Install verification: runtime verified (L5) · tested on dsh 0.2.1-rc.2 · last checked Install verification details →
What it doesAI
Builds and validates genome-scale metabolic models from whole-genome protein FASTA, with gap-filling and SBML plus model-card reports.
- Turns whole-genome protein FASTA into a draft GEM automatically
- Runs validation and gap-filling to repair model networks
- Exports SBML models plus a human-readable model card report
Capability tags are AI-inferred or rule-extracted from the README (see badge) — vocabulary-limited, not install-verified. AI = inferred; README = literal keyword from the readme.
Installation
dsh plugin --profile web add @dsh-bio/dsh-bio-gemInstall method: npm · runtime verified (L5)
Verification & Compatibility
Grouped by plugin version: each card lists the dsh versions actually tested against that artifact version and their install verdicts (L5 wins). Untested combinations are omitted — absence means untested, never assumed compatible. L1–L3 are a plugin-level static archive (independent of the dsh version — the same verdict on every dsh row): they sit in each row's level grid next to L4/L5, marked "static", while their evidence is stored once per plugin inside that row's "checks & evidence" instead of being duplicated per version.
External credentials (plugin-level): none detected
○ The author declares no dsh version requirement — install is not blocked by version.
| plugin ＼ dsh | dsh 0.2.1-rc.2 current | dsh 0.2.1-alpha.4 | dsh 0.2.1-alpha.2 |
|---|---|---|---|
| 0.1.18 | ✓ | ✓ | ✓ |
| v0.1.18 | · | · | · |
0.1.18npm✓ 3 runtime-verified2026-10-19
@dsh-bio/dsh-bio-gem
✓dsh 0.2.1-rc.2current2026-10-19L5 · runtime verified
- • Node.js: v24.14.0
- • DSH: 0.2.1-rc.2
- • Plugin artifact: npm · @dsh-bio/dsh-bio-gem@0.1.18
ID: dsh-bio-gem@0.1.18@dsh0.2.1-rc.2 · profile: l4-sandbox
Issued: 2026-10-19 · expires: 2026-10-26
View checks & evidence
active in loader tree (150 entries)
L1–L3 are plugin-level static conclusions (baseline, identical across dsh versions): evidence is stored once per plugin.
✓dsh 0.2.1-alpha.42026-10-17L5 · runtime verified
- • Node.js: v24.14.0
- • DSH: 0.2.1-alpha.4
- • Plugin artifact: npm · @dsh-bio/dsh-bio-gem@0.1.18
ID: dsh-bio-gem@0.1.18@dsh0.2.1-alpha.4 · profile: l4-sandbox
Issued: 2026-10-17 · expires: 2026-10-24
View checks & evidence
active in loader tree (150 entries)
L1–L3 are plugin-level static conclusions (baseline, identical across dsh versions): evidence is stored once per plugin.
✓dsh 0.2.1-alpha.22026-10-15L5 · runtime verified
- • Node.js: v24.14.0
- • DSH: 0.2.1-alpha.2
- • Plugin artifact: npm · @dsh-bio/dsh-bio-gem@0.1.18
ID: dsh-bio-gem@0.1.18@dsh0.2.1-alpha.2 · profile: l3-fullscan
Issued: 2026-10-15 · expires: 2026-10-22
View checks & evidence
active in loader tree (150 entries)
L1–L3 are plugin-level static conclusions (baseline, identical across dsh versions): evidence is stored once per plugin.
v0.1.18github2026-10-14
https://github.com/moonbowterfly/dsh-bio-gem
No runtime install test for this version (static scan only) — compatibility unknown, never assumed.
Author badges
Embed the official badges in your README to showcase security & install-test status:
`[](https://www.dsh.so/artifact/dsh-bio-gem/)``[](https://www.dsh.so/artifact/dsh-bio-gem/)`Security Report
Two automated layers, neither a manual review: a static scan (per-plugin rule checks) and a model-driven dynamic security audit that covers only the subset static-flagged at warn or above and never executes plugin code.
Static low, dynamic medium — stricter wins → overall medium.
v0.1.18dsh manifest0.1.18npm2026-10-210.1.18same versionclean · npmVet is an AST static scan (npm artifact or git source).
show static findings (6)
- warningchildProcess · code-exec
src/jobs.js:36const cp = spawn(py, args, { cwd: PYTHON_DIR, windowsHide: true }) - warningfsWrite · files
src/jobs.js:37const so = fs.createWriteStream(stdoutFile, { flags: 'a' }) - warningfsWrite · files
src/jobs.js:38const se = fs.createWriteStream(stderrFile, { flags: 'a' }) - warningfsWrite · files
src/jobs.js:63fs.writeFileSync(path.join(jobDir, 'result.json'), - warningchildProcess · code-exec
src/python.js:62const r = spawnSync(exe, ['-I', '-c', 'import cobra'], { - warningchildProcess · code-exec
src/python.js:128const cp = spawn(py, ['-I', script], { cwd: opts.cwd || PYTHON_DIR, windowsHide: true })
show 1 audit findings
- mediumUnvalidated jobId joined into filesystem paths allows directory listing / arbitrary-file probe
src/jobs.js:107readProgress(jobId)/jobStatus(jobId) take the caller-supplied jobId and concatenate it onto ~/.dsh/dsh-bio-gem/jobs without normalization or an allow-list check (startBuild-generated ids are the only legitimate values). A jobId such as '../../../../home/<user>' makes jobDir point anywhere; since no result.json exists there, jobStatus falls into the failure branch and returns jobDetail(jobDir), which does fs.readdirSync(jobDir) (names + byte sizes of every entry) and up to 800 chars of any file named stderr.txt/result.json/progress.jsonl in that directory. This is an information-disclosure prim
Bioinformatics GEM plugin spawns Python via argv arrays (no shell) and writes caller-chosen paths; the only concrete flaw is an unvalidated jobId joined into filesystem paths in jobs.js.
Rule: the dynamic audit can only raise risk, never lower it (raise-only, never an exemption); a wrong raise is withdrawn by human review and the tier falls back to the static verdict. Overall verdict = the stricter of the two layers.
Disclaimer: the static scan and the dynamic security audit are both automated analysis, not a security guarantee. Always review what you install.
Activity
Last commit 2026-10-11 · activity: Active
• Repo created: 2026-08-31
• Stars: ★ 0 · Forks: 0
• Health: Active — committed within last 30 days
Source
Author README
View on GitHub ↗The author's original README from the repository — fetched live, unedited (the English page loads the default README).