Compute assembly index for molecules via dynamic programming shortest-path analysis.
npx skills add https://github.com/plurigrid/asi --skill assembly-index
Please help me install this Agent Skill. Skill: assembly-index Source: https://github.com/plurigrid/asi/tree/main/skills/assembly-index Command: npx skills add https://github.com/plurigrid/asi --skill assembly-index
This Skill uses Assembly Index theory to quantify molecular complexity and identify biosignatures through minimal assembly steps and copy-number thresholds.
Compute assembly index for a molecule with assembly-index, then validate biosignature thresholds with assembly-validate, or compare assembly pathways with assembly-compare.
High-intent search queries and answers about installing and using this skill.
Assembly index quantifies the minimal assembly steps needed to construct a molecule from primitives. Use the assembly-index computation to calculate this metric, which serves as a foundation for detecting biosignatures through complexity analysis in molecular workflows.
Assembly index identifies biosignatures by combining molecular complexity with copy-number thresholds. Molecules with assembly index > 15 and copy counts > 1 signal potential biological origin, distinguishing synthetic or abiotic molecules from those likely produced by living systems.
Yes. Assembly index workflows support MS2 and SDF input formats, correlating mass spectrometry abundance data with assembly DAGs. This integration validates biosignature signals by cross-referencing molecular complexity with observed MS fragmentation patterns in laboratory and computational analyses.
Use assembly-validate to check biosignature thresholds against computed assembly indices, and assembly-compare to evaluate shortest construction paths across molecules. These tools enable pathway enumeration and DAG analysis for systematic biosignature identification.
Assembly index accepts SDF (structure data format) and MS2 (tandem mass spectrometry) files. SDF provides molecular structures for pathway computation, while MS2 data supplies abundance and fragmentation information for integrated biosignature validation.
Assembly index applies dynamic programming and DAG construction internally. You need familiarity with molecular complexity concepts and biosignature thresholds (MA > 15, copies > 1), but the Skill handles shortest-path computation and substructure enumeration automatically through its command-line interface.
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