dsh-bio-gem
Genome-scale metabolic model (GEM) builder and curator plugin for DeepSeek Harness.
Install
No clear install command was found in the current repository evidence.
Plugin Overview & Capabilities
AI-assisted organization based on the public repository snapshot. The content must be grounded in source evidence and does not replace compatibility or security verification.
Key Capabilities
- Automated GEM construction using CarveMe and optional gapseq engines from genome FASTA files
- Comprehensive multi-stage validation checks (G1-G6) covering element balance, growth plausibility, and ATP leakage
- Hierarchical gap-finding and gap-filling (L1 exchange, L2 transport, L3 internal pathways)
- Flux variability analysis (FVA), pFBA scanning, and flux space sampling (ACHR/OptGP)
- Gene essentiality scanning, double knockout synthetic lethality testing, and pathway enrichment
- Prediction ledger maintenance and structured target list export
- Read-only loopback integration endpoints for ecosystem pairing with dsh-bio-genie
Useful For
- Reconstructing and refining bacterial metabolic network models directly within DSH agent workflows
- Validating and debugging existing SBML models for blocked reactions, orphan metabolites, and elemental balance
- Performing in silico knockouts and phenotype predictions for metabolic engineering and target identification
Who It Fits
- Bioinformatics researchers and computational biologists
- Metabolic engineers analyzing microbial pathways
- DSH users building autonomous biological reasoning agents
Documented Limitations
- Requires a Python 3.10+ environment with cobra installed (or shared via dsh-bio-genie)
- gem_build requires separate installation of CarveMe and the external DIAMOND binary
- gapseq engine support is optional/experimental and relies on a configured WSL2 environment
DSH Compatibility
Version-specific runtime evidence collected by DSH Plugin. A missing result means we have not tested that combination yet.
Security Signals
Objective signals discovered from package metadata and source inspection. These are not a guarantee that a plugin is safe.
package.json declares 0 runtime, 0 development, 1 peer, and 0 optional dependencies.
package.json declares DSH bundle metadata.
GitHub reports the repository license as MIT.
A root package.json was captured and can be inspected by the registry.
Public GitHub source metadata is available for this registry snapshot.
Source & Registry Notes
Public provenance, Registry classification, and the latest source check for this entry, kept separate from runtime verification.
- Source repository
- moonbowterfly/dsh-bio-gem
- Registry source
- GitHub · dsh-plugin topic
- Registry classification
- Plugin
- Source checked
- d4d6a24 · 2026-11-13
This project is independently indexed from public source information. DSH Plugin is not affiliated with DeepSeek or the plugin author. Always check the author repository before installation.
Repository Activity
- GitHub stars
- 0GitHub stars
- Forks
- 0
- Open issues
- 0
- Last commit
- 2026-10-11
- Last release
- 2026-10-23
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