K-Dense-AI
Showing 121–174 of 174 skills · Page 3 of 3
K-Dense-AI / hugging-science
46.4kDiscovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. Used when selecting scientific ML resources in biology, chemistry, genomics, materials, climate, physics, astronomy, medicine, mathematics, protein design, single-cell analysis, or…
K-Dense-AI / labarchive-integration
46.4kIntegrates with the official LabArchives ELN REST-like API and Inventory API v1. Supports regional endpoint selection, signed-request construction, user authorization and UID flows, local LA container validation, and verified LabArchives integration workflows.
K-Dense-AI / marine-carbonate-chemistry
46.4kSolves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research.
K-Dense-AI / networkx
46.4kCreates, analyzes, and visualizes complex networks and graphs in Python with NetworkX
K-Dense-AI / openpiv
46.4kPerforms Particle Image Velocimetry (PIV) analysis with OpenPIV
K-Dense-AI / pyhealth
46.4kBuilds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes. Use for PyHealth dataset loading, MIMIC-III/IV, eICU or OMOP prediction tasks, patient-level evaluation, mortality/readmission/length-of-stay modeling, medication recommendation, sleep sta…
K-Dense-AI / pylabrobot
46.4kDevelops 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-lightning
46.4kDeep 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 / rdkit
46.4kCheminformatics 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 / statsmodels
46.4kFits 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 / tellurium
46.4kSimulates 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 / what-if-oracle
46.4kSupports structured what-if scenario analysis for research planning, experimental contingencies, and scientific project decisions. Explores favorable, reference, adverse, wild-card, contrarian, and second-order scenarios with explicit assumptions, evidence, and decision triggers.
K-Dense-AI / hypothesis-generation
46.4kFormulates 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-gpu
46.4kGPU-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 / relion
46.4kValidates 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 / research-grants
46.4kSupports research proposal preparation and review for NSF, NIH, DOE, DARPA, and Taiwan NSTC, including opportunity-specific requirements, aims, review criteria, budgets, broader impacts, forms, and resubmissions.
K-Dense-AI / cellprofiler
46.4kRuns 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-census
46.4kQueries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data
K-Dense-AI / dhdna-profiler
46.4kApplies the DHDNA framework as an exploratory rubric for reasoning and writing patterns in supplied text. Used for explicit requests for DHDNA, cognitive-style reflection, a thinking-pattern profile, or comparisons of textual reasoning.
K-Dense-AI / latex-posters
46.4kOpenRouter API key for optional schematic generation and review.
K-Dense-AI / nmrglue
46.4kProcesses calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration regions.
K-Dense-AI / nwb-conversion
46.4kConverts 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-notebook
46.4kInstance password used as the Bearer token when auth is enabled.
K-Dense-AI / paperzilla
46.4kReads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI. Supports recent recommendations, paper details, markdown-based summaries, recommendation feedback, JSON export, and Atom feed URLs.
K-Dense-AI / parallel-web
46.4kParallel API key; optional when CLI login credentials are available.
K-Dense-AI / pybamm
46.4kSimulates 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 / pyzotero
46.4kZotero library type: ''user'' or ''group'' (default ''user'').
K-Dense-AI / qiime2-amplicon
46.4kProcesses 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 / scientific-critical-thinking
46.4kEvaluates scientific claims and evidence quality. Applies to experimental design validity, biases and confounders, statistical interpretation, evidence grading frameworks (GRADE, Cochrane Risk of Bias), and teaching critical analysis.
K-Dense-AI / bgpt-paper-search
46.4kSearches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported statistics, scope, limitations, and provenance. Use for literature reviews, evidence synthesis, and finding experimental details beyond abstracts.
K-Dense-AI / fictiv
46.4kOperates Fictiv (app.fictiv.com), the on-demand manufacturing platform, end to end in the user's browser. Covers uploading CAD parts, configuring process, material, finish, threads, tolerances and inspections, getting instant or manual quotes, reading and fixing DFM feedback, choosing lead time and…
K-Dense-AI / pacsomatic
46.4kPrepares 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 / primekg
46.4kQueries 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 / autoskill
46.4kOptional Foundry access for drafting.
K-Dense-AI / biopython
46.4kNCBI API key to raise Entrez rate limits.
K-Dense-AI / bioservices
46.4kContact email for the EMBL-EBI hosted NCBI BLAST service.
K-Dense-AI / cantera
46.4kRuns Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement.
K-Dense-AI / cirq
46.4kGoogle quantum computing framework
K-Dense-AI / citation-management
46.4kOptional OpenAlex key for a higher account budget.
K-Dense-AI / generate-image
46.4kOpenRouter API key used for image generation.
K-Dense-AI / mageck
46.4kAnalyzes 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-analysis
46.4kFor optional Claude API calls.
K-Dense-AI / pi-agent
46.4kBuilds with and operates Pi, the minimal terminal coding harness. Use for installing Pi, configuring providers/models/settings/environment variables, creating Pi skills/extensions/packages/themes/prompt templates, embedding Pi through the SDK, integrating over RPC or JSON event streams, parsing sess…
K-Dense-AI / pycalphad
46.4kComputes finite-temperature CALPHAD equilibria, phase fractions, and phase compositions from thermodynamic TDB databases using pycalphad.
K-Dense-AI / research-lookup
46.4kOptional OpenRouter key for explicit Perplexity use.
K-Dense-AI / rowan
46.4kRowan computational chemistry API key.
K-Dense-AI / tamarind
46.4kTamarind Bio API key sent as the x-api-key header.
K-Dense-AI / benchling-integration
46.4kStaging API key (multi-env setups).
K-Dense-AI / infographics
46.4kOpenRouter API key for the skill's LLM-powered steps.
K-Dense-AI / omero-integration
46.4kSecure transport toggle; default true.
K-Dense-AI / protocolsio-integration
46.4kBearer token for authenticated protocols.io REST reads.
K-Dense-AI / ginkgo-cloud-lab
46.4kGuides protocol selection, input preparation, pricing checks, and browser ordering on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio). Applies to cell-free, E.
K-Dense-AI / modal
46.4kModal token secret.
K-Dense-AI / exa-search
46.4kExa search API key.