BioMASS ODE Model Builder

Construct, inspect, visualize, and simulate evidence-backed ODE models with BioMASS

Connector by marcorusc · GitHub account verified by the MCP Registry

IndexedGPL-3.0Local (stdio)★ 20

Install

Works with Claude Code, Codex, VS Code, Cursor, Windsurf, Claude Desktop. Read the repository before you give any tool access to your data.

npx agentmarket install connector/marcorusc-biomass

Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.

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About

Construct, inspect, visualize, and simulate evidence-backed ODE models with BioMASS

Use cases: data-analysis

Reviews

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Permissions

What this server can do and what it asks for, from its tool list, install config and code. Checked Oct 25, 2026.

Tools: 8 read · 13 write · 1 delete · 1 not yet classified
Secrets: None asked for
Install scripts: None found
Runs as: Python package

Tools by what they do 23

Read from the source code; the running server may list different tools.

Read 8 · Look things up without changing anything.

export_model_graph
inspect_model
inspect_reactions
list_artifact_sessions
list_generated_files
list_sessions
validate_model
visualize_model

Write 13 · Create, change, send or run things.

build_reactions
close_session
configure_model
create_session
export_model_bundle
generate_model
import_neko_handoff
import_text
import_text_file
restore_session
run_simulation
set_evidence

Show 1 more tools

set_reactions

Delete 1 · Delete, drop, revoke or wipe things.

clean_generated_files

Not yet classified 1 · We could not tell from the name and description.

guarded

Network hosts it talks to 1

github.com · found in code

Files it touches

Any path the agent passes to its tools

Tools (23)

Read from the source code; the running server may differ. Descriptions are the server’s own words; hidden characters are shown as [U+…].

build_reactions
Construct or edit reactions from a conversation, network, or existing file. Read docs://biomass/model_editing for template participants and examples. Scientific interpretation belongs to the calling agent. Metadata is optional; new records are unreviewed unless the agent explicitly annotates them.
clean_generated_files
Delete generated artifacts while preserving authoring state and source lineage.
close_session
Close a session, retaining its authoring snapshot and artifacts on disk.
configure_model
Configure observables, numerical defaults, conditions, time, and unit provenance.
create_session
Create an isolated, durable BioMASS authoring session.
export_model_bundle
Export a selected revision, evidence, graphs, runs, and reproduction script.
export_model_graph
Export BioMASS's directed species projection as DOT.
generate_model
Generate a new immutable BioMASS revision from the current authoring state.
guarded
import_neko_handoff
Verify and import a NeKo network and its complete reference provenance.
import_text
Import or replace standalone text and its line provenance atomically. Read docs://biomass/reaction_syntax and docs://biomass/authoring_examples before writing text. Only the documented Text2Model subset is supported.
import_text_file
Read a Text2Model file verbatim for expansion or editing with build_reactions. Source files are not modified. Read docs://biomass/model_editing for the versioned editing interface and preservation of line-based parameters.
inspect_model
Inspect authoring state, evidence, retained revisions, and edge coverage.
inspect_reactions
Inventory stable reaction IDs, text lines, and generated parameter names. Imported reactions initially use IDs such as line_3. This tool also works on an empty model or a document awaiting dependency repairs.
list_artifact_sessions
Discover artifact sessions saved on disk across server restarts.

Show 8 more tools

list_generated_files
List all nested session artifacts, including snapshots and diagnostics.
list_sessions
List active sessions and current generated revisions.
restore_session
Restore authoring state from a previously created BioMASS session.
run_simulation
Run bounded exploratory simulation, recording every condition's numerical values.
set_evidence
Store agent-extracted evidence, including contradictory or inaccessible sources.
set_reactions
Replace the COMPLETE ordered reaction list, retaining prior records explicitly. Before authoring, read docs://biomass/reaction_syntax, docs://biomass/authoring_examples, docs://biomass/network_to_reactions, and docs://biomass/model_editing for incremental edits that preserve configuration. Signed edges and PMID identifiers alone do not justify mechanisms or kinetics.
validate_model
Report syntax and optional generation validity independently of scientific validity.
visualize_model
Visualize a generated species graph without requiring simulation or calibration.

Signals

Stars: 20
Forks: 6
Open issues: 0
Contributors: 3
Weekly downloads: 423
Last commit (this folder): Oct 22, 2026 (5 days ago)
Last release: Oct 22, 2026 (5 days ago)
Last package publish: Oct 22, 2026 (5 days ago)

From GitHub (fetched Oct 24, 2026) and the package registry.

Details

Registry name: io.github.marcorusc/BioMASS
Version: 2.5.1
Auth: No auth
Packages: pypi mcp-biomodelling-servers
License: GPL-3.0
Repository: github.com/marcorusc/mcp-biomodelling-servers
First seen: Oct 24, 2026
Last checked: Oct 24, 2026
Source: Official MCP Registry github-graphql

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Cite this page

BioMASS ODE Model Builder MCP server. Agent Mart. https://agentmart.dev/connectors/marcorusc-biomass (last updated 2026-10-24)