@pikaa-ai/pikaa 0.3.22 → 0.3.24
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/assets/brand/orbit-logo-option4-whale.jpg +0 -0
- package/assets/brand/orbit-logo.jpg +0 -0
- package/assets/brand/orbit-logo.png +0 -0
- package/assets/brand/orbit-logo.svg +3 -0
- package/dist/cli.js +448 -181
- package/dist/index.js +22 -2
- package/package.json +1 -2
- package/skills/adaptyv/SKILL.md +0 -240
- package/skills/aeon/SKILL.md +0 -402
- package/skills/analytical-method-validation/SKILL.md +0 -299
- package/skills/anndata/SKILL.md +0 -431
- package/skills/arbor/SKILL.md +0 -152
- package/skills/arboreto/SKILL.md +0 -267
- package/skills/astropy/SKILL.md +0 -353
- package/skills/autoskill/SKILL.md +0 -233
- package/skills/benchling-integration/SKILL.md +0 -229
- package/skills/bgpt-paper-search/SKILL.md +0 -75
- package/skills/bids/SKILL.md +0 -237
- package/skills/biopython/SKILL.md +0 -472
- package/skills/bioservices/SKILL.md +0 -399
- package/skills/bulk-rnaseq/SKILL.md +0 -198
- package/skills/cellxgene-census/SKILL.md +0 -283
- package/skills/cirq/SKILL.md +0 -370
- package/skills/citation-management/SKILL.md +0 -329
- package/skills/clinical-decision-support/SKILL.md +0 -238
- package/skills/clinical-decision-support/references/README.md +0 -62
- package/skills/clinical-reports/SKILL.md +0 -248
- package/skills/clinical-reports/references/README.md +0 -34
- package/skills/cobrapy/SKILL.md +0 -496
- package/skills/consciousness-council/SKILL.md +0 -151
- package/skills/dask/SKILL.md +0 -482
- package/skills/database-lookup/SKILL.md +0 -386
- package/skills/datamol/SKILL.md +0 -200
- package/skills/deepchem/SKILL.md +0 -244
- package/skills/deepspot-m/SKILL.md +0 -175
- package/skills/deeptools/SKILL.md +0 -412
- package/skills/depmap/SKILL.md +0 -301
- package/skills/dhdna-profiler/SKILL.md +0 -184
- package/skills/diffdock/SKILL.md +0 -488
- package/skills/dnanexus-integration/SKILL.md +0 -325
- package/skills/docx/SKILL.md +0 -99
- package/skills/esm/SKILL.md +0 -334
- package/skills/etetoolkit/SKILL.md +0 -327
- package/skills/exa-search/SKILL.md +0 -102
- package/skills/executing-plans/SKILL.md +0 -14
- package/skills/experimental-design/SKILL.md +0 -234
- package/skills/exploratory-data-analysis/SKILL.md +0 -280
- package/skills/flowio/SKILL.md +0 -310
- package/skills/fluidsim/SKILL.md +0 -279
- package/skills/frontend-design/SKILL.md +0 -100
- package/skills/generate-image/SKILL.md +0 -304
- package/skills/geniml/SKILL.md +0 -310
- package/skills/genomic-coordinates/SKILL.md +0 -189
- package/skills/genomic-intelligence/SKILL.md +0 -243
- package/skills/geomaster/README.md +0 -105
- package/skills/geomaster/SKILL.md +0 -366
- package/skills/geopandas/SKILL.md +0 -250
- package/skills/get-available-resources/SKILL.md +0 -260
- package/skills/gget/SKILL.md +0 -153
- package/skills/ginkgo-cloud-lab/SKILL.md +0 -106
- package/skills/glycoengineering/SKILL.md +0 -339
- package/skills/gtars/SKILL.md +0 -282
- package/skills/guardian-rails/SKILL.md +0 -54
- package/skills/histolab/SKILL.md +0 -243
- package/skills/hugging-science/SKILL.md +0 -132
- package/skills/hypogenic/SKILL.md +0 -290
- package/skills/hypothesis-generation/SKILL.md +0 -264
- package/skills/imaging-data-commons/SKILL.md +0 -496
- package/skills/infographics/SKILL.md +0 -315
- package/skills/iso-standards-readiness/SKILL.md +0 -352
- package/skills/lab-hardware-cad/SKILL.md +0 -372
- package/skills/labarchive-integration/SKILL.md +0 -216
- package/skills/lamindb/SKILL.md +0 -408
- package/skills/latchbio-integration/SKILL.md +0 -227
- package/skills/latex-posters/SKILL.md +0 -369
- package/skills/latex-posters/references/README.md +0 -439
- package/skills/liteparse/SKILL.md +0 -295
- package/skills/literature-review/SKILL.md +0 -263
- package/skills/markdown-mermaid-writing/SKILL.md +0 -322
- package/skills/market-research-reports/SKILL.md +0 -337
- package/skills/markitdown/SKILL.md +0 -264
- package/skills/matchms/SKILL.md +0 -276
- package/skills/matlab/SKILL.md +0 -274
- package/skills/matplotlib/SKILL.md +0 -378
- package/skills/medchem/SKILL.md +0 -321
- package/skills/modal/SKILL.md +0 -468
- package/skills/molecular-dynamics/SKILL.md +0 -458
- package/skills/molfeat/SKILL.md +0 -348
- package/skills/ncats-arax/SKILL.md +0 -178
- package/skills/networkx/SKILL.md +0 -440
- package/skills/neurokit2/SKILL.md +0 -323
- package/skills/neuropixels-analysis/SKILL.md +0 -412
- package/skills/nextflow/SKILL.md +0 -195
- package/skills/omero-integration/SKILL.md +0 -222
- package/skills/onekgpd/SKILL.md +0 -371
- package/skills/ontology-term-resolution/SKILL.md +0 -147
- package/skills/open-notebook/SKILL.md +0 -297
- package/skills/openpiv/SKILL.md +0 -469
- package/skills/opentrons-integration/SKILL.md +0 -322
- package/skills/optimize-for-gpu/SKILL.md +0 -176
- package/skills/owasp-top10/SKILL.md +0 -48
- package/skills/pacsomatic/LICENSE +0 -21
- package/skills/pacsomatic/SKILL.md +0 -150
- package/skills/paper-lookup/SKILL.md +0 -263
- package/skills/paperclip/SKILL.md +0 -413
- package/skills/paperzilla/SKILL.md +0 -159
- package/skills/parallel-web/SKILL.md +0 -128
- package/skills/pathml/SKILL.md +0 -222
- package/skills/pathogen-variant-surveillance/SKILL.md +0 -208
- package/skills/pathway-enrichment/SKILL.md +0 -194
- package/skills/pdf/SKILL.md +0 -322
- package/skills/peer-review/SKILL.md +0 -288
- package/skills/penetration-testing/SKILL.md +0 -31
- package/skills/pennylane/SKILL.md +0 -240
- package/skills/phylogenetics/SKILL.md +0 -409
- package/skills/pi-agent/SKILL.md +0 -83
- package/skills/pkpd-modeling/SKILL.md +0 -381
- package/skills/polars/SKILL.md +0 -393
- package/skills/polars-bio/SKILL.md +0 -379
- package/skills/ponytail/SKILL.md +0 -31
- package/skills/ponytail-audit/SKILL.md +0 -18
- package/skills/pptx/SKILL.md +0 -246
- package/skills/pptx-posters/SKILL.md +0 -258
- package/skills/primekg/SKILL.md +0 -99
- package/skills/protocolsio-integration/SKILL.md +0 -236
- package/skills/pufferlib/SKILL.md +0 -328
- package/skills/pydeseq2/SKILL.md +0 -369
- package/skills/pydicom/SKILL.md +0 -381
- package/skills/pyhealth/SKILL.md +0 -124
- package/skills/pylabrobot/SKILL.md +0 -216
- package/skills/pymatgen/SKILL.md +0 -404
- package/skills/pymc/SKILL.md +0 -310
- package/skills/pymoo/SKILL.md +0 -276
- package/skills/pyopenms/SKILL.md +0 -179
- package/skills/pysam/SKILL.md +0 -330
- package/skills/pytdc/SKILL.md +0 -297
- package/skills/pytorch-lightning/SKILL.md +0 -191
- package/skills/pyzotero/SKILL.md +0 -137
- package/skills/qiskit/SKILL.md +0 -259
- package/skills/qutip/SKILL.md +0 -317
- package/skills/rdkit/SKILL.md +0 -94
- package/skills/relsa-severity-assessment/SKILL.md +0 -354
- package/skills/research-grants/SKILL.md +0 -296
- package/skills/research-grants/references/README.md +0 -287
- package/skills/research-lookup/README.md +0 -106
- package/skills/research-lookup/SKILL.md +0 -338
- package/skills/rowan/SKILL.md +0 -398
- package/skills/scanpy/SKILL.md +0 -303
- package/skills/scholar-evaluation/SKILL.md +0 -296
- package/skills/scientific-brainstorming/SKILL.md +0 -282
- package/skills/scientific-critical-thinking/SKILL.md +0 -180
- package/skills/scientific-schematics/SKILL.md +0 -370
- package/skills/scientific-slides/SKILL.md +0 -379
- package/skills/scientific-visualization/SKILL.md +0 -285
- package/skills/scientific-writing/SKILL.md +0 -356
- package/skills/scikit-bio/SKILL.md +0 -470
- package/skills/scikit-learn/SKILL.md +0 -324
- package/skills/scikit-survival/SKILL.md +0 -313
- package/skills/scvelo/SKILL.md +0 -328
- package/skills/scvi-tools/SKILL.md +0 -201
- package/skills/seaborn/SKILL.md +0 -254
- package/skills/security-auditor/SKILL.md +0 -37
- package/skills/shap/SKILL.md +0 -282
- package/skills/simpy/SKILL.md +0 -283
- package/skills/stable-baselines3/SKILL.md +0 -325
- package/skills/statistical-analysis/SKILL.md +0 -446
- package/skills/statistical-power/SKILL.md +0 -200
- package/skills/statsmodels/SKILL.md +0 -238
- package/skills/sympy/SKILL.md +0 -354
- package/skills/systematic-debugging/SKILL.md +0 -35
- package/skills/tamarind/SKILL.md +0 -285
- package/skills/tdd/SKILL.md +0 -26
- package/skills/tiledbvcf/SKILL.md +0 -456
- package/skills/timesfm-forecasting/SKILL.md +0 -408
- package/skills/timesfm-forecasting/examples/global-temperature/README.md +0 -178
- package/skills/torch-geometric/SKILL.md +0 -458
- package/skills/torchdrug/SKILL.md +0 -241
- package/skills/transformers/SKILL.md +0 -195
- package/skills/treatment-plans/SKILL.md +0 -174
- package/skills/treatment-plans/references/README.md +0 -19
- package/skills/umap-learn/SKILL.md +0 -488
- package/skills/uncertainty-and-units/SKILL.md +0 -384
- package/skills/usfiscaldata/SKILL.md +0 -171
- package/skills/vaex/SKILL.md +0 -204
- package/skills/venue-templates/SKILL.md +0 -269
- package/skills/verification-before-completion/SKILL.md +0 -22
- package/skills/waypoint-bio/SKILL.md +0 -273
- package/skills/what-if-oracle/SKILL.md +0 -184
- package/skills/writing-plans/SKILL.md +0 -15
- package/skills/xlsx/SKILL.md +0 -110
- package/skills/zarr-python/SKILL.md +0 -241
package/skills/lamindb/SKILL.md
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name: lamindb
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description: Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation with Bionty, collections, branches, storage, and workflow integrations.
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license: Apache-2.0 license
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metadata:
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version: "1.1"
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skill-author: K-Dense Inc.
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---
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# LaminDB
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## Overview
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LaminDB is an open-source, lineage-native lakehouse for biology. It makes datasets and models queryable, traceable, validated, reproducible, and FAIR (Findable, Accessible, Interoperable, Reusable) while storing data in open formats across local filesystems, S3, GCS, Hugging Face, SQLite, and Postgres.
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**Core Value Proposition:**
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- **Queryability**: Search and filter artifacts, records, runs, features, schemas, and collections
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- **Traceability**: Track inputs, outputs, parameters, source code, and environments for notebooks, scripts, functions, and pipelines
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- **Validation**: Curate DataFrame, AnnData, SpatialData, TileDB-SOMA, Parquet, Zarr, and other biological formats with schemas
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- **FAIR Compliance**: Standardize annotations with Bionty-backed ontologies and custom registries
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- **Change management**: Organize work with projects, branches, spaces, collections, and saved notes or plans
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## When to Use This Skill
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Use this skill when:
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- **Managing biological datasets**: scRNA-seq, bulk RNA-seq, spatial transcriptomics, flow cytometry, multi-modal data, EHR data
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- **Tracking computational workflows**: Notebooks, scripts, functions, shell scripts, and pipeline execution (Nextflow, Snakemake, Redun)
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- **Curating and validating data**: Schema validation, standardization, ontology-based annotation
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- **Working with biological ontologies**: Genes, proteins, cell types, tissues, diseases, pathways (via Bionty)
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- **Building data lakehouses**: Unified query interface across multiple datasets
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- **Ensuring reproducibility**: Automatic versioning, lineage tracking, environment capture
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- **Integrating ML pipelines**: Connecting with Weights & Biases, MLflow, Hugging Face, Lightning, scVI-tools
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- **Deploying data infrastructure**: Setting up local or cloud-based data management systems
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- **Collaborating on datasets**: Sharing curated, annotated data with standardized metadata
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## Core Capabilities
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LaminDB provides six interconnected capability areas, each documented in detail in the references folder.
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### 1. Core Concepts and Data Lineage
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**Core entities:**
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- **Artifacts**: Versioned datasets (DataFrame, AnnData, Parquet, Zarr, etc.)
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- **Records & ULabels**: Experimental entities, typed records, and simple labels
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- **Collections**: Versioned, immutable sets of artifacts
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- **Runs & Transforms**: Computational lineage tracking (what code produced what data)
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- **Features**: Typed metadata fields for annotation and querying
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- **Projects, Branches & Spaces**: Project grouping, change management, and access boundaries
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**Key workflows:**
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- Create and version artifacts from files or Python objects
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- Track notebook/script execution with `ln.track()` and `ln.finish()`
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- Track function workflows with `@ln.flow()` and `@ln.step()`
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- Annotate artifacts with records, ulabels, projects, and typed features
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- Visualize data lineage graphs with `artifact.view_lineage()`
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- Query by provenance (find all outputs from specific code/inputs)
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**Reference:** `references/core-concepts.md` - Read this for detailed information on artifacts, records, runs, transforms, features, versioning, and lineage tracking.
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### 2. Data Management and Querying
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**Query capabilities:**
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- Registry exploration and lookup with auto-complete
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- Single record retrieval with `get()`, `one()`, `one_or_none()`
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- Filtering with comparison operators (`__gt`, `__lte`, `__contains`, `__startswith`)
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- Feature-based queries, including expression-style queries with `Feature` objects
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- Cross-registry traversal with double-underscore syntax
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- Full-text search across registries
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- Advanced logical queries with `ln.Q` objects (AND, OR, NOT)
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- Streaming large datasets without loading into memory
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**Key workflows:**
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- Stream large files in chunks or with array slicing
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- Organize data with hierarchical keys
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**Reference:** `references/data-management.md` - Read this for comprehensive query patterns, filtering examples, streaming strategies, and data organization best practices.
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### 3. Annotation and Validation
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**Curation process:**
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1. **Validation**: Confirm datasets match desired schemas
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2. **Standardization**: Fix typos, map synonyms to canonical terms
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3. **Annotation**: Link datasets to metadata entities for queryability
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**Schema types:**
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- **Flexible schemas**: Validate only known columns, allow additional metadata
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**Supported data types:**
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- DataFrames (Parquet, CSV)
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- AnnData (single-cell genomics)
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- Use `DataFrameCurator`, `AnnDataCurator`, `SpatialDataCurator`, or `TiledbsomaExperimentCurator` for validation
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- Save curated artifacts with schema linkage
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- Query validated datasets by features
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**Reference:** `references/annotation-validation.md` - Read this for detailed curation workflows, schema design patterns, handling validation errors, and best practices.
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### 4. Biological Ontologies
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**Available ontologies (via Bionty):**
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- Genes (Ensembl), Proteins (UniProt)
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- Cell types (CL), Cell lines (CLO)
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- Tissues (Uberon), Diseases (Mondo, DOID)
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- Phenotypes (HPO), Pathways (GO)
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- Experimental factors (EFO), Developmental stages
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- Organisms (NCBItaxon), Drugs (DrugBank)
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**Key workflows:**
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- Import public ontologies with `bt.CellType.import_source()`
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- Search ontologies with keyword or exact matching
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- Standardize terms using synonym mapping
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- Explore hierarchical relationships (parents, children, ancestors)
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- Validate data against ontology terms
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- Annotate datasets with ontology records
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- Create custom terms and hierarchies
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- Handle multi-organism contexts (human, mouse, etc.)
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**Reference:** `references/ontologies.md` - Read this for comprehensive ontology operations, standardization strategies, hierarchy navigation, and annotation workflows.
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### 5. Integrations
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**Workflow managers:**
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- Nextflow: Track pipeline processes and outputs
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- Snakemake: Integrate into Snakemake rules
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- Redun: Combine with Redun task tracking
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- Lightning: Persist checkpoints and training metadata
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**MLOps platforms:**
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- Weights & Biases: Link experiments with data artifacts
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- MLflow: Track models and experiments
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- Hugging Face: Track model fine-tuning
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- scVI-tools: Single-cell analysis workflows
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**Storage systems:**
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- Local filesystem, AWS S3, Google Cloud Storage
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- S3-compatible (MinIO, Cloudflare R2)
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**Reference:** `references/integrations.md` - Read this for integration patterns, code examples, and troubleshooting for third-party systems.
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### 6. Setup and Deployment
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**Configuration:**
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**Deployment patterns:**
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**Reference:** `references/setup-deployment.md` - Read this for detailed installation, configuration, storage setup, database management, security best practices, and troubleshooting.
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## Safety and Security Defaults
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- Never display, log, or transmit actual API keys, cloud credentials, database passwords, or full connection strings that include secrets.
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- Prefer IAM roles, workload identity, secret managers, or named environment variables such as `LAMIN_DB_URL`, `AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY`, and `GOOGLE_APPLICATION_CREDENTIALS`; only check whether a named variable is present, not its value.
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- Before saving content from REST APIs, external databases, or user-provided files, validate and sanitize it with an explicit schema or curator.
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- For reproducible installs, pin package versions or use a lock file. Floating installs are acceptable only when the user explicitly wants the latest upstream release.
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## Common Use Case Workflows
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### Use Case 1: Single-Cell RNA-seq Analysis with Ontology Validation
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```python
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import anndata as ad
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# Start tracking a notebook/script run
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ln.track(params={"analysis": "scRNA-seq QC and annotation"})
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# Import cell type ontology
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bt.CellType.import_source()
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adata = ad.read_h5ad("raw_counts.h5ad")
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adata.obs["cell_type"] = bt.CellType.standardize(adata.obs["cell_type"])
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# Curate with schema
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curator = ln.curators.AnnDataCurator(adata, schema)
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curator.validate()
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artifact = curator.save_artifact(key="scrna/validated.h5ad")
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# Link ontology-backed annotations for queryability
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cell_types = bt.CellType.from_values(adata.obs["cell_type"])
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artifact.cell_types.add(*cell_types)
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ln.finish()
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```
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### Use Case 2: Building a Queryable Data Lakehouse
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```python
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import lamindb as ln
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# Register multiple experiments
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for i, file in enumerate(data_files):
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artifact = ln.Artifact.from_anndata(
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ad.read_h5ad(file),
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key=f"scrna/batch_{i}.h5ad",
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description=f"scRNA-seq batch {i}"
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).save()
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# Annotate with features
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artifact.features.set_values({
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"batch": i,
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"tissue": tissues[i],
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"condition": conditions[i]
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})
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# Query across all experiments by annotated features
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immune_datasets = ln.Artifact.filter(
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key__startswith="scrna/",
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tissue="PBMC",
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condition="treated"
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).to_dataframe()
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# Load specific datasets
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for artifact in immune_datasets:
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adata = artifact.load()
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# Analyze
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```
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-
|
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### Use Case 3: ML Pipeline with W&B Integration
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```python
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import lamindb as ln
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|
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import wandb
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|
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|
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# Initialize both systems
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|
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|
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wandb.init(project="drug-response", name="exp-42")
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ln.track(params={"model": "random_forest", "n_estimators": 100})
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# Load training data from LaminDB
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train_artifact = ln.Artifact.get(key="datasets/train.parquet")
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|
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train_data = train_artifact.load()
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|
-
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|
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# Train model
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|
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model = train_model(train_data)
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|
-
|
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|
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# Log to W&B
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|
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|
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wandb.log({"accuracy": 0.95})
|
|
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|
-
|
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|
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# Save model in LaminDB with W&B linkage
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|
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import joblib
|
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|
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joblib.dump(model, "model.pkl")
|
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|
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model_artifact = ln.Artifact("model.pkl", key="models/exp-42.pkl").save()
|
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|
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model_artifact.features.set_values({"wandb_run_id": wandb.run.id})
|
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|
-
|
|
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|
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ln.finish()
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|
301
|
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wandb.finish()
|
|
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|
-
```
|
|
303
|
-
|
|
304
|
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### Use Case 4: Nextflow Pipeline Integration
|
|
305
|
-
|
|
306
|
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```python
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|
307
|
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# In Nextflow process script
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|
308
|
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import lamindb as ln
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|
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|
-
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ln.track()
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|
-
|
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|
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# Load input artifact
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|
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input_artifact = ln.Artifact.get(key="raw/batch_${batch_id}.fastq.gz")
|
|
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|
-
input_path = input_artifact.cache()
|
|
315
|
-
|
|
316
|
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# Process (alignment, quantification, etc.)
|
|
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|
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# ... Nextflow process logic ...
|
|
318
|
-
|
|
319
|
-
# Save output
|
|
320
|
-
output_artifact = ln.Artifact(
|
|
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|
-
"counts.csv",
|
|
322
|
-
key="processed/batch_${batch_id}_counts.csv"
|
|
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|
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).save()
|
|
324
|
-
|
|
325
|
-
ln.finish()
|
|
326
|
-
```
|
|
327
|
-
|
|
328
|
-
For native Nextflow projects, prefer the `nf-lamin` plugin and current `nextflow.config` patterns when available; use inline Python tracking for small or custom pipeline steps.
|
|
329
|
-
|
|
330
|
-
## Getting Started Checklist
|
|
331
|
-
|
|
332
|
-
To start using LaminDB effectively:
|
|
333
|
-
|
|
334
|
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1. **Installation & Setup** (`references/setup-deployment.md`)
|
|
335
|
-
- Install pinned LaminDB and required extras
|
|
336
|
-
- Authenticate with `lamin login`
|
|
337
|
-
- Initialize instance with `lamin init --storage ...`
|
|
338
|
-
|
|
339
|
-
2. **Learn Core Concepts** (`references/core-concepts.md`)
|
|
340
|
-
- Understand Artifacts, Records, Runs, Transforms
|
|
341
|
-
- Practice creating and retrieving artifacts
|
|
342
|
-
- Implement `ln.track()`/`ln.finish()` or `@ln.flow()`/`@ln.step()` in workflows
|
|
343
|
-
|
|
344
|
-
3. **Master Querying** (`references/data-management.md`)
|
|
345
|
-
- Practice filtering and searching registries
|
|
346
|
-
- Learn feature-based queries and expression-style filters
|
|
347
|
-
- Experiment with streaming large files
|
|
348
|
-
|
|
349
|
-
4. **Set Up Validation** (`references/annotation-validation.md`)
|
|
350
|
-
- Define features relevant to research domain
|
|
351
|
-
- Create schemas for data types
|
|
352
|
-
- Practice curation workflows
|
|
353
|
-
|
|
354
|
-
5. **Integrate Ontologies** (`references/ontologies.md`)
|
|
355
|
-
- Import relevant biological ontologies (genes, cell types, etc.)
|
|
356
|
-
- Validate existing annotations
|
|
357
|
-
- Standardize metadata with ontology terms
|
|
358
|
-
|
|
359
|
-
6. **Connect Tools** (`references/integrations.md`)
|
|
360
|
-
- Integrate with existing workflow managers
|
|
361
|
-
- Link ML platforms for experiment tracking
|
|
362
|
-
- Configure cloud storage and compute
|
|
363
|
-
|
|
364
|
-
## Key Principles
|
|
365
|
-
|
|
366
|
-
Follow these principles when working with LaminDB:
|
|
367
|
-
|
|
368
|
-
1. **Track everything**: Use `ln.track()` at the start of every analysis for automatic lineage capture
|
|
369
|
-
|
|
370
|
-
2. **Validate early**: Define schemas and validate data before extensive analysis
|
|
371
|
-
|
|
372
|
-
3. **Use ontologies**: Leverage public biological ontologies for standardized annotations
|
|
373
|
-
|
|
374
|
-
4. **Organize with keys**: Structure artifact keys hierarchically (e.g., `project/experiment/batch/file.h5ad`)
|
|
375
|
-
|
|
376
|
-
5. **Query metadata first**: Filter and search before loading large files
|
|
377
|
-
|
|
378
|
-
6. **Version, don't duplicate**: Use built-in versioning instead of creating new keys for modifications
|
|
379
|
-
|
|
380
|
-
7. **Annotate with features**: Define typed features and use `artifact.features.set_values()` for queryable metadata
|
|
381
|
-
|
|
382
|
-
8. **Document thoroughly**: Add descriptions to artifacts, schemas, and transforms
|
|
383
|
-
|
|
384
|
-
9. **Leverage lineage**: Use `view_lineage()` to understand data provenance
|
|
385
|
-
|
|
386
|
-
10. **Start local, scale cloud**: Develop locally with SQLite, deploy to cloud with PostgreSQL
|
|
387
|
-
|
|
388
|
-
## Reference Files
|
|
389
|
-
|
|
390
|
-
This skill includes comprehensive reference documentation organized by capability:
|
|
391
|
-
|
|
392
|
-
- **`references/core-concepts.md`** - Artifacts, records, runs, transforms, features, versioning, lineage
|
|
393
|
-
- **`references/data-management.md`** - Querying, filtering, searching, streaming, organizing data
|
|
394
|
-
- **`references/annotation-validation.md`** - Schema design, curation workflows, validation strategies
|
|
395
|
-
- **`references/ontologies.md`** - Biological ontology management, standardization, hierarchies
|
|
396
|
-
- **`references/integrations.md`** - Workflow managers, MLOps platforms, storage systems, tools
|
|
397
|
-
- **`references/setup-deployment.md`** - Installation, configuration, deployment, troubleshooting
|
|
398
|
-
|
|
399
|
-
Read the relevant reference file(s) based on the specific LaminDB capability needed for the task at hand.
|
|
400
|
-
|
|
401
|
-
## Additional Resources
|
|
402
|
-
|
|
403
|
-
- **Official Documentation**: https://docs.lamin.ai
|
|
404
|
-
- **API Reference**: https://docs.lamin.ai/api
|
|
405
|
-
- **GitHub Repository**: https://github.com/laminlabs/lamindb
|
|
406
|
-
- **Tutorial**: https://docs.lamin.ai/tutorial
|
|
407
|
-
- **FAQ**: https://docs.lamin.ai/faq
|
|
408
|
-
|
|
@@ -1,227 +0,0 @@
|
|
|
1
|
-
---
|
|
2
|
-
name: latchbio-integration
|
|
3
|
-
description: Build, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP. Use when authoring or deploying Latch workflows, configuring resources or interfaces, moving data, integrating Registry, or launching and monitoring runs.
|
|
4
|
-
license: MIT
|
|
5
|
-
allowed-tools: Read Write Edit Bash
|
|
6
|
-
compatibility: Requires network access and a Latch account. The current stable SDK requires Python 3.9+; Python 3.12 is recommended. Uses uv for installation. Docker is needed for local image builds, while remote registration is the CLI default.
|
|
7
|
-
metadata:
|
|
8
|
-
version: "2.0"
|
|
9
|
-
skill-author: K-Dense Inc.
|
|
10
|
-
---
|
|
11
|
-
|
|
12
|
-
# LatchBio Integration
|
|
13
|
-
|
|
14
|
-
## Current Baseline
|
|
15
|
-
|
|
16
|
-
This skill targets **Latch SDK 2.76.8**, released July 10, 2026. The package
|
|
17
|
-
metadata supports Python 3.9–3.12 and declares Python 3.9+.
|
|
18
|
-
|
|
19
|
-
Treat the installed package and its changelog as authoritative when a guide
|
|
20
|
-
disagrees with the SDK. Some Latch guides retain older Python ranges or
|
|
21
|
-
compatibility-specific pre-release pins, especially the Snakemake v2 tutorial.
|
|
22
|
-
Never combine commands or imports from different tracks without checking their
|
|
23
|
-
version requirements.
|
|
24
|
-
|
|
25
|
-
## When to Use
|
|
26
|
-
|
|
27
|
-
Use this skill to:
|
|
28
|
-
|
|
29
|
-
- Create or maintain Python SDK workflows and task graphs
|
|
30
|
-
- Package and register Python, Nextflow, or Snakemake pipelines
|
|
31
|
-
- Configure task CPU, memory, storage, GPU, caching, retries, and timeouts
|
|
32
|
-
- Work with Latch Data through `LPath`, `LatchFile`, `LatchDir`, or the CLI
|
|
33
|
-
- Read or update Latch Registry projects, tables, and records
|
|
34
|
-
- Design workflow forms, launch plans, samplesheets, messages, and result links
|
|
35
|
-
- Stage and debug workflow images with `latch register --staging` and `latch develop`
|
|
36
|
-
- Launch and monitor workflows through Python or Latch MCP
|
|
37
|
-
- Discover and use ready-to-run Latch workflows
|
|
38
|
-
|
|
39
|
-
## Route to the Right Reference
|
|
40
|
-
|
|
41
|
-
Read only the references needed for the task:
|
|
42
|
-
|
|
43
|
-
| Need | Reference |
|
|
44
|
-
|---|---|
|
|
45
|
-
| Python workflows, tasks, maps, conditions, caching | `references/workflow-creation.md` |
|
|
46
|
-
| `LPath`, legacy file types, Latch URLs, data CLI | `references/data-management.md` |
|
|
47
|
-
| Registry reads, transactions, samplesheets | `references/registry.md` |
|
|
48
|
-
| CPU, memory, storage, GPU, dynamic resources | `references/resource-configuration.md` |
|
|
49
|
-
| Nextflow and Snakemake packaging | `references/nextflow-snakemake.md` |
|
|
50
|
-
| Metadata, forms, launch plans, messages, automations | `references/ui-and-automation.md` |
|
|
51
|
-
| Registration, development, execution, monitoring | `references/operations-and-debugging.md` |
|
|
52
|
-
| Ready-to-use workflows and `latch.verified` | `references/verified-workflows.md` |
|
|
53
|
-
| Remote MCP setup and tool workflow | `references/latch-mcp.md` |
|
|
54
|
-
|
|
55
|
-
Before relying on a symbol, run `scripts/inspect_latch_sdk.py` against the
|
|
56
|
-
target SDK version. It performs local imports only and does not authenticate or
|
|
57
|
-
make network requests.
|
|
58
|
-
|
|
59
|
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## Installation and Authentication
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60
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-
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61
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For a reproducible environment:
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-
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63
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```bash
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64
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uv venv --python 3.12
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65
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source .venv/bin/activate
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66
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uv pip install "latch==2.76.8"
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67
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```
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68
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-
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69
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On Windows, use WSL for the documented Linux workflow tooling.
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-
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71
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Authenticate through the supported OAuth flow; do not read, print, copy, or
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72
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parse `~/.latch/token` manually:
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-
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74
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```bash
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75
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latch login
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76
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latch workspace
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77
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```
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-
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79
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Select a workspace non-interactively when its numeric ID is already known:
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-
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81
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```bash
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latch workspace --id 12345
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83
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```
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84
|
-
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85
|
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`latch login` credentials are for the SDK and CLI. Latch MCP uses a separate
|
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86
|
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OAuth authorization and its credentials cannot be reused for general SDK
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87
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access.
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88
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-
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89
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## Fast Path
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90
|
-
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91
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Create and remotely register the maintained subprocess template:
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92
|
-
|
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93
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```bash
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94
|
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latch init covid-wf --template subprocess
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|
95
|
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latch register --yes --open covid-wf
|
|
96
|
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```
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97
|
-
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98
|
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Remote image building is the default. Use `--no-remote` only when a local
|
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99
|
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Docker daemon is available and a local build is intentional.
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100
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-
|
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101
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## Minimal Python Workflow
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103
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Keep workflow bodies declarative: invoke tasks and return their promises.
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104
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Perform computation and side effects inside tasks.
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105
|
-
|
|
106
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```python
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107
|
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from latch import small_task, workflow
|
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108
|
-
|
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109
|
-
|
|
110
|
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@small_task
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|
111
|
-
def reverse_complement(sequence: str) -> str:
|
|
112
|
-
table = str.maketrans("ACGTacgt", "TGCAtgca")
|
|
113
|
-
return sequence.translate(table)[::-1]
|
|
114
|
-
|
|
115
|
-
|
|
116
|
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@workflow
|
|
117
|
-
def reverse_complement_workflow(sequence: str) -> str:
|
|
118
|
-
"""Return the reverse complement of a DNA sequence."""
|
|
119
|
-
return reverse_complement(sequence=sequence)
|
|
120
|
-
```
|
|
121
|
-
|
|
122
|
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Use `@workflow(metadata)` when the generated interface needs custom labels,
|
|
123
|
-
sections, validation rules, samplesheets, or documentation links. Use `LatchFile` or
|
|
124
|
-
`LatchDir` for automatic task input staging and output upload; use `LPath` for
|
|
125
|
-
imperative remote path operations.
|
|
126
|
-
|
|
127
|
-
## Recommended Development Lifecycle
|
|
128
|
-
|
|
129
|
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1. **Inspect compatibility**
|
|
130
|
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- Confirm the installed SDK and Python version.
|
|
131
|
-
- Identify whether the project is Python, Nextflow, the legacy Snakemake
|
|
132
|
-
flag path, or the separately pinned Snakemake v2 tutorial track.
|
|
133
|
-
|
|
134
|
-
2. **Define a typed interface**
|
|
135
|
-
- Annotate every workflow and task input and output.
|
|
136
|
-
- Keep module import time free of network calls, data mutations, and secret
|
|
137
|
-
retrieval. Isolate documented exceptions such as `workflow_reference`,
|
|
138
|
-
which resolves the active workspace when its decorator is evaluated.
|
|
139
|
-
- Use dataclasses and enums for structured parameters.
|
|
140
|
-
|
|
141
|
-
3. **Configure metadata and resources**
|
|
142
|
-
- Match metadata parameter keys to the workflow signature.
|
|
143
|
-
- Start with named task decorators, then use `custom_task` only when measured
|
|
144
|
-
requirements justify it.
|
|
145
|
-
|
|
146
|
-
4. **Validate in the execution image**
|
|
147
|
-
|
|
148
|
-
Fresh Nextflow and Snakemake projects must generate their
|
|
149
|
-
version-compatible Python entrypoint before staging. In SDK 2.76.8, the
|
|
150
|
-
staging branch does not generate one from `--nf-script` or `--snakefile`.
|
|
151
|
-
|
|
152
|
-
```bash
|
|
153
|
-
latch register --staging .
|
|
154
|
-
latch develop .
|
|
155
|
-
```
|
|
156
|
-
|
|
157
|
-
Re-run staging registration after changing the Dockerfile or dependencies.
|
|
158
|
-
Edits made inside the development container are not synced back.
|
|
159
|
-
|
|
160
|
-
5. **Register deliberately**
|
|
161
|
-
|
|
162
|
-
```bash
|
|
163
|
-
latch register --yes --open .
|
|
164
|
-
```
|
|
165
|
-
|
|
166
|
-
Useful controls:
|
|
167
|
-
|
|
168
|
-
```bash
|
|
169
|
-
latch register --workspace-id 12345 .
|
|
170
|
-
latch register --mark-as-release .
|
|
171
|
-
latch register --workflow-module wf.custom_entrypoint .
|
|
172
|
-
```
|
|
173
|
-
|
|
174
|
-
Duplicate registration exits with status `2`; it is not the same as a build
|
|
175
|
-
failure.
|
|
176
|
-
|
|
177
|
-
6. **Launch only after reviewing cost and parameters**
|
|
178
|
-
- Prefer the Console or Latch MCP for interactive operation.
|
|
179
|
-
- Prefer `latch_cli.services.launch.launch_v2` for Python automation.
|
|
180
|
-
- Do not use the deprecated `latch launch` CLI as a new integration pattern.
|
|
181
|
-
|
|
182
|
-
7. **Monitor and verify**
|
|
183
|
-
- Check terminal status, task logs, result links, and scientific outputs.
|
|
184
|
-
- Treat successful orchestration as necessary but not sufficient scientific
|
|
185
|
-
validation.
|
|
186
|
-
|
|
187
|
-
## Operational Safety
|
|
188
|
-
|
|
189
|
-
- Ask for confirmation before launching paid compute, especially GPU or large
|
|
190
|
-
batch runs.
|
|
191
|
-
- Ask for confirmation before `LPath.rmr`, `latch rmr`, Registry deletion, or
|
|
192
|
-
overwriting shared destinations.
|
|
193
|
-
- Never log secrets, SDK tokens, signed URLs, or secret values.
|
|
194
|
-
- Call `get_secret()` only inside a task, use the returned value only for its
|
|
195
|
-
intended service, and never return it as workflow output.
|
|
196
|
-
- Do not pass untrusted strings through shell commands. Prefer argument lists
|
|
197
|
-
with `subprocess.run(..., check=True)`.
|
|
198
|
-
- Pin the SDK and workflow dependencies for releases. Upgrade only after
|
|
199
|
-
reviewing the changelog and re-running staging tests.
|
|
200
|
-
- Treat generated files as generated: customize the documented extension file
|
|
201
|
-
rather than editing output that the CLI will overwrite.
|
|
202
|
-
|
|
203
|
-
## Inspect the Installed SDK
|
|
204
|
-
|
|
205
|
-
From this skill directory:
|
|
206
|
-
|
|
207
|
-
```bash
|
|
208
|
-
uv run --no-project --python 3.12 --with "latch==2.76.8" \
|
|
209
|
-
python scripts/inspect_latch_sdk.py
|
|
210
|
-
```
|
|
211
|
-
|
|
212
|
-
Use JSON output for automated comparisons:
|
|
213
|
-
|
|
214
|
-
```bash
|
|
215
|
-
uv run --no-project --python 3.12 --with "latch==2.76.8" \
|
|
216
|
-
python scripts/inspect_latch_sdk.py --json
|
|
217
|
-
```
|
|
218
|
-
|
|
219
|
-
## Authoritative Sources
|
|
220
|
-
|
|
221
|
-
- Documentation index: https://wiki.latch.bio/llms.txt
|
|
222
|
-
- Workflow and SDK guides: https://wiki.latch.bio/workflows/overview
|
|
223
|
-
- SDK API reference: https://wiki.latch.bio/reference/sdk
|
|
224
|
-
- PyPI package: https://pypi.org/project/latch/
|
|
225
|
-
- SDK 2.76.8 release source: https://github.com/latchbio/latch/tree/0faa9dcd8186444ac008f50adf95d43f0fa30e06
|
|
226
|
-
- SDK changelog: https://github.com/latchbio/latch/blob/0faa9dcd8186444ac008f50adf95d43f0fa30e06/CHANGELOG.md
|
|
227
|
-
- Latch Console: https://console.latch.bio
|