design.
Execute synthetic peer-review process on EoE de novo binder-design manuscript (EoE_manuscript.md and EoE_supplementary.md) using the synthetic-peer-review skill. Evaluate in-silico computational design study with disclosed AI authorship as hackathon deliverable, focusing on computational methodology and design validation rather than experimental validation.
This session set out to run a synthetic peer-review process on an in-silico de novo binder-design manuscript for eosinophilic esophagitis (EoE), evaluating the computational methodology and design validation of a disclosed AI-authored hackathon deliverable rather than experimental results.
Draft and send a professional heads-up message to Biohub's legal team and AI research team lead informing them of hackathon work being conducted as approved professional development time and citizen science, noting potential biotech-leverageable insights for future IP discussion.
The session aimed to draft and send a professional heads-up message informing Biohub's legal team and AI research team lead about hackathon work related to eosinophilic esophagitis (EoE) protein therapeutics, framing it as approved professional development time and citizen science while flagging potential biotech-leverageable insights for future IP discussion.
Establish biotech company name, brand identity, and organizational structure. Define mission statement focused on personalized pMHC therapeutics for EoE patients and develop initial business entity documentation.
This session aimed to establish the biotech company's name, brand identity, organizational structure, and mission statement around personalized pMHC therapeutics for EoE patients, alongside initial business entity documentation.
Add wheat PDB file references to Blender and ChimeraX visualization scripts for pMHC demonstration clips. Review scripts for technical optimization and content alignment with Tolera's therapeutic narrative.
This session aimed to add wheat PDB file references into the Blender and ChimeraX visualization scripts used for pMHC demonstration clips, and to review those scripts for technical optimization and alignment with Tolera's therapeutic narrative.
Resolve IndentationError in Blender console script where kf_value() calls and return statement have unexpected indentation. Review and correct the indentation level of function body statements to match proper Python syntax.
This session set out to debug an IndentationError in a Blender console script (involving kf_value() calls and a return statement) as part of ongoing work on molecular/cellular animation tooling for the EoE protein therapeutics project.
Conduct a comprehensive 100+ page market report on the pMHC therapeutic space, documenting the development journey (from initial concept through post-market adoption) of all programs progressing to any stage. Focus on Tzield as FDA-approved example and celiac failures, incorporating patient-centered perspective, published PRO data, and PFDD timing across disease areas.
The session aimed to produce a 100+ page market report on the pMHC (peptide-MHC) therapeutic landscape, tracing program development from initial concept through post-market adoption, with Tzield as the FDA-approved case study, celiac program failures, and a patient-centered lens incorporating PRO data and PFDD timing.
Create a 5-minute survey on EoE patient experiences and vaccine interest with ≤1 short-answer question. Draft survey content, identify best distribution platform for anonymous responses (Google Forms, Typeform, or Qualtrics), and establish collection protocol for hackathon submission support.
Design a short (≤5-minute, ≤1 short-answer question) survey to gather EoE patient experiences and gauge interest in a tolerizing vaccine approach, plus a plan to distribute it anonymously for hackathon submission support.
Develop and publish a reusable skill to GitHub for generating patient-centered market reports and conducting patient community surveys. This skill will encapsulate the strategy and methodology for gathering market insights directly from patient perspectives.
This session aimed to develop and publish a reusable skill to GitHub for generating patient-centered market reports and conducting patient community surveys, encapsulating a methodology for gathering market insights directly from patient perspectives (in the context of protein therapeutics for eosinophilic esophagitis and related conditions).
Integrate insights from the patient-centered market report into business plan and pitch deck, incorporating findings on patient priorities, pMHC market dynamics, and regulatory strategies to strengthen deliverables.
This session aimed to integrate findings from a patient-centered market report — covering patient priorities, pMHC market dynamics, and regulatory strategy — into the business plan and pitch deck for the EoE-focused protein therapeutics project.
Update the "Rational design of multivalent nanoparticle-pMHC-II immunotherapies for food allergen tolerance induction in eosinophilic esophagitis" manuscript based on the newly refined scientific plan and business plan to ensure alignment across all strategic documents.
This session aimed to update the "Rational design of multivalent nanoparticle-pMHC-II immunotherapies for food allergen tolerance induction in eosinophilic esophagitis" manuscript so that it aligned with a newly refined scientific plan and business plan.
Prepare 1-2 line summary of ML/AI experience from this project for manager. Focus on key accomplishments: hypothesis generation pipeline development, GPU-optimized omics analysis, automated target-mining skill publication, and computational methods for disease modeling.
The session set out to prepare a 1-2 line summary of the project's ML/AI experience for a manager, highlighting hypothesis generation pipeline development, GPU-optimized omics analysis, automated target-mining skill publication, and computational methods for disease modeling.
Create a bare bones slide deck walking through the 3-minute hackathon video submission, starting from omics and DGE through target discovery and pMHC design, showcasing the evolution of skills, GitHub contributions, manuscript development, and the open-source AI-to-clinic pipeline built with Claude Science to serve the EoE patient community.
Build a bare-bones slide deck for a 3-minute hackathon video submission that walks through the project's arc from omics/DGE analysis through target discovery and pMHC design, highlighting skills evolution, GitHub contributions, manuscript progress, and the open-source AI-to-clinic pipeline for the EoE patient community.
Build a generalizable Claude Science tool that automates the complete therapeutic development pipeline for any disease: from understanding unmet needs and patient priorities, through data/literature mining for novel therapeutics, AI/ML validation (protein modeling, etc.), to generating scientific, regulatory, and commercial strategies. System should iteratively request human validation at decision points where confidence is insufficient.
The session aimed to build a generalizable "Claude Science" tool/skill that automates an end-to-end therapeutic development pipeline — from unmet-need and literature discovery through AI/ML validation to scientific, regulatory, and commercial strategy — with built-in checkpoints for human validation wherever confidence is low.
Design and develop a user-friendly interface enabling researchers to interact with a therapeutic program architect, receive real-time answers to questions, and obtain deliverables—all running on serverless infrastructure without requiring users to provide compute resources or server access.
This session set out to design and develop a user-friendly, serverless interface allowing researchers to interact with a therapeutic program architect tool, ask questions, and receive real-time answers and deliverables related to protein therapeutics for eosinophilic esophagitis (EoE) and related conditions.
Create a central website that showcases hackathon accomplishments with a high-level overview and role-based navigation directing visitors to relevant resources including GitHub repositories, therapeutic specialist agent, manuscripts (pMHC and CCL26/POSTN), biotech development plans, and more.
Build a central website showcasing hackathon accomplishments from an EoE-related protein therapeutics project, with a high-level overview and role-based navigation to relevant resources.
Execute the drug program pipeline for esophageal cancer research, including drug screening, efficacy analysis, and therapeutic candidate evaluation.
This session aimed to execute an end-to-end drug program pipeline for esophageal cancer (esophageal adenocarcinoma, EAC) research, covering drug/target screening, efficacy analysis, and therapeutic candidate evaluation.
Execute the manuscript specialist tool on the EAC (Eosinophilic Esophagitis) program to analyze and enhance manuscript quality and scientific rigor.
This session aimed to run a manuscript specialist tool on the EAC (Eosinophilic Esophagitis) program to analyze and improve the quality and scientific rigor of an associated manuscript.
Review completed work across therapeutics, software tools, business development, and AI/ML domains to identify skill gaps and propose new specialized agents that could enhance project capabilities and accelerate future research-to-commercialization workflows.
This session set out to review completed work across therapeutics, software tools, business development, and AI/ML domains for the EoE protein-design project in order to identify skill gaps and propose new specialized agents to accelerate future research-to-commercialization workflows.
Develop a lay summary for the CCL26/POSTN manuscript that explains the research findings and significance in accessible language for non-specialist audiences.
This session aimed to develop a lay summary for the CCL26/POSTN manuscript that translates the research findings and their significance into language accessible to non-specialist audiences.
Review and refine the 3 hackathon manuscripts for consistency in language, author/affiliation information, disclaimers about AI-generation and lack of peer review, and proper acknowledgments of the hackathon process.
This session aimed to review and refine the three Project Tolera hackathon manuscripts (CCL26/POSTN, pMHC, and EAC/EoE) for consistent language, author/affiliation details, AI-generation and no-peer-review disclaimers, and proper acknowledgment of the hackathon process.
Explore the genome-scale CD4+ T cell perturbseq dataset to identify insights for pMHC platform development and investigate potential CCL26/POSTN related findings that could inform therapeutic targets.
This session aimed to mine a genome-scale CD4+ T cell perturb-seq dataset for insights relevant to pMHC platform development, with a specific eye toward CCL26/POSTN-related findings that could inform therapeutic targets in eosinophilic esophagitis (EoE).
Create a short video that automatically displays each page of ruthannepai.netlify.app/biotech for 1.2 seconds per page to showcase the full site content.
The session set out to create a short video automatically cycling through each page of ruthannepai.netlify.app/biotech at 1.2 seconds per page to showcase the site's full content.
Create a shareable file/archive containing important chats, artifacts, and documentation from this project to be hosted on the Netlify website. This will enable collaborators and others to review the work and use it as a reference for tool development and future programs.
This session aimed to create a shareable archive of important chats, artifacts, and documentation from the EoE protein therapeutics project, to be hosted on Netlify for collaborators and future reference.
User Uploads
This session was intended to collect and centralize reference materials and external files relevant to the project's work on protein therapeutics for eosinophilic esophagitis and related conditions.