# scientific-agent-skills | K-Dense | Knowledge Base | Instagit

A set of ready to use Agent Skills for research, science, engineering, analysis, finance and writing.

GitHub Stars: 21.4k

Repository: https://github.com/K-Dense-AI/scientific-agent-skills

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## Articles

### [PyTDC vs DeepChem for ADMET Prediction: Key Differences and When to Use Each](/K-Dense-AI/scientific-agent-skills/pytdc-vs-deepchem-admet-prediction)

Compare PyTDC's benchmark datasets and DeepChem's ML stack for ADMET prediction. Learn key differences and choose the right tool for your project.

- Tags: comparison
- Published: 2026-05-14

### [How to Handle Censored Data with scikit-survival for Time-to-Event Modeling](/K-Dense-AI/scientific-agent-skills/handle-censored-data-scikit-survival-time-to-event)

Learn to handle censored data in time-to-event modeling using scikit-survival. Discover how scikit-survival natively respects censoring for advanced survival analysis.

- Tags: how-to-guide
- Published: 2026-05-14

### [Key Configuration Options for Modal Serverless GPU Workloads: A Complete Guide](/K-Dense-AI/scientific-agent-skills/modal-serverless-gpu-workloads-configuration-options)

Master Modal serverless GPU workloads. Explore key configuration options like gpu, cpu, and memory with the @app.function decorator for efficient distributed training and inference. Optimize cost and scale.

- Tags: how-to-guide
- Published: 2026-05-14

### [How the gtars Genomic Tokenization System Works for Machine Learning: A Technical Deep Dive](/K-Dense-AI/scientific-agent-skills/gtars-genomic-tokenization-system-ml-applications)

Discover how the gtars genomic tokenization system uses a Rust interval tree to convert genomic coordinates into integer tokens for efficient machine learning model training.

- Tags: deep-dive
- Published: 2026-05-14

### [Limitations of the aeon Time Series Library Compared to statsmodels for Forecasting](/K-Dense-AI/scientific-agent-skills/aeon-vs-statsmodels-time-series-forecasting-limitations)

Compare aeon vs statsmodels for time series forecasting. Discover aeon's machine learning strengths and statsmodels' statistical rigor, diagnostics, and reporting advantages.

- Tags: comparison
- Published: 2026-05-14

### [How to Debug Connection Issues with the Benchling API Integration: A Complete Guide](/K-Dense-AI/scientific-agent-skills/debug-benchling-api-connection-issues)

Debug Benchling API integration connection issues. Learn to validate API keys, environment variables, and test connectivity to resolve authentication, network, or rate-limiting problems.

- Tags: how-to-guide
- Published: 2026-05-14

### [Differences Between GPU Acceleration Libraries in the Optimize for GPU Skill](/K-Dense-AI/scientific-agent-skills/optimize-gpu-skill-gpu-acceleration-libraries)

Explore GPU acceleration libraries in K-Dense-AI's Optimize for GPU skill. Learn about RAPIDS, CuPy, cuDF, Warp, and KvikIO for efficient CUDA array data sharing and zero-copy performance.

- Tags: deep-dive
- Published: 2026-05-14

### [How the Open Notebook Skill Integrates with Self‑Hosted AI Providers: A LangChain & Esperanto Guide](/K-Dense-AI/scientific-agent-skills/open-notebook-skill-self-hosted-ai-integration)

Learn how the Open Notebook skill integrates with self hosted AI providers using LangChain and Esperanto. Connect seamlessly to local models via HTTP endpoints.

- Tags: how-to-guide
- Published: 2026-05-14

### [Common Causes of pyOpenMS Installation Failures: A Troubleshooting Guide](/K-Dense-AI/scientific-agent-skills/common-pyopenms-installation-failures)

Overcome pyOpenMS installation failures. Learn common causes like missing build tools, incompatible Python, or system libraries. Fix your setup now.

- Tags: how-to-guide
- Published: 2026-05-14

### [How to Configure FluidSim CFD for 2D vs 3D Turbulence Simulations](/K-Dense-AI/scientific-agent-skills/fluidsim-cfd-configure-2d-vs-3d-turbulence)

Learn how to configure FluidSim CFD for 2D and 3D turbulence simulations. Discover how to import solver classes and set spatial resolution for accurate results.

- Tags: how-to-guide
- Published: 2026-05-14

### [Security Implications of API Keys in the Scientific-Skills Framework: A Code-Level Analysis](/K-Dense-AI/scientific-agent-skills/scientific-skills-framework-api-key-security)

Explore security implications of API keys in the scientific-skills framework. Learn how the framework prevents hardcoded secrets, prioritizes explicit arguments, and restricts file discovery.

- Tags: deep-dive
- Published: 2026-05-14

### [How to Use the Neuropixels-Analysis Toolkit for Spike Sorting Quality Control](/K-Dense-AI/scientific-agent-skills/neuropixels-analysis-toolkit-spike-sorting-qc)

Master spike sorting quality control with Neuropixels-Analysis. Automate preprocessing, motion correction, and AI curation with this powerful Python toolkit.

- Tags: how-to-guide
- Published: 2026-05-14

### [How scVI-tools Reference Mapping (scArches) Works for Single-Cell Data Integration](/K-Dense-AI/scientific-agent-skills/scvi-tools-scarches-single-cell-data-integration)

Learn how scVI-tools reference mapping scArches integrates single-cell data. Project new datasets into a pretrained latent space for rapid integration without full model retraining.

- Tags: deep-dive
- Published: 2026-05-14

### [Common Issues Running TileDB-VCF on Cloud Storage (S3, Azure, GCS): Troubleshooting Guide](/K-Dense-AI/scientific-agent-skills/common-issues-tiledb-vcf-cloud-storage)

Troubleshoot common TileDB-VCF issues on cloud storage S3 Azure GCS. Learn essential configurations for credentials URI formatting and concurrency to optimize performance and avoid errors.

- Tags: how-to-guide
- Published: 2026-05-14

### [How to Set Up OAuth Authentication for Protocols.io API Integration: A Complete Guide](/K-Dense-AI/scientific-agent-skills/protocols-io-api-oauth-authentication-setup)

Learn to set up OAuth authentication for Protocols.io API integration using the Authorization Code grant flow. Securely authenticate your applications and access API resources.

- Tags: how-to-guide
- Published: 2026-05-14

### [Polars vs Pandas for Genomic Data Processing: Performance Architecture and Migration Guide](/K-Dense-AI/scientific-agent-skills/polars-vs-pandas-genomic-data-performance)

Discover Polars vs Pandas for genomic data processing. Polars offers massive speedups with columnar storage, lazy evaluation, and parallelism. Learn migration tips.

- Tags: performance
- Published: 2026-05-14

### [How to Integrate LaminDB with Nextflow and Snakemake Workflows](/K-Dense-AI/scientific-agent-skills/integrate-lamin-db-nextflow-snakemake-workflows)

Integrate LaminDB with Nextflow and Snakemake workflows. Seamlessly track data lineage and manage artifacts using ln.track() and ln.Artifact for robust scientific analysis pipelines.

- Tags: how-to-guide
- Published: 2026-05-14

### [SimPy Resource vs PriorityResource vs PreemptiveResource: Complete Guide to Resource Scheduling](/K-Dense-AI/scientific-agent-skills/simpy-resource-priorityresource-preemptive-resource-differences)

Understand SimPy Resource, PriorityResource, and PreemptiveResource differences. Learn how to manage queues and preemption for efficient scheduling in your simulations.

- Tags: deep-dive
- Published: 2026-05-14

### [How the Bionty Plugin Integrates Biological Ontologies into LaminDB](/K-Dense-AI/scientific-agent-skills/bionty-plugin-integrate-ontologies-lamin-db)

Learn how the Bionty plugin integrates biological ontologies into LaminDB for standardized gene, cell type, tissue, and disease validation and annotation via a unified Python API.

- Tags: how-to-guide
- Published: 2026-05-14

### [Best Practices for Querying Large Genomic Variant Datasets in TileDB-VCF: A Parallel Query Guide](/K-Dense-AI/scientific-agent-skills/best-practices-querying-tiledb-vcf-parallel)

Optimize genomic variant queries with TileDB-VCF. Learn best practices for parallel querying of large datasets achieving sub-second query times with partitioning and streaming.

- Tags: best-practices
- Published: 2026-05-14

### [How to Configure LaminDB with PostgreSQL or SQLite for Production](/K-Dense-AI/scientific-agent-skills/configure-lamin-db-postgresql-sqlite-production)

Learn how to configure LaminDB for production using PostgreSQL or SQLite. This guide covers installation, initialization, connection, and schema migration deployment for a robust setup.

- Tags: how-to-guide
- Published: 2026-05-14

### [TileDB-VCF vs Traditional VCF/BCF File Formats: A Technical Comparison](/K-Dense-AI/scientific-agent-skills/tile-db-vcf-vs-traditional-vcf-bcf-file-formats)

Discover the technical differences between TileDB-VCF and traditional VCF/BCF formats. Explore TileDB-VCF's advanced features for genomic variant storage, including incremental ingestion and parallel queries.

- Tags: analysis
- Published: 2026-05-14

### [How LaminDB Artifact Versioning and Lineage Tracking Works: A Technical Guide](/K-Dense-AI/scientific-agent-skills/how-does-lamin-db-artifact-versioning-and-lineage-tracking-work)

Discover how LaminDB artifact versioning and lineage tracking ensures full reproducibility. Learn how it links datasets, code, and environments for complete tracking.

- Tags: how-to-guide
- Published: 2026-05-14