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    138 repositories

    • BERIL-research-observatory

      Public
      BERIL Research Observatory - Exploring microbial ecology with the KBase Data Lakehouse
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •11•14•20•23•Updated Jun 22, 2026Jun 22, 2026

    • craft

      Public
      CRAFT — Co-Scientist Research Assessment & Framing Tools. Platform for the BERIL research-assessment skill stack (beril-adversarial + beril-paper-writer + beril…
      Python
      •
      MIT License
      •0•2•0•0•Updated Jun 11, 2026Jun 11, 2026

    • beril-adversarial-skill

      Public
      Harsh adversarial reviewer for BERIL deployments
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • beril-paper-writer-skill

      Public
      Python
      •
      MIT License
      •0•0•1•0•Updated Jun 11, 2026Jun 11, 2026

    • beril-presentation-maker-skill

      Public
      BERIL Presentation Maker — drafts evidence-grounded scientific presentations (talks + posters) from BERDL analysis projects, in KBase brand. Distributed as a Cl…
      Python
      •
      MIT License
      •0•0•1•0•Updated Jun 11, 2026Jun 11, 2026

    • cdm_iqtree

      Public
      iqtree image tor the cdm task service
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated May 26, 2026May 26, 2026

    • cdm_tool_skeleton

      Public
      Template skeleton for CTS (CDM Task Service) bioinformatics tool wrappers
      Python
      •
      MIT License
      •0•1•3•0•Updated May 23, 2026May 23, 2026

    • cdm_skani_gtdb

      Public
      CTS wrapper for skani paired with GTDB R232 reference sketches (reuses cdm_gtdbtk refdata bundle).
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 22, 2026May 22, 2026

    • cdm_skani

      Public
      CTS wrapper for skani (ANI calculator). Generic, no bundled refdata.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 22, 2026May 22, 2026

    • cdm_bakta_proteins

      Public
      CTS job wrapper for bakta_proteins (annotate pre-called proteins without re-predicting genes). Sibling to cdm_bakta.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 22, 2026May 22, 2026

    • cdm_gtdbtk

      Public
      CTS job wrapper for GTDB-Tk (taxonomic classification of bacterial/archaeal genomes against GTDB).
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 22, 2026May 22, 2026

    • cdm_bakta

      Public
      CTS job wrapper for Bakta bacterial genome annotation
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 15, 2026May 15, 2026

    • cdm_psortb

      Public
      CTS job wrapper for PSORTb bacterial protein subcellular localization
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 14, 2026May 14, 2026

    • cdm_kofamscan

      Public
      CTS job wrapper for KofamScan KEGG KO annotation
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 14, 2026May 14, 2026

    • cdm_mmseqs2

      Public
      CTS job wrapper for MMseqs2 sequence clustering
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 14, 2026May 14, 2026

    • CEPHplaypen

      Public
      Futzing around with CEPH investigations
      Python
      •
      MIT License
      •0•0•0•0•Updated May 4, 2026May 4, 2026

    • narrative_llm_agent

      Public
      A set of tools to use LLMs to help build and execute a KBase Narrative workflow.
      Jupyter Notebook
      •
      MIT License
      •0•0•11•2•Updated Mar 13, 2026Mar 13, 2026

    • kbase-security-dashboard

      Public
      A dashboard for KBase security
      Python
      •
      MIT License
      •0•0•1•5•Updated Mar 1, 2026Mar 1, 2026

    • vaast-app

      Public
      VAAST: Visual AI Assistant SynBio Toolkits
      Python
      •0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • opal-orchestrator

      Public
      OPAL Orchestration Chatbot - AI-powered cross-lab research planning for DOE national laboratories
      Python
      •0•0•0•3•Updated Feb 9, 2026Feb 9, 2026

    • kbase-ui-components

      Public
      KBase-created React components for usage in kbase uis.
      TypeScript
      •
      MIT License
      •1•1•0•3•Updated Jan 21, 2026Jan 21, 2026

    • kbase-ui-lib

      Public
      TypeScript
      •
      MIT License
      •0•1•0•3•Updated Jan 21, 2026Jan 21, 2026

    • cdm_jupyterlab_brand_extension

      Public
      Example Jupyter extension providing custom branded logos
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • CDM_Tasks_jplfaria

      Public
      To make it easy to share progress on CDM related tasks
      Jupyter Notebook
      •0•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • KBase_CDM_Ontologies

      Public
      KBase CDM Ontologies Pipeline - Containerized pipeline for processing and merging biological ontologies at scale
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • cdm-ts-plugin-template

      Public
      0•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • security_dashboard

      Public
      security_dashboard
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

    • kbase-chat-assistant

      Public
      KBase help chat assistant
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

    • kbaseincubator.github.io

      Public
      HTML
      •
      MIT License
      •0•0•0•1•Updated Feb 21, 2025Feb 21, 2025

    • catalog_test_module

      Public
      A repository used for unit tests of the catalog
      MIT License
      •1•0•0•0•Updated Jan 27, 2025Jan 27, 2025
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