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13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics. Use for 13C-MFA, carbon tracing, mass isotopomer distributions (MDVs/MIDs), positional isotopomers, parallel tracer experiments, and determining w…
neuropixels-analysis
Analyzes Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and unit curation (threshold-based, model-based UnitRefine, and AI-assisted visual review). Use when working with Neuropixels 1.0/2.0 recordings…
tooluniverse-aging-senescence
Aging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic drug discovery (dasatinib+quercetin, fisetin, navitoclax), epigenetic clocks, telomere biology, and longevity GWAS. Use for senescence-pathway analysis, age-related disease genetics, senolytic-target discovery, an…
tooluniverse-toxicology
Drug and chemical toxicity assessment via adverse outcome pathways (AOPs), real-world FAERS adverse event signals, FDA labels, toxicogenomic associations, and EPA CompTox quantitative hazard/high-throughput bioactivity data. Triangulates molecular initiating event to cellular outcome to organ-level toxicity to clinical adverse event. Use for hepatotoxicity/…
tooluniverse-aging-senescence
Aging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic drug discovery (dasatinib+quercetin, fisetin, navitoclax), epigenetic clocks, telomere biology, and longevity GWAS. Use for senescence-pathway analysis, age-related disease genetics, senolytic-target discovery, an…
tooluniverse-toxicology
Drug and chemical toxicity assessment via adverse outcome pathways (AOPs), real-world FAERS adverse event signals, FDA labels, toxicogenomic associations, and EPA CompTox quantitative hazard/high-throughput bioactivity data. Triangulates molecular initiating event to cellular outcome to organ-level toxicity to clinical adverse event. Use for hepatotoxicity/…
bio-imaging-mass-cytometry-spatial-analysis
Analyze spatial cell-cell interactions, neighborhoods, and niches in IMC/MIBI data with squidpy and imcRtools, covering neighborhood-enrichment permutation nulls, the abundance-vs-density confound, inhomogeneous Ripley's K, cellular-neighborhood discovery, graph-construction (contact vs proximity), and edge effects. Use when testing whether cell types co-lo…
bio-spatial-transcriptomics-high-resolution-binning
Reconstructs single cells from sub-cellular spatial capture units (Visium HD 2um bins, Stereo-seq DNB spots, Slide-seqV2 beads) by aggregating bins UP into cells rather than deconvolving a mixture DOWN. Use when choosing a bin size and recognizing the sparsity-vs-mixture dilemma (2um bins are too sparse to cluster, but binning to 8/16um re-creates the multi…
procedural-generation
Use when implementing procedural generation — noise-based terrain, BSP dungeons, cellular automata caves, wave function collapse, and seeded randomness in Godot 4.3+
spikeinterface-skill
Domain knowledge for building extracellular electrophysiology pipelines with SpikeInterface: loading data with extractors, preprocessing, running spike sorters, post-processing via SortingAnalyzer, quality metrics, curation, comparison, visualization, and export.
spike-sorting
Automated spike sorting pipeline using SpikeInterface with Kilosort2/Mountainsort5, quality metrics, and Phy export for extracellular neural recordings.
13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics. Use for 13C-MFA, carbon tracing, mass isotopomer distributions (MDVs/MIDs), positional isotopomers, parallel tracer experiments, and determining w…
basic-discovery-translational-opportunity-finder
Finds translational opportunities that connect basic-research discoveries to clinically meaningful use cases such as diagnosis, stratification, prognosis, treatment response prediction, monitoring, or therapeutic development. Use this skill when a user wants to turn a mechanism finding, pathway signal, cellular phenotype, experimental observation, or omics …
bio-spatial-transcriptomics-spatial-communication
Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer intercellular signaling, identify communication pathways, and visualize interaction networks. Use when analyzing cell-cell communication in spatial context.
bio-spatial-transcriptomics-spatial-multiomics
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
cell
Cellular biology fundamentals
cellchat-cell-communication
Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network centrality (senders/receivers/influencers) → chord/heatmap/bubble plots → cross-condition compare. Human, mo…
cellular-neuroscientist
Expert-thinking profile for Cellular Neuroscientist (wet-lab / patch-clamp electrophysiology / live-cell imaging / culture-slice-iPSC preparations / synaptic physiology): Treat the neuron as a cable with active channels, not a point integrator unless you have shown it is one for your question. Separate voltage, calcium, and fluorescence observables. GCaMP r…
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