Docs & Writing

cyberstrikeus Skill

Test, validate, and document changes to the system before finalizing the implementation of the changes.

cyberstrikeus Skill

Identify, report, and correct system flaws;

cyberstrikeus Skill

Use [organization-defined] to: Document proposed changes to the system; Notify [organization-defined] of proposed changes to the system and request ch

cyberstrikeus Skill

Report system vulnerabilities associated with reported incidents to [organization-defined].

cyberstrikeus Skill

Documentation of Activities

cyberstrikeus Skill

Use software and associated documentation in accordance with contract agreements and copyright laws;

cyberstrikeus Skill

Identify, report, and correct system flaws.

cyberstrikeus Skill

Ensure the App Usage Report is reviewed regularly for anomalies

holobiomicslab Skill

Use when an ASB skill proved wrong, stale, missing or wasteful in practice — its steps failed, no skill covered the task, the leaves existed but nothing composed them, or the tool has changed. Turns that friction into a redacted, dedupable report the user approves before anything is filed.

holobiomicslab Skill

Use when when you have JSON-formatted curation data organized in a directory structure (e.g., the MIBiG `data` directory) and need to extract a specific nested field (e.g., `cluster.status`) across all entries to build an index, summary table, or quality report.

holobiomicslab Skill

Use when when a project README or documentation embeds badge endpoints that report real-time status (e.g., Travis CI build, Landscape.

holobiomicslab Skill

Use when when a user uploads a JSON project document to the Pairing Omics Data Platform and you need to determine whether it satisfies the platform's data structure requirements, including all mandatory fields, proper data types, and constraint satisfaction for paired omics metadata (e.

holobiomicslab Skill

Use when after performing statistical tests (t-test, Mann–Whitney U, ANOVA) on matched lipid abundance data grouped by experimental condition, to report not only whether differences are statistically significant but also the magnitude and direction of change.

holobiomicslab Skill

Use when your PSM input file (e.g., from MaxQuant or other search engines that do not report fixed modifications) lacks modification annotations for residues that were chemically modified during sample preparation (e.g., carbamidomethylation of cysteines, TMT labeling of lysines and N-termini).

holobiomicslab Skill

Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, call qc_summary() to obtain a structured report of which ions passed or failed each filter.

holobiomicslab Skill

Use when a software package claims to bundle or install a specific number of tools (documented or approximate) but the tool names, versions, and sources are not enumerated in the primary README or documentation.

holobiomicslab Skill

Use when after running feature clustering (Gravity) or drift correction (Blueshift) on LCMS data, when you have a processed feature table and need to standardize its structure, validate metadata completeness, enforce missing-value thresholds, and generate a QC report documenting pass/fail status.

holobiomicslab Skill

Use when after applying jsonschema validation to a parsed mwTab file against MS or NMR schema definitions, when you have collected validation errors, warnings, and metadata column matching results and need to communicate findings to data curators or submitters in a structured, machine-readable.

holobiomicslab Skill

Use when when you need to validate that a development build release workflow (such as dev_build_release.yml for a mass spectrometry data processing project) executes without failure and generates artifacts for downstream testing or distribution.

holobiomicslab Skill

Use when after sub-clusters have been detected by PRESTO-STAT or PRESTO-TOP statistical methods on tokenised and redundancy-filtered BGCs, and you need to report their precise genomic positions, gene locus tags, and orientations for integration with natural product substructure predictions or for.

holobiomicslab Skill

Use when when a software project has reached a stable milestone (v-tagged commit) and you need to produce official distribution artifacts with verified version metadata, checksums, and release documentation that can be validated against a published GitHub release record.

holobiomicslab Skill

Use when when you need to understand how a complex feature or architectural pattern was implemented in a codebase, particularly when the current README or documentation does not fully explain the control flow, decision criteria, or parameter passing between subsystems.

holobiomicslab Skill

Use when you are starting a new mass spectrometry analysis task or feature request where the problem scope is unclear, the tool chain (e.g., OpenMS + Python + KNIME integration) is not yet selected, or acceptance criteria (code quality, test coverage, documentation) have not been established.

holobiomicslab Skill

Use when a bioinformatics package claims to install a large number of tools (e.g., ~89 for untargeted metabolomics pipelines) but the article or main documentation does not enumerate them explicitly.

holobiomicslab Skill

Use when you have identified all pinned software dependencies for a Python project (typically from README, setup.py, or environment documentation) and need to create a machine-readable artifact that can reliably reconstruct that exact environment.

holobiomicslab Skill

Use when you have claims in a paper or tool documentation that one peak picking method outperforms others (e.g., 'IDSL.IPA outperforms MZmine 2 and xcms'), but the specific comparison metrics, numerical results, and source tables are not provided in the abstract or introduction.

holobiomicslab Skill

Use when after generating a numerical visualization (e.g., confusion matrix, heatmap, or similarity array) using matplotlib, when you need to add axis labels, class names, colormaps, normalization annotations, colorbars, titles, and export the figure in a publication-ready format (PNG or PDF).

holobiomicslab Skill

Use when when you need to verify that a software package (such as MassQL) passes its periodic integration test suite as indicated by CI workflow badges in the project documentation, or when you must reproduce pass/fail results for package-testing workflows distinct from unit tests to establish.

holobiomicslab Skill

Use when when you have loaded a project JSON document from the Pairing Omics Data Platform and need to identify and document constraint violations (such as whitespace in URL fields) defined in the JSON schema.

holobiomicslab Skill

Use when when initializing a new Python project environment, reproducing a published analysis, or building documentation that requires external dependencies. Specifically apply this skill when you have a requirements.txt file listing pinned versions and need to ensure all downstream tools (e.

holobiomicslab Skill

Use when you have obtained a repository containing simulation scripts (e.g., Type I error or power analysis scripts) and need to verify that executing those scripts produces the same summary statistics and findings reported in the associated publication or documentation.

holobiomicslab Skill

Use when when you have raw HPLC column specifications from RepoRT or similar metadata repositories and need to prepare them as input features for machine learning models. Apply this skill before featurizing molecular structures or training graph transformers for retention time prediction.

holobiomicslab Skill

Use when you need to understand how a complex MS/MS spectral search system routes query spectra through multiple parallel processing pipelines with different objectives (e.g., reliable exact matching vs. fast approximate matching).

holobiomicslab Skill

Use when when you have identified all software dependencies and their exact pinned versions from project documentation (README, setup files, or supplementary materials) and need to create portable environment specifications for a scientific implementation.

holobiomicslab Skill

Use when preparing a scientific application (such as a metabolite annotation tool) for deployment to a shared or production app server, particularly when the deployment requires external database access, Java library dependencies, and credential management.

holobiomicslab Skill

Use when your R package wraps a compiled .NET assembly or binary executable and you need to expose the version of that dependency to users at runtime for troubleshooting, validation, or documentation purposes.