Python · 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

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

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

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

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

Builds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy.

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

Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries.

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

Scales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask.

K-Dense-AI/scientific-agent-skills

Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding.

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

Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.

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

Extracts and preprocesses whole-slide histology image tiles with Histolab.

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

Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs.

K-Dense-AI/scientific-agent-skills

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

K-Dense-AI/scientific-agent-skills

GPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster.

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

Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review.

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

Supports machine learning in Python with scikit-learn. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Builds, evaluates, and audits right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model selection, probability prediction, and…

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

Processes large tabular scientific datasets with Vaex expressions, filtered views, streamed statistics, binned visualizations, and file conversion.

K-Dense-AI/scientific-agent-skills