Research & Science · Python · By K-Dense-AI

Finds papers in OpenAlex, PubMed and Google Scholar, turns DOIs, PMIDs and arXiv IDs into clean BibTeX, and validates citations for a manuscript or thesis.

K-Dense-AI/claude-scientific-writer

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

Builds conference-size scientific posters in LaTeX with beamerposter, tikzposter or baposter, including figure preparation, compilation and print preflight checks.

K-Dense-AI/claude-scientific-writer

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

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

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

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

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

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

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

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage…

K-Dense-AI/scientific-agent-skills

Analyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen.

K-Dense-AI/scientific-agent-skills

Designs custom laboratory hardware as parametric build123d models and exports fabrication artifacts as STEP, STL, and DXF files - microfluidic chips and molds, optomechanical mounts and breadboard…

K-Dense-AI/scientific-agent-skills

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or…

K-Dense-AI/scientific-agent-skills

Tracks physical units and propagates measurement uncertainty in scientific calculations using pint and uncertainties.

K-Dense-AI/scientific-agent-skills

Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology.

K-Dense-AI/scientific-agent-skills

Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem.

K-Dense-AI/scientific-agent-skills

Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer compatibility, and assess consensus universes.

K-Dense-AI/scientific-agent-skills

Queries 20+ bioinformatics resources through CLI/Python. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and…

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

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 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

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

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

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

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

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

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