Research & Science · By K-Dense-AI

Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage…

K-Dense-AI/scientific-agent-skills

Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query…

K-Dense-AI/scientific-agent-skills

Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX.

K-Dense-AI/scientific-agent-skills

Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows.

K-Dense-AI/scientific-agent-skills

Searches and reads biomedical papers, FDA/PMDA/EMA documents, clinical trials, and protein records with the GXL Paperclip CLI and Python SDK.

K-Dense-AI/scientific-agent-skills

Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows.

K-Dense-AI/scientific-agent-skills

Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference.

K-Dense-AI/scientific-agent-skills

Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data.

K-Dense-AI/scientific-agent-skills

Reads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data.

K-Dense-AI/scientific-agent-skills

Solves and validates single-, multi-, and many-objective optimization with pymoo, including NSGA-II, NSGA-III, MOEA/D, constraints, Pareto approximations, reference directions, and ZDT/DTLZ…

K-Dense-AI/scientific-agent-skills

Processes mass spectrometry data with pyOpenMS. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Provides Python/HTSlib workflows for genomic files. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance.

K-Dense-AI/scientific-agent-skills

Validates and executes RELION single-particle cryo-EM refinement and half-map postprocessing.

K-Dense-AI/scientific-agent-skills

Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression.

K-Dense-AI/scientific-agent-skills

Calculates sample sizes and statistical power for study planning.

K-Dense-AI/scientific-agent-skills

Performs exact symbolic mathematics with SymPy for algebra, calculus, equation solving, symbolic linear algebra, physics, and lambdify or LaTeX code generation.

K-Dense-AI/scientific-agent-skills

Provides access to a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required.

K-Dense-AI/scientific-agent-skills

Stores and retrieves genomic variant calls with TileDB-VCF. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and…

K-Dense-AI/scientific-agent-skills

Supports structured what-if scenario analysis for research planning, experimental contingencies, and scientific project decisions.

K-Dense-AI/scientific-agent-skills

Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement.

K-Dense-AI/scientific-agent-skills

Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported statistics, scope, limitations, and provenance.

K-Dense-AI/scientific-agent-skills

Predicts regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights.

K-Dense-AI/scientific-agent-skills

Queries and downloads public cancer imaging data from NCI Imaging Data Commons.

K-Dense-AI/scientific-agent-skills

Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez).

K-Dense-AI/scientific-agent-skills

Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results.

K-Dense-AI/scientific-agent-skills

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem.

K-Dense-AI/scientific-agent-skills

Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model validation for…

K-Dense-AI/scientific-agent-skills

Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.

K-Dense-AI/scientific-agent-skills

Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple…

K-Dense-AI/scientific-agent-skills

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis.

K-Dense-AI/scientific-agent-skills

Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML.

K-Dense-AI/scientific-agent-skills

Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI.

K-Dense-AI/scientific-agent-skills

Manages Zotero reference libraries using the pyzotero Python client: retrieves, creates, updates, and deletes items, collections, tags, and attachments via the Zotero Web API v3 or local API.

K-Dense-AI/scientific-agent-skills

Evaluates scientific claims and evidence quality. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Uses Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and recurring web monitoring.

K-Dense-AI/scientific-agent-skills

Use Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and recurring web monitoring.

K-Dense-AI/claude-scientific-writer

Queries documented public database APIs with explicit endpoints, filters, pagination, and provenance.

K-Dense-AI/scientific-agent-skills

Guides protocol selection, input preparation, pricing checks, and browser ordering on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio).

K-Dense-AI/scientific-agent-skills

Applies Judea Pearl's causal reasoning frameworks to distinguish correlation from causation, evaluate AI capabilities, and make counterfactual decisions.

K-Dense-AI/mimeo

Use after framing a question and before designing an analysis, or when choosing a method, judging whether a result is novel, or needing a prior effect size for a power calculation

K-Dense-AI/science-superpowers

A skill your agent uses whenever you are reasoning about large-scale scientific projects, genomics, bioethics, data infrastructure, or long-term medical translation.

K-Dense-AI/mimeographs

A skill your agent uses whenever you are reasoning about public health policy, cancer prevention, epidemiological study design, clinical risk models, or weight management advice.

K-Dense-AI/mimeographs

Applies the Neoplatonic and mathematical reasoning of Hypatia of Alexandria.

K-Dense-AI/mimeographs

A skill your agent uses to reason like JoAnn E. An agent skill from K-Dense-AI/mimeographs.

K-Dense-AI/mimeographs

A skill your agent uses to apply the rigorous epidemiological reasoning of Julie E.

K-Dense-AI/mimeographs

This skill applies the analytical frameworks of Ronald C. An agent skill from K-Dense-AI/mimeographs.

K-Dense-AI/mimeographs