@bgicli/bgicli 2.1.1 → 2.2.0

package/data/skills/pptx-posters/SKILL.md

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+---
+name: pptx-posters
+description: Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.
+allowed-tools: Read Write Edit Bash
+license: MIT license
+metadata:
+    skill-author: K-Dense Inc.
+---
+
+# PPTX Research Posters (HTML-Based)
+
+## Overview
+
+**⚠️ USE THIS SKILL ONLY WHEN USER EXPLICITLY REQUESTS PPTX/POWERPOINT POSTER FORMAT.**
+
+For standard research posters, use the **latex-posters** skill instead, which provides better typographic control and is the default for academic conferences.
+
+This skill creates research posters using HTML/CSS, which can then be exported to PDF or converted to PowerPoint format. The web-based approach offers:
+- Modern, responsive layouts
+- Easy integration of AI-generated visuals
+- Quick iteration and preview in browser
+- Export to PDF via browser print function
+- Conversion to PPTX if specifically needed
+
+## When to Use This Skill
+
+**ONLY use this skill when:**
+- User explicitly requests "PPTX poster", "PowerPoint poster", or "PPT poster"
+- User specifically asks for HTML-based poster
+- User needs to edit poster in PowerPoint after creation
+- LaTeX is not available or user requests non-LaTeX solution
+
+**DO NOT use this skill when:**
+- User asks for a "poster" without specifying format → Use latex-posters
+- User asks for "research poster" or "conference poster" → Use latex-posters
+- User mentions LaTeX, tikzposter, beamerposter, or baposter → Use latex-posters
+
+## AI-Powered Visual Element Generation
+
+**STANDARD WORKFLOW: Generate ALL major visual elements using AI before creating the HTML poster.**
+
+This is the recommended approach for creating visually compelling posters:
+1. Plan all visual elements needed (hero image, intro, methods, results, conclusions)
+2. Generate each element using scientific-schematics or Nano Banana Pro
+3. Assemble generated images in the HTML template
+4. Add text content around the visuals
+
+**Target: 60-70% of poster area should be AI-generated visuals, 30-40% text.**
+
+---
+
+### CRITICAL: Poster-Size Font Requirements
+
+**⚠️ ALL text within AI-generated visualizations MUST be poster-readable.**
+
+When generating graphics for posters, you MUST include font size specifications in EVERY prompt. Poster graphics are viewed from 4-6 feet away, so text must be LARGE.
+
+**MANDATORY prompt requirements for EVERY poster graphic:**
+
+```
+POSTER FORMAT REQUIREMENTS (STRICTLY ENFORCE):
+- ABSOLUTE MAXIMUM 3-4 elements per graphic (3 is ideal)
+- ABSOLUTE MAXIMUM 10 words total in the entire graphic
+- NO complex workflows with 5+ steps (split into 2-3 simple graphics instead)
+- NO multi-level nested diagrams (flatten to single level)
+- NO case studies with multiple sub-sections (one key point per case)
+- ALL text GIANT BOLD (80pt+ for labels, 120pt+ for key numbers)
+- High contrast ONLY (dark on white OR white on dark, NO gradients with text)
+- MANDATORY 50% white space minimum (half the graphic should be empty)
+- Thick lines only (5px+ minimum), large icons (200px+ minimum)
+- ONE SINGLE MESSAGE per graphic (not 3 related messages)
+```
+
+**⚠️ BEFORE GENERATING: Review your prompt and count elements**
+- If your description has 5+ items → STOP. Split into multiple graphics
+- If your workflow has 5+ stages → STOP. Show only 3-4 high-level steps
+- If your comparison has 4+ methods → STOP. Show only top 3 or Our vs Best Baseline
+
+**Example - WRONG (7-stage workflow):**
+```bash
+# ❌ Creates tiny unreadable text
+python scripts/generate_schematic.py "Drug discovery workflow: Stage 1 Target ID, Stage 2 Synthesis, Stage 3 Screening, Stage 4 Lead Opt, Stage 5 Validation, Stage 6 Clinical Trial, Stage 7 FDA Approval with metrics." -o figures/workflow.png
+```
+
+**Example - CORRECT (3 mega-stages):**
+```bash
+# ✅ Same content, simplified to readable poster format
+python scripts/generate_schematic.py "POSTER FORMAT for A0. ULTRA-SIMPLE 3-box workflow: 'DISCOVER' → 'VALIDATE' → 'APPROVE'. Each word in GIANT bold (120pt+). Thick arrows (10px). 60% white space. ONLY these 3 words. NO substeps. Readable from 12 feet." -o figures/workflow_simple.png
+```
+
+---
+
+### CRITICAL: Preventing Content Overflow
+
+**⚠️ POSTERS MUST NOT HAVE TEXT OR CONTENT CUT OFF AT EDGES.**
+
+**Prevention Rules:**
+
+**1. Limit Content Sections (MAXIMUM 5-6 sections):**
+```
+✅ GOOD - 5 sections with room to breathe:
+   - Title/Header
+   - Introduction/Problem
+   - Methods
+   - Results (1-2 key findings)
+   - Conclusions
+
+❌ BAD - 8+ sections crammed together
+```
+
+**2. Word Count Limits:**
+- **Per section**: 50-100 words maximum
+- **Total poster**: 300-800 words MAXIMUM
+- **If you have more content**: Cut it or make a handout
+
+---
+
+## Core Capabilities
+
+### 1. HTML/CSS Poster Design
+
+The HTML template (`assets/poster_html_template.html`) provides:
+- Fixed poster dimensions (36×48 inches = 2592×3456 pt)
+- Professional header with gradient styling
+- Three-column content layout
+- Block-based sections with modern styling
+- Footer with references and contact info
+
+### 2. Poster Structure
+
+**Standard Layout:**
+```
+┌─────────────────────────────────────────┐
+│  HEADER: Title, Authors, Hero Image     │
+├─────────────┬─────────────┬─────────────┤
+│ Introduction│   Results   │  Discussion │
+│             │             │             │
+│   Methods   │   (charts)  │ Conclusions │
+│             │             │             │
+│  (diagram)  │   (data)    │   (summary) │
+├─────────────┴─────────────┴─────────────┤
+│  FOOTER: References & Contact Info      │
+└─────────────────────────────────────────┘
+```
+
+### 3. Visual Integration
+
+Each section should prominently feature AI-generated visuals:
+
+**Hero Image (Header):**
+```html
+<img src="figures/hero.png" class="hero-image">
+```
+
+**Section Graphics:**
+```html
+<div class="block">
+  <h2 class="block-title">Methods</h2>
+  <div class="block-content">
+    <img src="figures/workflow.png" class="block-image">
+    <ul>
+      <li>Brief methodology point</li>
+    </ul>
+  </div>
+</div>
+```
+
+### 4. Generating Visual Elements
+
+**Before creating the HTML, generate all visual elements:**
+
+```bash
+# Create figures directory
+mkdir -p figures
+
+# Hero image - SIMPLE, impactful
+python scripts/generate_schematic.py "POSTER FORMAT for A0. Hero banner: '[TOPIC]' in HUGE text (120pt+). Dark blue gradient background. ONE iconic visual. Minimal text. Readable from 15 feet." -o figures/hero.png
+
+# Introduction visual - ONLY 3 elements
+python scripts/generate_schematic.py "POSTER FORMAT for A0. SIMPLE visual with ONLY 3 icons: [icon1] → [icon2] → [icon3]. ONE word labels (80pt+). 50% white space. Readable from 8 feet." -o figures/intro.png
+
+# Methods flowchart - ONLY 4 steps
+python scripts/generate_schematic.py "POSTER FORMAT for A0. SIMPLE flowchart with ONLY 4 boxes: STEP1 → STEP2 → STEP3 → STEP4. GIANT labels (100pt+). Thick arrows. 50% white space. NO sub-steps." -o figures/workflow.png
+
+# Results visualization - ONLY 3 bars
+python scripts/generate_schematic.py "POSTER FORMAT for A0. SIMPLE bar chart with ONLY 3 bars: BASELINE (70%), EXISTING (85%), OURS (95%). GIANT percentages ON bars (120pt+). NO axis, NO legend. 50% white space." -o figures/results.png
+
+# Conclusions - EXACTLY 3 key findings
+python scripts/generate_schematic.py "POSTER FORMAT for A0. EXACTLY 3 cards: '95%' (150pt) 'ACCURACY' (60pt), '2X' (150pt) 'FASTER' (60pt), checkmark 'READY' (60pt). 50% white space. NO other text." -o figures/conclusions.png
+```
+
+---
+
+## Workflow for PPTX Poster Creation
+
+### Stage 1: Planning
+
+1. **Confirm PPTX is explicitly requested**
+2. **Determine poster requirements:**
+   - Size: 36×48 inches (most common) or A0
+   - Orientation: Portrait (most common)
+3. **Develop content outline:**
+   - Identify 1-3 core messages
+   - Plan 3-5 visual elements
+   - Draft minimal text (300-800 words total)
+
+### Stage 2: Generate Visual Elements (AI-Powered)
+
+**CRITICAL: Generate SIMPLE figures with MINIMAL content.**
+
+```bash
+mkdir -p figures
+
+# Generate each element with POSTER FORMAT specifications
+# (See examples in Section 4 above)
+```
+
+### Stage 3: Create HTML Poster
+
+1. **Copy the template:**
+   ```bash
+   cp skills/pptx-posters/assets/poster_html_template.html poster.html
+   ```
+
+2. **Update content:**
+   - Replace placeholder title and authors
+   - Insert AI-generated images
+   - Add minimal supporting text
+   - Update references and contact info
+
+3. **Preview in browser:**
+   ```bash
+   open poster.html  # macOS
+   # or
+   xdg-open poster.html  # Linux
+   ```
+
+### Stage 4: Export to PDF
+
+**Browser Print Method:**
+1. Open poster.html in Chrome or Firefox
+2. Print (Cmd/Ctrl + P)
+3. Select "Save as PDF"
+4. Set paper size to match poster dimensions
+5. Remove margins
+6. Enable "Background graphics"
+
+**Command Line (if Chrome available):**
+```bash
+# Chrome headless PDF export
+google-chrome --headless --print-to-pdf=poster.pdf \
+  --print-to-pdf-no-header \
+  --no-margins \
+  poster.html
+```
+
+### Stage 5: Convert to PPTX (If Required)
+
+**Option 1: PDF to PPTX conversion**
+```bash
+# Using LibreOffice
+libreoffice --headless --convert-to pptx poster.pdf
+
+# Or use online converters for simple cases
+```
+
+**Option 2: Direct PPTX creation with python-pptx**
+```python
+from pptx import Presentation
+from pptx.util import Inches, Pt
+
+prs = Presentation()
+prs.slide_width = Inches(48)
+prs.slide_height = Inches(36)
+
+slide = prs.slides.add_slide(prs.slide_layouts[6])  # Blank
+
+# Add images from figures/
+slide.shapes.add_picture("figures/hero.png", Inches(0), Inches(0), width=Inches(48))
+# ... add other elements
+
+prs.save("poster.pptx")
+```
+
+---
+
+## HTML Template Structure
+
+The provided template (`assets/poster_html_template.html`) includes:
+
+### CSS Variables for Customization
+
+```css
+/* Poster dimensions */
+body {
+  width: 2592pt;   /* 36 inches */
+  height: 3456pt;  /* 48 inches */
+}
+
+/* Color scheme - customize these */
+.header {
+  background: linear-gradient(135deg, #1a365d 0%, #2b6cb0 50%, #3182ce 100%);
+}
+
+/* Typography */
+.poster-title { font-size: 108pt; }
+.authors { font-size: 48pt; }
+.block-title { font-size: 52pt; }
+.block-content { font-size: 34pt; }
+```
+
+### Key Classes
+
+| Class | Purpose | Font Size |
+|-------|---------|-----------|
+| `.poster-title` | Main title | 108pt |
+| `.authors` | Author names | 48pt |
+| `.affiliations` | Institutions | 38pt |
+| `.block-title` | Section headers | 52pt |
+| `.block-content` | Body text | 34pt |
+| `.key-finding` | Highlight box | 36pt |
+
+---
+
+## Quality Checklist
+
+### Step 0: Pre-Generation Review (MANDATORY)
+
+**For EACH planned graphic, verify:**
+- [ ] Can describe in 3-4 items or less? (NOT 5+)
+- [ ] Is it a simple workflow (3-4 steps, NOT 7+)?
+- [ ] Can describe all text in 10 words or less?
+- [ ] Does it convey ONE message (not multiple)?
+
+**Reject these patterns:**
+- ❌ "7-stage workflow" → Simplify to "3 mega-stages"
+- ❌ "Multiple case studies" → One case per graphic
+- ❌ "Timeline 2015-2024 annual" → "ONLY 3 key years"
+- ❌ "Compare 6 methods" → "ONLY 2: ours vs best"
+
+### Step 2b: Post-Generation Review (MANDATORY)
+
+**For EACH generated figure at 25% zoom:**
+
+**✅ PASS criteria (ALL must be true):**
+- [ ] Can read ALL text clearly
+- [ ] Count: 3-4 elements or fewer
+- [ ] White space: 50%+ empty
+- [ ] Understand in 2 seconds
+- [ ] NOT a complex 5+ stage workflow
+- [ ] NOT multiple nested sections
+
+**❌ FAIL criteria (regenerate if ANY true):**
+- [ ] Text small/hard to read → Regenerate with "150pt+"
+- [ ] More than 4 elements → Regenerate "ONLY 3 elements"
+- [ ] Less than 50% white space → Regenerate "60% white space"
+- [ ] Complex multi-stage → SPLIT into 2-3 graphics
+- [ ] Multiple cases cramped → SPLIT into separate graphics
+
+### After Export
+
+- [ ] NO content cut off at ANY of the 4 edges (check carefully)
+- [ ] All images display correctly
+- [ ] Colors render as expected
+- [ ] Text readable at 25% scale
+- [ ] Graphics look SIMPLE (not like complex 7-stage workflows)
+
+---
+
+## Common Pitfalls to Avoid
+
+**AI-Generated Graphics Mistakes:**
+- ❌ Too many elements (10+ items) → Keep to 3-5 max
+- ❌ Text too small → Specify "GIANT (100pt+)" in prompts
+- ❌ No white space → Add "50% white space" to every prompt
+- ❌ Complex flowcharts (8+ steps) → Limit to 4-5 steps
+
+**HTML/Export Mistakes:**
+- ❌ Content exceeding poster dimensions → Check overflow in browser
+- ❌ Missing background graphics in PDF → Enable in print settings
+- ❌ Wrong paper size in PDF → Match poster dimensions exactly
+- ❌ Low-resolution images → Use 300 DPI minimum
+
+**Content Mistakes:**
+- ❌ Too much text (over 1000 words) → Cut to 300-800 words
+- ❌ Too many sections (7+) → Consolidate to 5-6
+- ❌ No clear visual hierarchy → Make key findings prominent
+
+---
+
+## Integration with Other Skills
+
+This skill works with:
+- **Scientific Schematics**: Generate all poster diagrams and flowcharts
+- **Generate Image / Nano Banana Pro**: Create stylized graphics and hero images
+- **LaTeX Posters**: DEFAULT skill for poster creation (use this instead unless PPTX explicitly requested)
+
+---
+
+## Template Assets
+
+Available in `assets/` directory:
+
+- `poster_html_template.html`: Main HTML poster template (36×48 inches)
+- `poster_quality_checklist.md`: Pre-submission validation checklist
+
+## References
+
+Available in `references/` directory:
+
+- `poster_content_guide.md`: Content organization and writing guidelines
+- `poster_design_principles.md`: Typography, color theory, and visual hierarchy
+- `poster_layout_design.md`: Layout principles and grid systems
+

package/data/skills/precision-oncology-agent/SKILL.md

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+<!--
+# COPYRIGHT NOTICE
+# This file is part of the "Universal Biomedical Skills" project.
+# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
+# All Rights Reserved.
+#
+# This code is proprietary and confidential.
+# Unauthorized copying of this file, via any medium is strictly prohibited.
+#
+# Provenance: Authenticated by MD BABU MIA
+
+-->
+
+---
+name: precision-oncology-agent
+description: Fuse genomic variants, pathology findings, and clinical context to draft evidence-linked therapy options for tumor board review.
+allowed-tools:
+  - read_file
+  - run_shell_command
+---
+
+## At-a-Glance
+- **description (10-20 chars):** Tumor board copilot
+- **keywords:** oncology, genomics, OncoKB, therapy-ranking, evidence
+- **measurable_outcome:** Deliver a ranked therapy list with OncoKB/NCCN citations plus data-gap checklist for every case within 10 minutes of receiving inputs.
+
+## Inputs
+- `vcf_path` (hg38 preferred) plus optional CNV/fusion summaries.
+- `pathology_report` text for histology/grade/biomarkers.
+- `clinical_context` dict capturing tumor type, stage, prior lines, ECOG.
+
+## Outputs
+1. Ranked treatment options (approved, off-label, clinical trials) with evidence strength + contraindications.
+2. Variant interpretation table (pathogenicity, tier, therapy linkage).
+3. Biomarker summary (TMB, MSI, PD-L1 if provided) and missing-test checklist.
+
+## Workflow
+1. **Ingest & normalize:** Harmonize gene symbols, genome build, and variant effects.
+2. **Annotate:** Query OncoKB/NCCN + internal knowledge for actionability tiers.
+3. **Contextualize:** Blend pathology + prior therapy info to filter contraindicated options.
+4. **Recommend:** Present therapies ordered by evidence + patient fit; cite sources.
+5. **Gaps:** Highlight assays or confirmations still required before treatment.
+
+## Guardrails
+- No autonomous treatment decisions—flag outputs as advisory.
+- Cite evidence rigorously (guideline version, publication).
+- Highlight resistance mechanisms and prior exposure conflicts.
+
+## References
+- See `README.md` for detailed workflow plus cited Nature Cancer study.
+
+
+<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

package/data/skills/prior-auth-coworker/SKILL.md

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+<!--
+# COPYRIGHT NOTICE
+# This file is part of the "Universal Biomedical Skills" project.
+# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
+# All Rights Reserved.
+#
+# This code is proprietary and confidential.
+# Unauthorized copying of this file, via any medium is strictly prohibited.
+#
+# Provenance: Authenticated by MD BABU MIA
+
+-->
+
+---
+name: 'prior-auth-coworker'
+description: 'Prior Auth Review'
+measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
+allowed-tools:
+  - read_file
+  - run_shell_command
+---
+
+
+# Prior Authorization Coworker
+
+This skill acts as an automated utilization management reviewer. It takes unstructured clinical notes and a procedure code, compares them against internal policy criteria (e.g., conservative therapy failure), and renders a decision.
+
+## When to Use This Skill
+
+*   When a user asks to "review a prior auth request".
+*   When checking if a patient qualifies for a specific procedure (e.g., MRI).
+*   When you need to generate a structured approval/denial letter justification.
+
+## Core Capabilities
+
+1.  **Policy Matching**: Checks against specific criteria (e.g., "Pain > 6 weeks").
+2.  **Trace Generation**: Produces an "Anthropic-style" `<thinking>` trace for auditability.
+3.  **Structured Output**: Returns a JSON object with decision, reasoning, and timestamps.
+
+## Workflow
+
+1.  **Extract Data**: Parse the clinical note and procedure code from the user's input.
+2.  **Execute Review**: Run the coworker script.
+3.  **Present Decision**: Output the JSON decision and the reasoning trace.
+
+## Example Usage
+
+**User**: "Check if this patient qualifies for an MRI of the Lumbar Spine: Patient has had back pain for 2 months, tried PT but it didn't work."
+
+**Agent Action**:
+```bash
+python3 Skills/Clinical/Prior_Authorization/anthropic_coworker.py --code "MRI-L-SPINE" --note "Patient has back pain > 2 months. Failed PT."
+```
+
+## Supported Policies
+
+*   `MRI-L-SPINE` (Lumbar Spine MRI)
+
+
+<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->