opencode-knowledge-work 0.0.0-stage → 0.1.0

package/content/bio-research/README.md

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+# Bio-Research Plugin
+
+Connect to preclinical research tools and databases (literature search, genomics analysis, target prioritization) to accelerate early-stage life sciences R&D. Use with [Cowork](https://claude.com/product/cowork) or install directly in Claude Code.
+
+This plugin consolidates 11 MCP server integrations and 5 analysis skills into a single package for life science researchers.
+
+## What's Included
+
+### MCP Servers (Data Sources & Tools)
+
+> If you see unfamiliar placeholders or need to check which tools are connected, see [CONNECTORS.md](CONNECTORS.md).
+
+| Provider | What It Does | Category/Placeholder |
+|----------|-------------|---------------------|
+| U.S. National Library of Medicine | Search biomedical literature and research articles | `~~literature` |
+| deepsense.ai | Access preprints from bioRxiv and medRxiv | `~~literature` |
+| Consensus | AI-powered search and synthesis of peer-reviewed research | `~~literature` |
+| John Wiley & Sons | Access academic research and publications | `~~journal access` |
+| Sage Bionetworks | Collaborative research data management | `~~data repository` |
+| deepsense.ai | Bioactive drug-like compound database | `~~chemical database` |
+| OpenTargets | Drug target discovery and prioritization | `~~drug targets` |
+| deepsense.ai | NIH/NLM clinical trial registry | `~~clinical trials` |
+| BioRender | Scientific illustration creation | `~~scientific illustration` |
+| Owkin | AI for biology — histopathology and drug discovery | `~~AI research` |
+| Benchling\* | Lab data management platform | `~~lab platform` |
+
+### Optional Binary MCP Servers
+
+These require a separate binary download:
+
+- **10X Genomics txg-mcp** (`~~genomics platform`) — Cloud analysis data and workflows ([GitHub](https://github.com/10XGenomics/txg-mcp/releases))
+- **ToolUniverse** (`~~tool database`) — AI tools for scientific discovery from Harvard MIMS ([GitHub](https://github.com/mims-harvard/ToolUniverse/releases))
+
+### Skills (Analysis Workflows)
+
+#### Single-Cell RNA QC
+Automated quality control for scRNA-seq data following scverse best practices. Supports `.h5ad` and `.h5` files with MAD-based filtering and comprehensive visualizations.
+
+#### scvi-tools
+Deep learning toolkit for single-cell omics. Covers scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, and sysVI models for integration, batch correction, label transfer, and multi-modal analysis.
+
+#### Nextflow Pipelines
+Run nf-core bioinformatics pipelines on local or public GEO/SRA sequencing data:
+- **rnaseq** — Gene expression and differential expression
+- **sarek** — Germline and somatic variant calling (WGS/WES)
+- **atacseq** — Chromatin accessibility analysis
+
+#### Instrument Data to Allotrope
+Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) format. Supports 40+ instrument types including cell counters, spectrophotometers, plate readers, qPCR, and chromatography systems.
+
+#### Scientific Problem Selection
+Systematic framework for research problem selection based on Fischbach & Walsh's framework. Includes 9 skills covering ideation, risk assessment, optimization, decision trees, adversity planning, and synthesis.
+
+## Getting Started
+
+```bash
+# Install the plugin
+/install anthropics/knowledge-work-plugins bio-research
+
+# Run the start command to see available tools
+/start
+```
+
+## Common Workflows
+
+**Literature Review**
+Search ~~literature database for papers, access full-text through ~~journal access, and create figures with ~~scientific illustration.
+
+**Single-Cell Analysis**
+Run QC on scRNA-seq data, then use scvi-tools for integration, batch correction, and cell type annotation.
+
+**Sequencing Pipeline**
+Download public data from GEO/SRA, run nf-core pipelines (RNA-seq, variant calling, ATAC-seq), and verify outputs.
+
+**Drug Discovery**
+Search ~~chemical database for bioactive compounds, use ~~drug target database for target prioritization, and review clinical trial data.
+
+**Research Strategy**
+Pitch a new idea, troubleshoot a stuck project, or evaluate strategic decisions using the scientific problem selection framework.
+
+## License
+
+Skills are licensed under Apache 2.0. MCP servers are provided by their respective authors — see individual server documentation for terms.

package/content/bio-research/skills/bio-research-instrument-data-to-allotrope/LICENSE.txt

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package/content/bio-research/skills/bio-research-instrument-data-to-allotrope/SKILL.md

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+---
+name: instrument-data-to-allotrope
+description: Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full ASM JSON, flattened CSV for easy import, and exportable Python code for data engineers. Common triggers include converting instrument files, standardizing lab data, preparing data for upload to LIMS/ELN systems, or generating parser code for production pipelines.
+---
+
+# Instrument Data to Allotrope Converter
+
+Convert instrument files into standardized Allotrope Simple Model (ASM) format for LIMS upload, data lakes, or handoff to data engineering teams.
+
+> **Note: This is an Example Skill**
+>
+> This skill demonstrates how skills can support your data engineering tasks—automating schema transformations, parsing instrument outputs, and generating production-ready code.
+>
+> **To customize for your organization:**
+> - Modify the `references/` files to include your company's specific schemas or ontology mappings
+> - Use an MCP server to connect to systems that define your schemas (e.g., your LIMS, data catalog, or schema registry)
+> - Extend the `scripts/` to handle proprietary instrument formats or internal data standards
+>
+> This pattern can be adapted for any data transformation workflow where you need to convert between formats or validate against organizational standards.
+
+## Workflow Overview
+
+1. **Detect instrument type** from file contents (auto-detect or user-specified)
+2. **Parse file** using allotropy library (native) or flexible fallback parser
+3. **Generate outputs**:
+   - ASM JSON (full semantic structure)
+   - Flattened CSV (2D tabular format)
+   - Python parser code (for data engineer handoff)
+4. **Deliver** files with summary and usage instructions
+
+> **When Uncertain:** If you're unsure how to map a field to ASM (e.g., is this raw data or calculated? device setting or environmental condition?), ask the user for clarification. Refer to `references/field_classification_guide.md` for guidance, but when ambiguity remains, confirm with the user rather than guessing.
+
+## Quick Start
+
+```python
+# Install requirements first
+pip install allotropy pandas openpyxl pdfplumber --break-system-packages
+
+# Core conversion
+from allotropy.parser_factory import Vendor
+from allotropy.to_allotrope import allotrope_from_file
+
+# Convert with allotropy
+asm = allotrope_from_file("instrument_data.csv", Vendor.BECKMAN_VI_CELL_BLU)
+```
+
+## Output Format Selection
+
+**ASM JSON (default)** - Full semantic structure with ontology URIs
+- Best for: LIMS systems expecting ASM, data lakes, long-term archival
+- Validates against Allotrope schemas
+
+**Flattened CSV** - 2D tabular representation
+- Best for: Quick analysis, Excel users, systems without JSON support
+- Each measurement becomes one row with metadata repeated
+
+**Both** - Generate both formats for maximum flexibility
+
+## Calculated Data Handling
+
+**IMPORTANT:** Separate raw measurements from calculated/derived values.
+
+- **Raw data** → `measurement-document` (direct instrument readings)
+- **Calculated data** → `calculated-data-aggregate-document` (derived values)
+
+Calculated values MUST include traceability via `data-source-aggregate-document`:
+
+```json
+"calculated-data-aggregate-document": {
+  "calculated-data-document": [{
+    "calculated-data-identifier": "SAMPLE_B1_DIN_001",
+    "calculated-data-name": "DNA integrity number",
+    "calculated-result": {"value": 9.5, "unit": "(unitless)"},
+    "data-source-aggregate-document": {
+      "data-source-document": [{
+        "data-source-identifier": "SAMPLE_B1_MEASUREMENT",
+        "data-source-feature": "electrophoresis trace"
+      }]
+    }
+  }]
+}
+```
+
+**Common calculated fields by instrument type:**
+| Instrument | Calculated Fields |
+|------------|-------------------|
+| Cell counter | Viability %, cell density dilution-adjusted values |
+| Spectrophotometer | Concentration (from absorbance), 260/280 ratio |
+| Plate reader | Concentrations from standard curve, %CV |
+| Electrophoresis | DIN/RIN, region concentrations, average sizes |
+| qPCR | Relative quantities, fold change |
+
+See `references/field_classification_guide.md` for detailed guidance on raw vs. calculated classification.
+
+## Validation
+
+Always validate ASM output before delivering to the user:
+
+```bash
+python scripts/validate_asm.py output.json
+python scripts/validate_asm.py output.json --reference known_good.json  # Compare to reference
+python scripts/validate_asm.py output.json --strict  # Treat warnings as errors
+```
+
+**Validation Rules:**
+- Based on Allotrope ASM specification (December 2024)
+- Last updated: 2026-01-07
+- Source: https://gitlab.com/allotrope-public/asm
+
+**Soft Validation Approach:**
+Unknown techniques, units, or sample roles generate **warnings** (not errors) to allow for forward compatibility. If Allotrope adds new values after December 2024, the validator won't block them—it will flag them for manual verification. Use `--strict` mode to treat warnings as errors if you need stricter validation.
+
+**What it checks:**
+- Correct technique selection (e.g., multi-analyte profiling vs plate reader)
+- Field naming conventions (space-separated, not hyphenated)
+- Calculated data has traceability (`data-source-aggregate-document`)
+- Unique identifiers exist for measurements and calculated values
+- Required metadata present
+- Valid units and sample roles (with soft validation for unknown values)
+
+## Supported Instruments
+
+See `references/supported_instruments.md` for complete list. Key instruments:
+
+| Category | Instruments |
+|----------|-------------|
+| Cell Counting | Vi-CELL BLU, Vi-CELL XR, NucleoCounter |
+| Spectrophotometry | NanoDrop One/Eight/8000, Lunatic |
+| Plate Readers | SoftMax Pro, EnVision, Gen5, CLARIOstar |
+| ELISA | SoftMax Pro, BMG MARS, MSD Workbench |
+| qPCR | QuantStudio, Bio-Rad CFX |
+| Chromatography | Empower, Chromeleon |
+
+## Detection & Parsing Strategy
+
+### Tier 1: Native allotropy parsing (PREFERRED)
+**Always try allotropy first.** Check available vendors directly:
+
+```python
+from allotropy.parser_factory import Vendor
+
+# List all supported vendors
+for v in Vendor:
+    print(f"{v.name}")
+
+# Common vendors:
+# AGILENT_TAPESTATION_ANALYSIS  (for TapeStation XML)
+# BECKMAN_VI_CELL_BLU
+# THERMO_FISHER_NANODROP_EIGHT
+# MOLDEV_SOFTMAX_PRO
+# APPBIO_QUANTSTUDIO
+# ... many more
+```
+
+**When the user provides a file, check if allotropy supports it before falling back to manual parsing.** The `scripts/convert_to_asm.py` auto-detection only covers a subset of allotropy vendors.
+
+### Tier 2: Flexible fallback parsing
+**Only use if allotropy doesn't support the instrument.** This fallback:
+- Does NOT generate `calculated-data-aggregate-document`
+- Does NOT include full traceability
+- Produces simplified ASM structure
+
+Use flexible parser with:
+- Column name fuzzy matching
+- Unit extraction from headers
+- Metadata extraction from file structure
+
+### Tier 3: PDF extraction
+For PDF-only files, extract tables using pdfplumber, then apply Tier 2 parsing.
+
+## Pre-Parsing Checklist
+
+Before writing a custom parser, ALWAYS:
+
+1. **Check if allotropy supports it** - Use native parser if available
+2. **Find a reference ASM file** - Check `references/examples/` or ask user
+3. **Review instrument-specific guide** - Check `references/instrument_guides/`
+4. **Validate against reference** - Run `validate_asm.py --reference <file>`
+
+## Common Mistakes to Avoid
+
+| Mistake | Correct Approach |
+|---------|------------------|
+| Manifest as object | Use URL string |
+| Lowercase detection types | Use "Absorbance" not "absorbance" |
+| "emission wavelength setting" | Use "detector wavelength setting" for emission |
+| All measurements in one document | Group by well/sample location |
+| Missing procedure metadata | Extract ALL device settings per measurement |
+
+## Code Export for Data Engineers
+
+Generate standalone Python scripts that scientists can hand off:
+
+```python
+# Export parser code
+python scripts/export_parser.py --input "data.csv" --vendor "VI_CELL_BLU" --output "parser_script.py"
+```
+
+The exported script:
+- Has no external dependencies beyond pandas/allotropy
+- Includes inline documentation
+- Can run in Jupyter notebooks
+- Is production-ready for data pipelines
+
+## File Structure
+
+```
+instrument-data-to-allotrope/
+├── SKILL.md                          # This file
+├── scripts/
+│   ├── convert_to_asm.py            # Main conversion script
+│   ├── flatten_asm.py               # ASM → 2D CSV conversion
+│   ├── export_parser.py             # Generate standalone parser code
+│   └── validate_asm.py              # Validate ASM output quality
+└── references/
+    ├── supported_instruments.md     # Full instrument list with Vendor enums
+    ├── asm_schema_overview.md       # ASM structure reference
+    ├── field_classification_guide.md # Where to put different field types
+    └── flattening_guide.md          # How flattening works
+```
+
+## Usage Examples
+
+### Example 1: Vi-CELL BLU file
+```
+User: "Convert this cell counting data to Allotrope format"
+[uploads viCell_Results.xlsx]
+
+Claude:
+1. Detects Vi-CELL BLU (95% confidence)
+2. Converts using allotropy native parser
+3. Outputs:
+   - viCell_Results_asm.json (full ASM)
+   - viCell_Results_flat.csv (2D format)
+   - viCell_parser.py (exportable code)
+```
+
+### Example 2: Request for code handoff
+```
+User: "I need to give our data engineer code to parse NanoDrop files"
+
+Claude:
+1. Generates self-contained Python script
+2. Includes sample input/output
+3. Documents all assumptions
+4. Provides Jupyter notebook version
+```
+
+### Example 3: LIMS-ready flattened output
+```
+User: "Convert this ELISA data to a CSV I can upload to our LIMS"
+
+Claude:
+1. Parses plate reader data
+2. Generates flattened CSV with columns:
+   - sample_identifier, well_position, measurement_value, measurement_unit
+   - instrument_serial_number, analysis_datetime, assay_type
+3. Validates against common LIMS import requirements
+```
+
+## Implementation Notes
+
+### Installing allotropy
+```bash
+pip install allotropy --break-system-packages
+```
+
+### Handling parse failures
+If allotropy native parsing fails:
+1. Log the error for debugging
+2. Fall back to flexible parser
+3. Report reduced metadata completeness to user
+4. Suggest exporting different format from instrument
+
+### ASM Schema Validation
+Validate output against Allotrope schemas when available:
+```python
+import jsonschema
+# Schema URLs in references/asm_schema_overview.md
+```