Agentic Biological Modelling

Plugin agentic-system-for-modelling in marcorusc/agentic_system_for_modelling. Commands read from the repo's manifest — 12 days ago.

Skills (12)

• biomass-workflow

  Route authorized ODE construction, Text2Model editing, BioMASS validation, provisional candidate preservation and approved exploratory simulation through the isolated ODE specialist.

• checkpoint-model

  Checkpoints the biological modelling project before compaction, clearing, stage transition, or session exit.

• maboss-workflow

  Operational guide for the MaBoSS MCP server — sessions, loading a BNET or NeKo handoff, inspecting nodes/rules/rates, restricting output nodes, summary readouts, running and analysing durable simulation runs, mutation studies, and debugging slow or hanging runs. Preloaded into the boolean-dynamics-m

• model-archive

  Create a named, Git-backed archive of the current biological-model state. Use only when the user explicitly invokes /model-archive and supplies an archive name.

• model-list

  List the currently loaded biological-model attempt and named Git-backed archives. Use only when the user invokes /model-list or asks which model states are available.

• model-restart

  Safely discard the current modelling direction and reset scientific state to pristine templates. Use only when the user explicitly invokes /model-restart.

• model-restore

  Restore a named biological-model archive without rolling back agent configuration or inputs. Use only when the user explicitly invokes /model-restore with an archive name.

• neko-workflow

  Operational guide for the NeKo MCP server — session/network creation, connectivity auditing, connection strategies (connect_targeted_nodes, bridge_components, apply_global_connection), history navigation, export, and debugging exploded or disconnected networks. Preloaded into the network-curator sub

• physicell-workflow

  Operational guide for the PhysiCell MCP server — domain, substrate, and cell-type setup, parameter and substrate-interaction patches, signal-behavior rules, PhysiBoSS integration, and XML/cell-rules export. Preloaded into the multicellular-configurator subagent; in the main session, delegate PhysiCe

• review-literature-evidence

  Reviews PubMed evidence for biological interactions and model assumptions using an explicit evidence matrix.

• validate-stage

  Coordinates independent scientific review and reproducibility audit before approving a modelling-stage transition.

• biomodelling-orchestrator

  Coordinate this repository's staged biological-modelling workflow, specialist routing, approvals, lineage, and durable state. Use for end-to-end model work or deciding the next permitted stage.