K-Dense-AI/scientific-agent-skills

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with…

K-Dense-AI/scientific-agent-skills

Skill Claude CodeCodex

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

K-Dense-AI/scientific-agent-skills

Skill Claude CodeCodex

Build with and use 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 sessions, running local…

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug monitoring. Use when…

K-Dense-AI/scientific-agent-skills

Skill Claude Code

High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

High-performance DataFrame library for Python ETL, analytics, and pandas migration. Use for expression-based data manipulation with lazy query optimization, parallel execution, streaming out-of-core processing, Arrow interoperability, and optional GPU execution.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Create and audit editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets. Use when the requested deliverable is a PowerPoint research/conference poster and exact physical, printer, accessibility, provenance, and package-security checks are required.

K-Dense-AI/scientific-agent-skills

Skill Claude CodeCodex needs its repo

Use this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx or .potx file (even if the extracted content will be used elsewhere, like in an email or summary)…

K-Dense-AI/scientific-agent-skills

Skill Claude CodeCodex

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Read, validate, and safely export protocols.io data with current official REST/MCP contracts, or create non-executing mutation plans. The bundled client makes bounded official-host GET requests only with explicit --execute. Use only for tasks explicitly targeting protocols.io or an exact protocols.io protocol version.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Version-aware guidance for PufferLib reinforcement-learning environments, vectorization, policies, PuffeRL training, evaluation, and safe checkpoint review. Use when adapting Gymnasium/PettingZoo environments to published PufferLib 3.0.0 or working with the redesigned native 4.0 source line.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Differential gene expression analysis for bulk RNA-seq with PyDESeq2, including formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.

K-Dense-AI/scientific-agent-skills

Skill Claude CodeCodex

Use pydicom to read, inspect, write, transform, and safely preflight local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression plugins, frames, private elements, JSON, and bounded de-identification review.

K-Dense-AI/scientific-agent-skills

Skill Claude CodeCodex

Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD coding, EEG events), instantiating models (Transformer…

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Develop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Use for PyLabRobot protocols or API questions; keep physical execution behind an explicit operator safety gate.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Analyze, validate, convert, and transform materials structures and computed materials data with current pymatgen APIs, including local phase diagrams, symmetry sensitivity, electronic-structure I/O, and explicitly bounded Materials Project queries.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Complete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free and isobaric quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral…

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Python/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Use Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset access, task-aware splits, evaluator metrics, benchmark groups, and bounded molecular-oracle workflows.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Deep 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 training.

K-Dense-AI/scientific-agent-skills

Skill Claude Code

Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations…

K-Dense-AI/scientific-agent-skills

Skill Claude CodeCodex

Build, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitives, target-aware transpilation, local or noisy simulation, IBM QPU execution, Runtime sessions or batches, error mitigation, and Qiskit ecosystem…