Skip to content

Instantly share code, notes, and snippets.

View jasonclark's full-sized avatar

Jason A. Clark jasonclark

126 followers · 113 following
View GitHub Profile
@jasonclark
jasonclark / research-analysis-prompts.md
Created March 6, 2026 15:00
research-analysis-prompts.md

Research Analysis Prompts

Inspired by https://github.com/eseckel/ai-for-grant-writing.

The “So what?” Vetting - Prompt

"I am a researcher in [Field] considering a project on [Topic]. Act as a critical peer reviewer for a major funding agency. Evaluate my idea for 'novelty' and 'significance.' Identify 3 potential 'fatal flaws' in the logic or scope and suggest how I might narrow the focus to address a specific, high-impact gap in current knowledge."

Systematic Gap Analysis (The Literature Review) - Prompt

“Based on the current state of research in [Specific Sub-field], perform a systematic gap analysis. Map the 'Current State' (what we know) vs. 'Emerging Opportunities.' Specifically, identify:

  • Methodological limitations in recent major studies.
  • Contradictory findings that need reconciliation.
  • Populations or contexts that have been under-researched.”
@jasonclark
jasonclark / claude_desktop_config.json
Created November 12, 2025 01:20
Model Context Protocol - Server and Configuration Files (Claude Desktop Integration)
{
"mcpServers": {
"expertise-search": {
"command": "/ADD-FILEPATH-TO-YOUR-PYTHON-VIRTUAL-ENVIRONMENT/.venv/bin/python",
"args": ["/ADD-FILEPATH-TO-YOUR-LOCAL-MCP-SERVER-FILE/server.py"],
"env": {
"PYTHONPATH": "/ADD-FILEPATH-TO-YOUR-LOCAL-MCP-SERVER-DIRECTORY",
"GOOGLE_API_KEY": "ADD-YOUR-OWN-API-KEY"
}
}
@jasonclark
jasonclark / msu-research-agent-prompt.md
Last active November 21, 2025 05:40
Example system prompts for a research agents: First file (msu-research-agent-prompt.md) is a system prompt that works with a consumer LLM (optimized for Claude, but will work with most consumer LLMs); Second file (system-prompt.md) is system prompt for a small language model implementation of an agentic search tool.

MSU Research Agent Prompt

Role and Goal

You are a Research Assistant for Montana State University (MSU). Your sole goal is to answer user queries by gathering, evaluating, and synthesizing information using web search and fetch tools, focusing exclusively on MSU expertise.

Core Process: The ReAct Cycle

You MUST operate using the Thought -> Action -> Observation cycle until the query is fully answered.

Source of Truth and Reasoning:

  1. Observations are your absolute source of truth. You must rely only on the information returned in your Observation: steps.
@jasonclark
jasonclark / gist:9586f8bace7ee3b56235a8bd4952ec76
Created November 10, 2023 18:06
<meta> tags - article markup for Google Scholar
<head>
<title>Identification and Characterization of Bacteria-Derived Antibiotics for the Biological Control of Pea Aphanomyces Root Rot</title>
<link rel="schema.DCTERMS" href="http://purl.org/dc/terms/" />
<link rel="schema.DC" href="http://purl.org/dc/elements/1.1/" />
<meta name="DC.creator" content="Lai, Xiao" />
<meta name="DC.creator" content="Niroula, Dhirendra" />
<meta name="DC.creator" content="Burrows, Mary" />
<meta name="DC.creator" content="Wu, Xiaogang" />
<meta name="DC.creator" content="Yan, Qing" />
<meta name="DCTERMS.dateAccepted" content="2023-11-09T23:34:06Z" scheme="DCTERMS.W3CDTF" />
@jasonclark
jasonclark / gist:9ea832d8abd335d9bc8477b01ac345b2
Last active October 6, 2023 19:59
msu journal home page json-ld markup - Mountains and Minds example
<script type="application/ld+json">
{
"@context": "https://schema.org",
"@type": "Periodical",
"@id": "https://www.montana.edu/news/mountainsandminds/",
"hasPart": {
"@id": "ADD INDIVIDUAL ARTICLE URL HERE",
"@type": "Article"
},
"name": "Mountains and Minds",
@jasonclark
jasonclark / gist:f203f702ac4b10426f8081f306e57cc9
Last active October 6, 2023 20:16
msu article json-ld -> Mountains and Minds individual article example
<script type="application/ld+json">
{ "@context": "https://schema.org",
"@type": "Article",
"isPartOf": {
"@id": "https://www.montana.edu/news/mountainsandminds/"
},
"headline": "Addressing Montana's Veterinary Shortage",
"alternativeHeadline": "Efforts MSU began decades ago have helped transform Bozeman into a thriving center of the photonics industry",
"image": "https://...ADD FULL IMAGE pathe HERE/Article Example_files/rockgirlz.jpg",
"author": "Marshall Swearingen",
@jasonclark
jasonclark / msu-program-schema-json-ld
Last active December 6, 2022 20:57
montana.edu/academics create json-ld to define programs generically Action: Ready to share with Brooke and Philip on December 6 https://schema.org/CollegeOrUniversity https://schema.org/EducationalOccupationalProgram https://schema.org/educationalCredentialAwarded https://schema.org/Course https://schema.org/hasCourseInstance
<script type="application/ld+json">
{
"@context": "https://schema.org/",
"@type": "EducationalOccupationalProgram",
"name": "Undergraduate Accounting degree from Montana State University",
"description": "Accounting – B.S. in Business, Accounting EmphasisAccounting is designed to help students develop the necessary technical expertise and broad-based business knowledge required for long-term success in careers such as auditing, assurance, tax consulting, corporate or non-profit accounting and finance, financial analysis, venture capital and financial planning."
"url": "https://www.montana.edu/academics/accounting/",
"provider": {
"@type": "CollegeOrUniversity",
"name": "Montana State University",
@jasonclark
jasonclark / gist:01e6b363f6dbfe5d94aeea6c7043b6d0
Created December 16, 2017 04:33
Testing hero image swap
<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>HTML5 boilerplate – all you really need…</title>
<style>
section.heroimg {
display: flex;
align-items: flex-end;
margin-bottom: 2rem;
@jasonclark
jasonclark / css-diagnostic-for-https.css
Created August 23, 2016 13:13
CSS as privacy diagnostic tool - mark all unsecure or unencrypted content/links. Add this to your CSS to see a red frowny face next to your non-SSL content.
.content [href^="http:"]::after {
content: "\2639\ (unencrypted link)";
display: inline-block;
width: .8em;
height: .8em;
text-indent: .8em;
white-space: nowrap;
color: red;
}
@jasonclark
jasonclark / data-model-people.sql
Created July 28, 2016 16:44
Data model for @msulibrary people app
--
-- Database: `people`
--
-- --------------------------------------------------------
--
-- Table structure for table `create_action`
--