K-Dense-AI/scientific-agent-skills

Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.

K-Dense-AI/scientific-agent-skills

Plans, runs, and documents analytical method validation, verification, or transfer studies under ICH Q2(R2)/Q14, USP, ICH M10, CLSI EP, or ISO/IEC 17025.

K-Dense-AI/scientific-agent-skills

Runs Cantera constant-volume or constant-pressure ignition simulations and reports temperature-based ignition delay with mechanism provenance and checks.

K-Dense-AI/scientific-agent-skills

Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.

K-Dense-AI/scientific-agent-skills

Plans and audits runs of the HypoGeniC and HypoRefine packages, which propose hypotheses from labeled text datasets, with local checks before any model call.

K-Dense-AI/scientific-agent-skills

Organizes scope, controlled documents, risk files and traceability into draft evidence for human review against ISO 13485, 14971, 17025 and 15189.

K-Dense-AI/scientific-agent-skills

Creates research posters in LaTeX using beamerposter, tikzposter, or baposter.

K-Dense-AI/scientific-agent-skills

Runs systematic, scoping or narrative literature reviews across PubMed, arXiv, bioRxiv and Semantic Scholar, with citation checks and Markdown or PDF output.

K-Dense-AI/scientific-agent-skills

Builds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows.

K-Dense-AI/scientific-agent-skills

Analyzes Neuropixels extracellular recordings end-to-end with SpikeInterface.

K-Dense-AI/scientific-agent-skills

Processes calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration regions.

K-Dense-AI/scientific-agent-skills

Converts neuroscience acquisition data to Neurodata Without Borders files with NeuroConv and PyNWB, preserves metadata and timebases, checks evidence-based clock alignment, and produces schema…

K-Dense-AI/scientific-agent-skills

Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence…

K-Dense-AI/scientific-agent-skills

Designs and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates.

K-Dense-AI/scientific-agent-skills

Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, checks mesh and solver sensitivity, and compares predicted voltage curves with…

K-Dense-AI/scientific-agent-skills

Computes finite-temperature CALPHAD equilibria, phase fractions, and phase compositions from thermodynamic TDB databases using pycalphad.

K-Dense-AI/scientific-agent-skills

Builds and checks Bayesian models with PyMC, including hierarchical models, NUTS MCMC, variational inference, mutable-data predictions, posterior predictive checks, diagnostics, and PSIS-LOO model…

K-Dense-AI/scientific-agent-skills

Supports multivariate severity assessment and exploratory endpoint-time score forecasting for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast…

K-Dense-AI/scientific-agent-skills

Creates and audits truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly.

K-Dense-AI/scientific-agent-skills

Simulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter perturbations, and exports and replays SBML plus…

K-Dense-AI/scientific-agent-skills

Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API.

K-Dense-AI/scientific-agent-skills

Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC…

K-Dense-AI/scientific-agent-skills

Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3.

K-Dense-AI/scientific-agent-skills

Analyzes user-requested Screenpipe history windows to detect repeated research workflows, match existing scientific skills, and stage new skill drafts or composition recipes for review.

K-Dense-AI/scientific-agent-skills

Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression.

K-Dense-AI/scientific-agent-skills

Operates Fictiv (app.fictiv.com), the on-demand manufacturing platform, end to end in the user's browser.

K-Dense-AI/scientific-agent-skills

Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO.

K-Dense-AI/scientific-agent-skills

Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strategies, and supported FlowJo 10 workspaces.

K-Dense-AI/scientific-agent-skills

Plans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks.

K-Dense-AI/scientific-agent-skills

Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis.

K-Dense-AI/scientific-agent-skills

Supports geospatial research workflows for remote sensing, vector and raster GIS, spatial statistics, terrain and network analysis, and machine learning for Earth observation.

K-Dense-AI/scientific-agent-skills

Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan evidence, and preparing NetNGlyc, NetOGlyc and…

K-Dense-AI/scientific-agent-skills

Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP.

K-Dense-AI/scientific-agent-skills

Local document and PDF parsing that returns spatial text with bounding boxes.

K-Dense-AI/scientific-agent-skills

Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and library QC, and produces gene hit rankings with effect…

K-Dense-AI/scientific-agent-skills

Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research.

K-Dense-AI/scientific-agent-skills

Processes, cleans, compares, and searches tandem mass spectra with matchms.

K-Dense-AI/scientific-agent-skills

Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships.

K-Dense-AI/scientific-agent-skills

Builds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, variability, and complexity.

K-Dense-AI/scientific-agent-skills

Inspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs.

K-Dense-AI/scientific-agent-skills

Resolves free-text scientific labels to ontology term IDs and validates existing CURIEs against the EBI Ontology Lookup Service (OLS4).

K-Dense-AI/scientific-agent-skills

Organizes research with the self-hosted Open Notebook alternative to NotebookLM.

K-Dense-AI/scientific-agent-skills

Performs Particle Image Velocimetry (PIV) analysis with OpenPIV.

K-Dense-AI/scientific-agent-skills

Authors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots.

K-Dense-AI/scientific-agent-skills

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs.

K-Dense-AI/scientific-agent-skills

Supports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path storage, multiplex quantification, spatial graphs, and bounded model inference.

K-Dense-AI/scientific-agent-skills

Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies.

K-Dense-AI/scientific-agent-skills

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results.

K-Dense-AI/scientific-agent-skills