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Apply prettier formatting to project files
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‎src/content/projects/RDF-knowledge-graph-construction.md‎

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title: "RDF Knowledge Graph Construction"
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description: "Transforming Pathogen Data Network Resources to RDF using Large Language Models"
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tags: ["Knowledge Graphs", "RDF", "Linked Data", "Semantic Web", "Data Integration"]
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tags:
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["Knowledge Graphs", "RDF", "Linked Data", "Semantic Web", "Data Integration"]
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github: "https://github.com/NIAID-BRC-Codeathons/RDF-knowledge-graph-construction"
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‎src/content/projects/ai-co-scientist-protein-function.md‎

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title: "AI Co-Scientist for Protein Function Prediction and Hypothesis Generation"
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description: "Extending the Co-Scientist framework to build reasoning agents for protein function prediction using CEPI and BV-BRC datasets for priority pathogens"
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tags: ["AI Co-Scientist", "Protein Function", "Hypothesis Generation", "Reasoning Agents", "Jnana"]
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tags:
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[
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"AI Co-Scientist",
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"Protein Function",
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"Hypothesis Generation",
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"Reasoning Agents",
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"Jnana",
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]
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github: "https://github.com/NIAID-BRC-Codeathons/ai-co-scientist-protein-function"
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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| -------------------- | -------------------------------- | --------------------------------------- |
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| Arvind Ramanathan | Argonne National Laboratory | Principal Investigator, AI Systems Architect |
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| Ozan | Argonne National Laboratory | RAG and Data Integration Specialist |
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| BV-BRC Developers | - | Model integration and deployment |
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| CEPI Scientists | - | Use-case definition and validation |
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| Name | Affiliation | Role / Expertise |
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| ----------------- | --------------------------- | -------------------------------------------- |
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| Arvind Ramanathan | Argonne National Laboratory | Principal Investigator, AI Systems Architect |
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| Ozan | Argonne National Laboratory | RAG and Data Integration Specialist |
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| BV-BRC Developers | - | Model integration and deployment |
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| CEPI Scientists | - | Use-case definition and validation |
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**Project Summary**
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**Data and Resources Required**
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| Resource Type | Source / Link | Description / Purpose |
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| ----------------- | -------------------------------------- | ---------------------------------- |
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| Data | BV-BRC genomes, CEPI curated datasets | Training and evaluation data |
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| Tools / Services | Jnana (Co-Scientist GitHub repo) | Agentic reasoning system |
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| LLMs / AI Models | GPT-4, Claude 3 | Reasoning and synthesis agents |
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| Compute / Storage | Argonne HPC | Experimentation environment |
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| Resource Type | Source / Link | Description / Purpose |
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| ----------------- | ------------------------------------- | ------------------------------ |
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| Data | BV-BRC genomes, CEPI curated datasets | Training and evaluation data |
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| Tools / Services | Jnana (Co-Scientist GitHub repo) | Agentic reasoning system |
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| LLMs / AI Models | GPT-4, Claude 3 | Reasoning and synthesis agents |
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| Compute / Storage | Argonne HPC | Experimentation environment |
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**Expected Outcomes / Deliverables**
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‎src/content/projects/hiperrag-literature-extraction.md‎

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title: "HiPerRAG for Literature-based Data Extraction on Priority Pathogens"
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description: "Leveraging high-performance retrieval-augmented generation to extract and curate structured biological data for CEPI priority pathogens from scientific literature"
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tags: ["HiPerRAG", "Literature Mining", "Knowledge Extraction", "RAG", "Priority Pathogens"]
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tags:
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[
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"HiPerRAG",
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"Literature Mining",
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"Knowledge Extraction",
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"RAG",
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"Priority Pathogens",
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]
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github: "https://github.com/NIAID-BRC-Codeathons/hiperrag-literature-extraction"
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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| -------------------- | -------------------------------- | --------------------------------------- |
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| Ozan | Argonne National Laboratory | AI/ML Engineer, Data Curation Lead |
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| Arvind Ramanathan | Argonne National Laboratory | Scientific Advisor |
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| BV-BRC Analysts | - | Data integration and validation |
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| CEPI collaborators | - | Priority Pathogen Data Alignment |
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| Name | Affiliation | Role / Expertise |
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| ------------------ | --------------------------- | ---------------------------------- |
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| Ozan | Argonne National Laboratory | AI/ML Engineer, Data Curation Lead |
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| Arvind Ramanathan | Argonne National Laboratory | Scientific Advisor |
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| BV-BRC Analysts | - | Data integration and validation |
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| CEPI collaborators | - | Priority Pathogen Data Alignment |
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**Project Summary**
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**Data and Resources Required**
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| Resource Type | Source / Link | Description / Purpose |
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| ----------------- | -------------------------------------- | -------------------------------------------- |
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| Data | PubMed, BV-BRC text corpora | Literature sources for entity/relation extraction |
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| Tools / Services | HiPerRAG (ArXiv:2505.04846) | RAG-based extraction framework |
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| LLMs / AI Models | Mistral Large, GPT-4 via Rhea | Entity normalization and summarization |
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| Compute / Storage | Argonne HPC, BRC clusters | Parallel literature processing |
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| Resource Type | Source / Link | Description / Purpose |
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| ----------------- | ----------------------------- | ------------------------------------------------- |
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| Data | PubMed, BV-BRC text corpora | Literature sources for entity/relation extraction |
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| Tools / Services | HiPerRAG (ArXiv:2505.04846) | RAG-based extraction framework |
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| LLMs / AI Models | Mistral Large, GPT-4 via Rhea | Entity normalization and summarization |
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| Compute / Storage | Argonne HPC, BRC clusters | Parallel literature processing |
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**Expected Outcomes / Deliverables**
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‎src/content/projects/pubmed-miner.md‎

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title: "PubMed Miner: AI-Powered Sequence Feature Extraction from Literature"
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description: "Automated extraction of viral sequence features, mutations, and epitopes from PubMed literature using LLMs to accelerate outbreak response and genomic analysis"
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tags: ["LLM", "PubMed", "Literature Mining", "Sequence Features", "Mutation Detection"]
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tags:
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[
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"LLM",
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"PubMed",
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"Literature Mining",
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"Sequence Features",
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"Mutation Detection",
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]
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github: "https://github.com/NIAID-BRC-Codeathons/pubmed-miner"
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‎src/content/projects/rhea-workflow-automation.md‎

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**Suggested Team Members and Roles \[4-6 members\]**
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| Name | Affiliation | Role / Expertise |
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| --------------------- | -------------------------------- | ------------------------------------------ |
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| Chris Grams | Argonne National Laboratory | Lead Developer, Galaxy Integration |
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| Oleksandr Narykov | Argonne National Laboratory | Workflow Automation Engineer |
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| Arvind Ramanathan | Argonne National Laboratory | AI Systems Integration Advisor |
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| CEPI collaborators | - | Use-case Alignment and Testing |
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| Name | Affiliation | Role / Expertise |
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| ------------------ | --------------------------- | ---------------------------------- |
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| Chris Grams | Argonne National Laboratory | Lead Developer, Galaxy Integration |
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| Oleksandr Narykov | Argonne National Laboratory | Workflow Automation Engineer |
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| Arvind Ramanathan | Argonne National Laboratory | AI Systems Integration Advisor |
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| CEPI collaborators | - | Use-case Alignment and Testing |
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**Project Summary**
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**Data and Resources Required**
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| Resource Type | Source / Link | Description / Purpose |
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| ----------------- | ------------------------------------------ | ------------------------------- |
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| Data | BV-BRC genomes, CEPI priority pathogen datasets | Training and workflow inputs |
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| Tools / Services | BV-BRC APIs, Galaxy server | Workflow integration and execution |
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| LLMs / AI Models | Rhea MCP model, GPT-5 | Tool reasoning and synthesis |
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| Compute / Storage | Argonne HPC / Galaxy cluster | Execution backend |
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| Resource Type | Source / Link | Description / Purpose |
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| ----------------- | ----------------------------------------------- | ---------------------------------- |
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| Data | BV-BRC genomes, CEPI priority pathogen datasets | Training and workflow inputs |
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| Tools / Services | BV-BRC APIs, Galaxy server | Workflow integration and execution |
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| LLMs / AI Models | Rhea MCP model, GPT-5 | Tool reasoning and synthesis |
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| Compute / Storage | Argonne HPC / Galaxy cluster | Execution backend |
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**Expected Outcomes / Deliverables**
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‎src/content/projects/viral-phylogenetics.md‎

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title: "Viral Structural Phylogenetics"
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description: "Optimizing protein language model to predict viral protein structures at scale"
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tags: ["AI", "Structural Biology", "Phylogenetics", "Protein Language Models", "Virology"]
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tags:
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[
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"AI",
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"Structural Biology",
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"Phylogenetics",
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"Protein Language Models",
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"Virology",
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]
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github: "https://github.com/NIAID-BRC-Codeathons/viral-phylogenetics"
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