KBase Incubator Projects
Official@kbaseincubator
This organization is for beginning or alpha-quality KBase repositories. Use at your own risk.
Agent Skills by KBase Incubator Projects
Showing 13 vetted skills indexed across 1 GitHub repositories.
kbaseincubatorberdl_start
Guide users through the BERIL Research Observatory and its BERDL data lakehouse.
kbaseincubatorremote-compute
Execute arbitrary bash scripts on remote KBase compute nodes via CTS.
kbaseincubatorsubmit
Submit projects to the BERDL lakehouse after validation and AI review.
kbaseincubatorphenix
Orchestrate protein structure determination and refinement with X-ray crystallography and cryo-EM data.
kbaseincubatorberdl-minio
Configure the MinIO client and transfer files with BERDL credentials.
kbaseincubatorpitfall-capture
Detect and document BERDL data analysis pitfalls in docs/pitfalls.md.
kbaseincubatorliterature-review
Search and synthesize biological literature across PubMed, arXiv, bioRxiv, and Google Scholar.
kbaseincubatorberdl-discover
Introspect BERDL databases via API and generate Markdown documentation modules.
kbaseincubatorlinkml-schema
Generate LinkML schema YAML from markdown, Excel, or text descriptions.
kbaseincubatorsuggest-research
Analyze completed projects and BERDL data to recommend novel research topics.
kbaseincubatorberdl
Query KBase BERDL Data Lakehouse for microbial genomic and biochemical data via SQL.
kbaseincubatorberdl-query
Execute SQL queries against a remote BERDL Spark cluster via secure proxy.
kbaseincubatorsynthesize
Synthesize project analysis outputs into a structured REPORT.md with literature context.
Frequently Asked Questions About KBase Incubator Projects
FAQPage SchemaWhat specific research tasks are enabled by these repositories?▼
These repositories enable microbial genomic data querying, protein structure determination, and automated synthesis of biological literature. Users can perform complex SQL operations on the BERDL lakehouse, manage MinIO file transfers, and generate structured research reports by integrating experimental outputs with external academic databases like PubMed and arXiv.
Which personas benefit most from these research modules?▼
Bioinformaticians, structural biologists, and computational researchers working within the KBase ecosystem are the primary target users. These modules are designed for scientists requiring high-performance access to microbial datasets, protein refinement pipelines, and systematic literature review capabilities to support novel research discovery and data documentation.
What are the prerequisites for accessing the BERDL data lakehouse?▼
Access requires valid KBase credentials and configuration of the MinIO client for secure file transfers. Users must also ensure their project environments are compatible with the BERDL Spark cluster proxy and that their data schemas adhere to the LinkML standards required for successful submission to the incubator.