Kit Finder

Phase 2: Ask User for Preferences

Before searching, present the extracted reagent list and ask the user:

# Reagents Identified for Your Protocol

I've identified the following reagents/kits needed:

## Step 1: [Step Name]
1. [Reagent A] — e.g., TRIzol or equivalent lysis reagent
2. [Reagent B] — e.g., chloroform
...

## Step 2: [Step Name]
1. [Reagent C] — e.g., reverse transcription kit
...

**Do you already have preferred kits or catalog numbers for any of these?**
For example: "We use SYBR Select Master Mix (Cat# 4472908)" or "We prefer QIAGEN kits for RNA extraction."

Reply with your preferences, or say "search all" to have me find options for everything.

Phase 3: Search for Options

For each reagent where the user did not provide a specific catalog number:

1. Search vendor websites using targeted queries:

   • Query format: "[reagent name]" site:[vendor-domain] catalog number
   • Priority vendor domains (search in this order):
     • thermofisher.com
     • qiagen.com
     • neb.com (New England Biolabs)
     • bio-rad.com
     • sigmaaldrich.com / emdmillipore.com
     • takarabio.com
     • promega.com
     • idtdna.com (for primers/oligos)
   • If user specified --vendor, prioritize that vendor's domain

2. For each reagent, find 2-3 options from different vendors when possible. For each option, collect:

   • Product name (exact, as listed by vendor)
   • Catalog number (specific, not a product family)
   • Vendor name
   • Direct product URL (the specific product page, not a search results page)
   • Pack size / unit (e.g., "500 mL", "200 rxns", "100 µg")
   • Key specifications (e.g., concentration, format, compatibility)

3. Verify product links — fetch product URLs when possible to confirm:

   • The catalog number matches the product page
   • The product is currently available (not discontinued)
   • The pack size and specifications are correct

Phase 4: Present Options for Confirmation

Present the findings organized by protocol step, with a recommended option highlighted:

# Kit & Reagent Options: [Protocol Name]

---

## Step 1: [Step Name]

### 1.1 [Reagent Category] (e.g., Lysis Reagent)

| # | Product | Catalog # | Vendor | Pack Size | Link |
|---|---------|-----------|--------|-----------|------|
| ▸ **A** | **[Recommended Product]** | **[Cat#]** | **[Vendor]** | **[Size]** | **[URL]** |
| B | [Alternative 1] | [Cat#] | [Vendor] | [Size] | [URL] |
| C | [Alternative 2] | [Cat#] | [Vendor] | [Size] | [URL] |

> **Recommendation:** Option A because [reason — e.g., most widely cited, includes all components, best value].

### 1.2 [Next Reagent Category]
...

---

## Step 2: [Step Name]
...

---

## Summary of Recommendations

| Step | Reagent | Recommended Product | Catalog # | Vendor | Link |
|------|---------|-------------------|-----------|--------|------|
| 1 | Lysis reagent | [Product] | [Cat#] | [Vendor] | [URL] |
| 1 | Chloroform | [Product] | [Cat#] | [Vendor] | [URL] |
| 2 | RT Kit | [Product] | [Cat#] | [Vendor] | [URL] |
| ... | ... | ... | ... | ... | ... |

**Please confirm your selections or specify changes** (e.g., "Use option B for the RT kit", "Change chloroform to Fisher brand").

Phase 5: Finalize and Output

After user confirmation, produce a final Bill of Materials document:

# Bill of Materials: [Protocol Name]

**Date:** [current date]
**Confirmed by:** User

| # | Product Name | Catalog # | Vendor | Pack Size | Product Link | Notes |
|---|-------------|-----------|--------|-----------|-------------|-------|
| 1 | [Exact product name] | [Cat#] | [Vendor] | [Size] | [URL] | [Any notes] |
| 2 | ... | ... | ... | ... | ... | ... |

## Ordering Notes
- [Any special ordering instructions, e.g., "Ships on dry ice", "Requires hazmat shipping"]
- [Storage requirements upon receipt]
- [Items that may already be in common lab stock]

Phase 6: Download Kit Documentation

After the Bill of Materials is finalized, download or save the PDF documentation (product manuals, protocols, safety data sheets) for each selected kit:

1. For each confirmed kit/reagent, search for its product documentation:

   • Query format: "[product name]" "[catalog number]" manual PDF site:[vendor-domain]
   • Look for: product manual, user guide, protocol sheet, or technical data sheet
   • Also check the product page URL (from the BOM) for documentation download links

2. Download each PDF to the project's references/kit-docs/ directory:

   • Filename format: [Vendor]_[ProductName]_[CatalogNumber].pdf (spaces replaced with hyphens)
   • Example: ThermoFisher_TRIzol-Reagent_15596026.pdf
   • If a direct PDF URL is not available, save the product page content as markdown instead: [Vendor]_[ProductName]_[CatalogNumber]_product-page.md

3. Report the results to the user:

# Kit Documentation Downloaded

| # | Product | Catalog # | File | Status |
|---|---------|-----------|------|--------|
| 1 | [Product] | [Cat#] | [filename] | Downloaded |
| 2 | [Product] | [Cat#] | [filename] | PDF not found — product page saved |
| 3 | [Product] | [Cat#] | — | No documentation found |

Files saved to: `references/kit-docs/`

Important Guidelines

• Catalog numbers must be specific — never use product family codes or generic numbers. For example, use 4472908 (SYBR Select Master Mix, 10 × 5 mL), not just the product family page.
• Links must point to the specific product page — not search results, not product family overviews. The URL should contain the catalog number or lead directly to the product with that catalog number visible.
• Distinguish pack sizes — the same product often has multiple catalog numbers for different quantities (e.g., 50 rxns vs. 200 rxns). Present the most common lab-scale size unless the user specifies.
• Flag discontinued products — if a product appears to be discontinued, note it and suggest the replacement.
• Note kit contents — for kits that bundle multiple components, list what's included so the user knows what they do NOT need to order separately.
• Consider compatibility — when recommending across steps (e.g., RT kit + qPCR master mix), prefer products from the same vendor or that are explicitly validated together.
• Common lab stock items — for commodity chemicals (ethanol, isopropanol, chloroform, water), still provide catalog numbers but note these may already be available in the lab.
• Always include web references with direct URLs for every product listed.
• Do not guess catalog numbers — if you cannot verify a catalog number through web search, explicitly state that and provide the best product page link you found so the user can verify.