Skills/PyPI/mcp-biomodelling-servers

mcp-biomodelling-servers@2.5.2

CAUTION· not started

Publisher claims: "MCP servers for NeKo signalling-network construction, MaBoSS Boolean simulation, PhysiCell configuration, and BioMASS ODE construction" Observed in sandbox: no network, touches nothing outside the project, writes no memory.

Registry PyPI (MCP server)Publisher marcorusc · publishing for 212 daysInstalls 1,519Last detonated 8d ago
What would fix thisWatchDispute verdict

Coverage

Not started: dependency install failed; the server itself was not observed.
Tested
the dependency install step · every file read, file written and host contacted by what ran
Not tested
server startup · the tool list · tool behavior

What this means for the label: Caution here covers what ran. The server's tools were not exercised with a real credential, so nothing about their behavior is asserted; the credential summary below says what to do with that.

Before you give it your token

Code inventory arrives with this version's next honeypot run.
It will ask for
unknown until the next run
Where it talks to
unknown until the next run
What the honeypot saw
no credential files read · no network
What we could not test
server startup · the tool list · tool behavior

Not enough was observed to say yet. Not started: dependency install failed; the server itself was not observed. This version's code has not been inventoried for credentials and hosts either; both arrive with its next honeypot run (popular servers first). `vet-skills try mcp-biomodelling-servers` runs it now and prints the full answer.

Never paste a credential into a chat, a ticket or a report, including ours. How the guard holds it.

Is [email protected] safe to install?

KillerSkills ran it in the KillerSkills honeypot sandbox (2 scenarios; not started: dependency install failed; the server itself was not observed) on 2026-11-07 and scored it 77/100 (Caution). It is not known to be malicious, but it has behaviour or code a security policy should decide on before install. Notable findings: Access to sensitive file paths; Access to sensitive file paths; Access to sensitive file paths. Summary: no network, touches nothing outside the project, writes no memory.

Behavior trace

Honeypot run · 0 s · 2 scenarios · 0 deviations
t+CategoryObserved action
0.0sprocessno install scripts in bundle
0.1sprocessdependency install exit 1
0.2sprocessexec /usr/bin/date
0.2sprocessexec /usr/bin/timeout
0.2sprocessexec .venv/bin/mcp-neko-server
0.2sclaimedno tools/list reply (exit 0)
0.2sprocessscript backend runs setup only
0.2sprocessno install scripts to re-run

Static findings

HIGH
Access to sensitive file pathspyproject.toml:103 · Access to sensitive file paths — SSH keys, AWS credentials, env files, or system files"**/.env",Fix: Stop enumerating or reading credential locations; take secrets from a declared environment variable the user sets on purpose.
AST05
MEDIUM
Python subprocess execution detectedBioMASS/services/artifacts.py:98 · Python subprocess execution detectedprocess = subprocess.Popen(Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
File type combined with upload actionPhysiCell/server.py:2394 · File type combined with upload action — agent may exfiltrate local data filesfilename: NonEmptyString = Field(default="PhysiCell_settings.xml", description="Output filename for the XML configuration file."),Fix: Remove the call, or declare the host in frontmatter and explain in the README what is sent and why.
AST07
HIGH
Access to sensitive file pathspyproject.toml:133 · Access to sensitive file paths — SSH keys, AWS credentials, env files, or system files"**/.env.*",Fix: Stop enumerating or reading credential locations; take secrets from a declared environment variable the user sets on purpose.
AST05
MEDIUM
Process kill commandMaBoSS/services/engine.py:8 · Process kill command — agent can terminate processeskill the server. Results keep the file-backed interface of pyMaBoSS's ownFix: Build commands from fixed arguments; do not interpolate untrusted strings into a shell.
AST05
MEDIUM
Python subprocess execution detectedMaBoSS/services/engine.py:27 · Python subprocess execution detectedreturn subprocess.run(Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
HIGH
Access to sensitive file pathspyproject.toml:104 · Access to sensitive file paths — SSH keys, AWS credentials, env files, or system files"**/.env.*",Fix: Stop enumerating or reading credential locations; take secrets from a declared environment variable the user sets on purpose.
AST05
HIGH
Access to sensitive file pathspyproject.toml:132 · Access to sensitive file paths — SSH keys, AWS credentials, env files, or system files"**/.env",Fix: Stop enumerating or reading credential locations; take secrets from a declared environment variable the user sets on purpose.
AST05
MEDIUM
File type combined with upload actionPhysiCell/server.py:2487 · File type combined with upload action — agent may exfiltrate local data filesfilename: NonEmptyString = Field(default="cell_rules.csv", description="Output filename for the cell rules CSV file."),Fix: Remove the call, or declare the host in frontmatter and explain in the README what is sent and why.
AST07

Cost to the agent

Instructions loaded
≈76 tok
1 file · 81 in bundle
Tool list per prompt
≈0 tok
0 tools · 0 per tool
Handshake
no reply
launch to tools/list, stdio
Undocumented tools
0
description under 20 chars · avg 0

Tokens estimated at four characters each. The tool list is re-read by the agent on every turn, so it is the number to compare between servers that do the same job: ranked across the index.

Known vulnerabilities

No advisories in OSV for mcp-biomodelling-servers@2.5.2 as of 7 h ago. This is the package itself, not its dependencies.

What would make this Verified

3 points to 80 · weights: behavior 45%, static 25%, prompt 15%, publisher 15%
  1. Unclaimed publisher≈ +8 on the totalClaim marcorusc: a verified publisher gets +50 on publisher trust. It is free and usually instant with GitHub sign-in.
  2. Access to sensitive file paths≈ +4 on the totalStop enumerating or reading credential locations; take secrets from a declared environment variable the user sets on purpose.
  3. New publisher≈ +3 on the totalTime clears this on its own after 14 and 30 days. Claiming the handle (+50) is the fastest way past it.
  4. Python subprocess execution detected≈ +2 on the totalBuild commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
  5. File type combined with upload action≈ +2 on the totalRemove the call, or declare the host in frontmatter and explain in the README what is sent and why.
  6. Process kill command≈ +2 on the totalBuild commands from fixed arguments; do not interpolate untrusted strings into a shell.
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