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cantera
【效率与协作】Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kinetics, closed adiabatic ideal-gas constant-volume or constant-pressure ignition, temperature histories, or mechanism-specific ignition-delay comparisons.
conservation-assessment
【文档与办公】Assess condition of artworks and cultural objects, develop treatment proposals, and document conservation interventions following AIC ethical guidelines
tooluniverse-comparative-genomics
【数据与研究】Cross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to identify orthologs, paralogs, sequence conservation, functional conservation across species, and lineage-specific gene gains/losses. Use for phylogenetic gene tracing, model-organism mapping, and evolutionary…
tooluniverse-ecology-biodiversity
【数据与研究】Ecology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive species impact, ecosystem dynamics, conservation status (IUCN), niche ecology. Use for biodiversity questions, species comparison, invasion biology, conservation prioritization, and ecology-related literature search.
tooluniverse-vaccine-design
【设计与创意】Computational vaccine candidate design: peptide/subunit vaccines via MHC-I/MHC-II epitope prediction (IEDB), population HLA coverage optimization, B-cell epitope identification, and cross-strain conservation analysis. Use for vaccine epitope prediction, HLA allele coverage, multi-epitope construct design, and immunogenicity assessment. Combines predi…
tooluniverse-variant-predictor-dms-validation
【数据与研究】Validate a variant-effect predictor (AlphaMissense, ESM-C SAE, ESM logits, EVE, conservation scores, or any per-variant numeric score) against experimental deep mutational scanning (DMS) data. Computes per-variant predictor scores, splits variants into neutral vs disruptive groups by DMS effect, runs a Mann-Whitney U test on the predictor scores, and…
tooluniverse-comparative-genomics
【数据与研究】Cross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to identify orthologs, paralogs, sequence conservation, functional conservation across species, and lineage-specific gene gains/losses. Use for phylogenetic gene tracing, model-organism mapping, and evolutionary…
tooluniverse-ecology-biodiversity
【数据与研究】Ecology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive species impact, ecosystem dynamics, conservation status (IUCN), niche ecology. Use for biodiversity questions, species comparison, invasion biology, conservation prioritization, and ecology-related literature search.
tooluniverse-vaccine-design
【设计与创意】Computational vaccine candidate design: peptide/subunit vaccines via MHC-I/MHC-II epitope prediction (IEDB), population HLA coverage optimization, B-cell epitope identification, and cross-strain conservation analysis. Use for vaccine epitope prediction, HLA allele coverage, multi-epitope construct design, and immunogenicity assessment. Combines predi…
tooluniverse-variant-predictor-dms-validation
【数据与研究】Validate a variant-effect predictor (AlphaMissense, ESM-C SAE, ESM logits, EVE, conservation scores, or any per-variant numeric score) against experimental deep mutational scanning (DMS) data. Computes per-variant predictor scores, splits variants into neutral vs disruptive groups by DMS effect, runs a Mann-Whitney U test on the predictor scores, and…
bio-alignment-io
【数据与研究】Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
bio-alignment-msa-statistics
【效率与协作】Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
bio-alignment-multiple
【数据与研究】Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.
bio-ecological-genomics-conservation-genetics
【效率与协作】Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic…
bio-genome-intervals-bigwig-tracks
【数据与研究】Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wid…
bio-rna-structure-ncrna-search
【效率与协作】Searches for non-coding RNA homologs and classifies RNA families with Infernal covariance models against Rfam, scoring sequence AND secondary-structure conservation jointly. Use when deciding whether a covariance model is the right tool versus BLAST/nhmmer (structured ncRNA versus lncRNA or mature miRNA); choosing the Rfam gathering threshold over a …
simulation-validator
【效率与协作】Validate simulations before, during, and after execution. Use for pre-flight checks, runtime monitoring, post-run validation, diagnosing failed simulations, checking convergence, detecting NaN/Inf, or verifying mass/energy conservation.
simulation-validator
【数据与研究】Validate simulations across three stages — run pre-flight checks on configuration files (parameter ranges, required fields, disk space), monitor runtime logs for residual growth, NaN/Inf, and adaptive dt collapse, and perform post-flight validation of results (physical bounds, mass/energy conservation, convergence). Diagnose failed simulations with p…