1,133 skills found · Page 5 of 38
K-Dense-AI / pylabrobotDevelops and reviews PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Supports PyLabRobot protocols and API questions; keep physical execution behind an explicit operator safety gate.
K-Dense-AI / pytorch-lightningDeep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network traini…
K-Dense-AI / rdkitCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit).
K-Dense-AI / statsmodelsFits and diagnoses Python statistical models including OLS, GLM, discrete and mixed models, ARIMA and SARIMAX. Supports coefficient inference, marginal effects, model comparison and time series forecasting with explicit design and uncertainty checks.
K-Dense-AI / telluriumSimulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter perturbations, and exports and replays SBML plus SED-ML COMBINE archives.
K-Dense-AI / hypothesis-generationFormulates evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready analysis plans.
K-Dense-AI / optimize-for-gpuGPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster. Use for CUDA/GPU optimization; CPU-bound NumPy, SciPy, pandas, scikit-learn, NetworkX, scikit-image, vector-search, image-processing, graph, simulation, or file-I/O workloads; CuPy, cuDF, cuML, c…
K-Dense-AI / relionValidates and executes RELION single-particle cryo-EM refinement and half-map postprocessing. Supports STAR optics/acquisition checks, particle-stack consistency, gold-standard half sets, soft-mask validation, diagnostic Fourier shell correlation, and restart guidance.
K-Dense-AI / cellprofilerRuns reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/channel manifests, headless batch execution, segmentation overlays, and measurement QC for 2D fluorescence assays.
K-Dense-AI / cellxgene-censusQueries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data
K-Dense-AI / latex-postersOpenRouter API key for optional schematic generation and review.
K-Dense-AI / nmrglueProcesses calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration regions.
K-Dense-AI / nwb-conversionConverts neuroscience acquisition data to Neurodata Without Borders files with NeuroConv and PyNWB, preserves metadata and timebases, checks evidence-based clock alignment, and produces schema validation, NWB Inspector findings and round-trip checks.
K-Dense-AI / open-notebookInstance password used as the Bearer token when auth is enabled.
K-Dense-AI / parallel-webParallel API key; optional when CLI login credentials are available.
K-Dense-AI / pybammSimulates 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 measured cycling data.
K-Dense-AI / pyzoteroZotero library type: ''user'' or ''group'' (default ''user'').
K-Dense-AI / qiime2-ampliconProcesses paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer orientation diagnostics, predicted post-trimming overlap, sample IDs, runtime versions and read retention, and guides selection of compatible taxonomic clas…
K-Dense-AI / pacsomaticPrepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting.
K-Dense-AI / primekgQueries a pinned Precision Medicine Knowledge Graph (PrimeKG) CSV for typed gene, drug, disease, and phenotype nodes, direct associations, disease context, and one- or two-hop paths.
K-Dense-AI / biopythonNCBI API key to raise Entrez rate limits.
K-Dense-AI / bioservicesContact email for the EMBL-EBI hosted NCBI BLAST service.
K-Dense-AI / canteraRuns Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement.
K-Dense-AI / cirqGoogle quantum computing framework
K-Dense-AI / citation-managementOptional OpenAlex key for a higher account budget.
K-Dense-AI / generate-imageOpenRouter API key used for image generation.
K-Dense-AI / mageckAnalyzes 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 sizes and FDR.
K-Dense-AI / neuropixels-analysisFor optional Claude API calls.
K-Dense-AI / pycalphadComputes finite-temperature CALPHAD equilibria, phase fractions, and phase compositions from thermodynamic TDB databases using pycalphad.
K-Dense-AI / research-lookupOptional OpenRouter key for explicit Perplexity use.
