From 445f95978bb11462c058b31bb8aae5f465247b0f Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 13 May 2026 15:36:46 -0400 Subject: [PATCH 1/5] Update site for the 2026 codeathon. Swap dates and titles over to NIAID BRC AI Codeathon 2.0 (September 16-18, 2026), pull in the new two-focus-area framing (Literature RAG/LLM + MCP/agentic workflow automation) and goals from the announcement doc, and replace the schedule with the new Argonne agenda. Kept the 2025 project pages around -- relabeled the nav as "Past Projects" and added a banner on the listing pointing back to the 2026 announcement so visitors aren't confused about which event the projects belong to. Application form link is still a placeholder since the form isn't ready yet; deadline shown as August 15, 2026. --- src/components/Header.astro | 2 +- src/consts.ts | 9 +-- src/pages/index.astro | 100 ++++++++++++++++++++++----------- src/pages/projects/index.astro | 43 +++++++++++++- src/pages/schedule.astro | 53 +++++++++++------ 5 files changed, 150 insertions(+), 57 deletions(-) diff --git a/src/components/Header.astro b/src/components/Header.astro index 5a8c7d3..02b7c1b 100644 --- a/src/components/Header.astro +++ b/src/components/Header.astro @@ -8,7 +8,7 @@ import HeaderLink from "./HeaderLink.astro";

{SITE_TITLE}

Home - Projects + Past Projects Schedule
diff --git a/src/consts.ts b/src/consts.ts index 55c50d2..2b94661 100644 --- a/src/consts.ts +++ b/src/consts.ts @@ -1,10 +1,11 @@ // Place any global data in this file. // You can import this data from anywhere in your site by using the `import` keyword. -export const SITE_TITLE = "NIAID BRC AI Codeathon 2025"; +export const SITE_TITLE = "NIAID BRC AI Codeathon 2026"; export const SITE_DESCRIPTION = - "NIAID-BRC AI Codeathon for Infectious Disease Research - November 12-14, 2025 at Argonne National Laboratory"; + "NIAID-BRC AI Codeathon 2.0 for Infectious Disease Research - September 16-18, 2026 at Argonne National Laboratory"; -export const EVENT_DATE = "November 12-14, 2025"; +export const EVENT_DATE = "September 16-18, 2026"; export const EVENT_LOCATION = "Argonne National Laboratory, Lemont, IL"; -export const EVENT_YEAR = "2025"; +export const EVENT_YEAR = "2026"; +export const APPLICATION_DEADLINE = "August 15, 2026"; diff --git a/src/pages/index.astro b/src/pages/index.astro index eadb8e3..6f74daf 100644 --- a/src/pages/index.astro +++ b/src/pages/index.astro @@ -2,7 +2,13 @@ import BaseHead from "../components/BaseHead.astro"; import Footer from "../components/Footer.astro"; import Header from "../components/Header.astro"; -import { SITE_DESCRIPTION, SITE_TITLE } from "../consts"; +import { + APPLICATION_DEADLINE, + EVENT_DATE, + EVENT_LOCATION, + SITE_DESCRIPTION, + SITE_TITLE, +} from "../consts"; --- @@ -13,76 +19,102 @@ import { SITE_DESCRIPTION, SITE_TITLE } from "../consts";
-

NIAID BRC AI Codeathon 2025

+

NIAID BRC AI Codeathon 2.0

Accelerating FAIR Data and Tools with AI

- November 12–14, 2025
- Argonne National Laboratory, Lemont, IL + {EVENT_DATE}
+ {EVENT_LOCATION}

The NIAID Bioinformatics Resource Centers (BRCs) invite researchers, - data scientists, and developers to a three-day AI Codeathon focused on - improving 2026 NIAID-BRC AI Codeathon for Infectious Disease Research, + a three-day, in-person event focused on advancing infectious disease + research through artificial intelligence (AI), large language models + (LLMs), and agentic frameworks. +

+ +

+ Building on the success of the previous codeathon, participants will + collaborate in small teams to develop prototype tools and workflows + that improve the Findability, Accessibility, Interoperability, and Reusability (FAIR-ness) of BRC data and tools using artificial intelligence (AI) and large language - models (LLMs). + > of BRC data, resources, and analysis tools.

-

Event Goals

+

Project Focus Areas

+

This year's codeathon will emphasize two focus areas:

  • - Apply AI and LLMs to improve accessibility and usability of BRC data - and tools + Automated Knowledge Extraction and Curation from Literature — Using Retrieval-Augmented Generation (RAG) and LLM frameworks to extract, + structure, and integrate biological and epidemiological knowledge from + the scientific literature into BRC platforms.
    • -
  • Enhance interoperability and reuse of BRC resources
  • - Foster collaboration between infectious disease researchers, AI - developers, and bioinformaticians -
    • -
  • - Deliver openly available prototypes that can serve as seeds for - long-term community solutions + Bioinformatics Workflow Automation — Designing + agent-based systems that translate research questions into executable + workflows using Model Context Protocol (MCP)-enabled tools and + services.
-

Project Topics

-

Participants will form teams around proposed themes:

+

Event Goals

  • - Virtual BRC Helpdesk - AI-powered helpdesk to guide users - through bioinformatics tasks + Apply AI and LLMs to enable scalable knowledge extraction and + integration from scientific literature
  • - Automated Workflow Generation - Generate and run workflows - from user descriptions + Develop intelligent systems for automated bioinformatics workflow + design and execution
  • - Knowledge Extraction and Curation - Extract biological - insights from literature + Enhance interoperability and reuse of BRC data, tools, and services
  • - Function Assignment - Predict functions for uncharacterized - genes + Foster collaboration among infectious disease researchers, AI + developers, bioinformaticians, and data scientists
  • - Outbreak Monitoring - Track and process outbreak data - for real-time monitoring + Deliver openly available prototypes that can seed long-term community + solutions
    • +
+ +

Who Should Apply?

+
    +
  • Infectious disease researchers and domain experts
    • +
  • + Data scientists and AI/ML researchers interested in biological and + biomedical applications +
    • +
  • Bioinformaticians and computational biologists
    • +
  • Software developers and research engineers
  • - Virtual AI Co-scientist - Multi-agent system for hypothesis - generation and ranking + Students, postdoctoral researchers, and trainees interested in AI and + data-driven infectious disease research
+

Application and Registration

+

+ Participation is free, but space is limited.
+ Application deadline: + {APPLICATION_DEADLINE}.
+ Application form and additional details coming soon. +

+

- View Projects + View Schedule

diff --git a/src/pages/projects/index.astro b/src/pages/projects/index.astro index 6612271..a7ec654 100644 --- a/src/pages/projects/index.astro +++ b/src/pages/projects/index.astro @@ -4,7 +4,7 @@ import { getCollection } from "astro:content"; import BaseHead from "../../components/BaseHead.astro"; import Footer from "../../components/Footer.astro"; import Header from "../../components/Header.astro"; -import { SITE_DESCRIPTION, SITE_TITLE } from "../../consts"; +import { SITE_TITLE } from "../../consts"; const projects = (await getCollection("projects")).sort((a, b) => a.data.title.localeCompare(b.data.title) @@ -14,11 +14,34 @@ const projects = (await getCollection("projects")).sort((a, b) => - + diff --git a/src/components/Header.astro b/src/components/Header.astro index 02b7c1b..948e006 100644 --- a/src/components/Header.astro +++ b/src/components/Header.astro @@ -1,76 +1,147 @@ --- -import { SITE_TITLE } from "../consts"; import HeaderLink from "./HeaderLink.astro"; ---
- + - +
+
+ diff --git a/src/components/HeaderLink.astro b/src/components/HeaderLink.astro index 3091a69..c832a73 100644 --- a/src/components/HeaderLink.astro +++ b/src/components/HeaderLink.astro @@ -12,13 +12,3 @@ const isActive = href === pathname || href === "/" + (subpath?.[0] || ""); - diff --git a/src/layouts/ProjectPost.astro b/src/layouts/ProjectPost.astro index 7c0d9a8..40b631d 100644 --- a/src/layouts/ProjectPost.astro +++ b/src/layouts/ProjectPost.astro @@ -17,55 +17,143 @@ const editUrl = `https://github.com/NIAID-BRC-Codeathons/NIAID-BRC-Codeathons.gi @@ -74,64 +162,56 @@ const editUrl = `https://github.com/NIAID-BRC-Codeathons/NIAID-BRC-Codeathons.gi
+ + { + heroImage && ( +
+ +
+ ) + } + +
diff --git a/src/pages/index.astro b/src/pages/index.astro index 6f74daf..09734da 100644 --- a/src/pages/index.astro +++ b/src/pages/index.astro @@ -15,108 +15,588 @@ import { +
-

NIAID BRC AI Codeathon 2.0

-

Accelerating FAIR Data and Tools with AI

- -

- {EVENT_DATE}
- {EVENT_LOCATION} -

- -

- The NIAID Bioinformatics Resource Centers (BRCs) invite researchers, - data scientists, developers, bioinformaticians, and students to the - 2026 NIAID-BRC AI Codeathon for Infectious Disease Research, - a three-day, in-person event focused on advancing infectious disease - research through artificial intelligence (AI), large language models - (LLMs), and agentic frameworks. -

- -

- Building on the success of the previous codeathon, participants will - collaborate in small teams to develop prototype tools and workflows - that improve the Findability, Accessibility, Interoperability, and Reusability - (FAIR-ness) of BRC data, resources, and analysis tools. -

- -

Project Focus Areas

-

This year's codeathon will emphasize two focus areas:

-
    -
  • - Automated Knowledge Extraction and Curation from Literature — Using Retrieval-Augmented Generation (RAG) and LLM frameworks to extract, - structure, and integrate biological and epidemiological knowledge from - the scientific literature into BRC platforms. -
    • -
  • - Bioinformatics Workflow Automation — Designing - agent-based systems that translate research questions into executable - workflows using Model Context Protocol (MCP)-enabled tools and - services. -
    • -
- -

Event Goals

-
    -
  • - Apply AI and LLMs to enable scalable knowledge extraction and - integration from scientific literature -
    • -
  • - Develop intelligent systems for automated bioinformatics workflow - design and execution -
    • -
  • - Enhance interoperability and reuse of BRC data, tools, and services -
    • -
  • - Foster collaboration among infectious disease researchers, AI - developers, bioinformaticians, and data scientists -
    • -
  • - Deliver openly available prototypes that can seed long-term community - solutions -
    • -
- -

Who Should Apply?

-
    -
  • Infectious disease researchers and domain experts
    • -
  • - Data scientists and AI/ML researchers interested in biological and - biomedical applications -
    • -
  • Bioinformaticians and computational biologists
    • -
  • Software developers and research engineers
    • -
  • - Students, postdoctoral researchers, and trainees interested in AI and - data-driven infectious disease research -
    • -
- -

Application and Registration

-

- Participation is free, but space is limited.
- Application deadline: - {APPLICATION_DEADLINE}.
- Application form and additional details coming soon. -

- -

- - View Schedule - -

+
+
+ Sept 16 — 18, 2026 · Argonne National Lab + +
+ +
+

+ AI Codeathon 2.0 +

+

+ Accelerating FAIR data and tools for infectious disease research. +

+
+ +
+
+ Dates +
{EVENT_DATE}
+
3 days · in person · Wed → Fri
+
+
+ Venue +
{EVENT_LOCATION}
+
Bldg 240 · Room 1416
+
+
+ Applications close +
{APPLICATION_DEADLINE}
+
Form coming soon
+
+
+ +
+ View Schedule → + 2025 Project Archive + Applications open soon +
+
+ +
+
+ About the event +
+
+

+ The NIAID Bioinformatics Resource Centers (BRCs) invite researchers, + data scientists, developers, bioinformaticians, and students to a + three-day in-person codeathon focused on advancing infectious + disease research through AI, large language models, and agentic + frameworks. +

+

+ Building on the success of the previous codeathon, participants + will collaborate in small teams to develop prototype tools and + workflows that improve the + Findability, Accessibility, Interoperability, and Reusability + of BRC data, resources, and analysis tools. +

+
+
+ +
+
+ Focus Areas, 2026 +

+ Two directions.
One common goal. +

+
+ +
    +
  1. +
    01
    +
    +
    RAG · LLM
    +

    + Automated knowledge extraction & curation from literature +

    +
    +

    + AI-driven systems that automatically extract, structure, and + integrate biological and epidemiological knowledge from the + scientific literature using Retrieval-Augmented Generation and + large language models — linked back to BRC schemas with + provenance. +

    +
    2. + +
  2. +
    02
    +
    +
    MCP · Agentic AI
    +

    + Bioinformatics workflow automation +

    +
    +

    + Agent-based systems that translate research questions into + executable bioinformatics workflows by leveraging Model Context + Protocol (MCP)-enabled tools and services — adaptive, multi-step, + and reproducible. +

    +
    3. +
+
+ +
+
+ Goals +

What we hope to ship.

+
    +
  • + Apply AI and LLMs to enable scalable knowledge extraction from + scientific literature +
    • +
  • + Develop intelligent systems for automated workflow design & + execution +
    • +
  • + Enhance interoperability and reuse of BRC data, tools, and + services +
    • +
  • + Foster collaboration across infectious disease, AI, and + bioinformatics communities +
    • +
  • + Deliver openly available prototypes that seed long-term community + solutions +
    • +
+
+ +
+ Who should apply +

Bring your discipline.

+
    +
  • Infectious disease researchers and domain experts
    • +
  • Data scientists and AI/ML researchers
    • +
  • Bioinformaticians and computational biologists
    • +
  • Software developers and research engineers
    • +
  • Students, postdocs, and trainees
    • +
+
+
+ +
+
+ Apply +

+ Three days at Argonne.
Free to attend. +

+

+ Participation is free, but space is limited. Application form and + additional details on registration, project themes, and logistics + will be announced soon. +

+ View Full Schedule → +
+
+ Application Deadline +
{APPLICATION_DEADLINE}
+

+ Notifications shortly after. Confirmed teams begin bi-weekly + preparatory calls. +

+
+