Scientific Agent Skills

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server, returning 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions.

Conduct systematic literature reviews by searching multiple academic databases, synthesizing findings, and generating professionally formatted documents with verified citations.

Access microscopy images and metadata via the OMERO Python API: retrieve datasets, analyze pixels, manage ROIs and annotations, and batch-process for high-content screening workflows.

Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), and distributed training (DDP, FSDP, DeepSpeed) for scalable neural network training.

Build visually engaging scientific slide decks for conferences, seminars, defenses, and research talks with structured planning, design templates, and automated image generation.

Train reinforcement learning agents using PPO, SAC, DQN, TD3, DDPG, and A2C algorithms with a scikit-learn-like API. Supports custom Gymnasium environments, vectorized environments, callbacks, and model persistence.

Calculate sample sizes, minimum detectable effects, and power curves for study planning using closed-form formulas or Monte Carlo simulation.

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces).

Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Covers over-representation analysis (ORA), Gene Set Enrichment Analysis (GSEA), and single-sample scoring using gseapy, g:Profiler, and Enrichr libraries.

Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.

Write scientific manuscripts in full paragraphs using IMRAD structure, with citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA) for research papers and journal submissions.

Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries.

Design experiments and studies before data collection — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable.

Design custom laboratory hardware as parametric build123d models and export fabrication-ready STEP, STL, and DXF files - microfluidic chips and molds, optomechanical mounts and breadboard adapters, cuvette and microplate holders, tube racks, animal-behavior rigs, and 3D-printed instrument fixtures. Use when a research task needs a physical part that must mate with standardized labware, an optical table, a cage system, or a printer, CNC, or laser process.

Forecast any univariate time series (sales, sensors, energy, vitals, weather) zero-shot using Google's TimesFM foundation model, with point forecasts and prediction intervals from CSV, DataFrame, or array inputs.

Build and deploy apps/applets on the DNAnexus cloud genomics platform, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution.

Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Access large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.

Build and deploy bioinformatics workflows as serverless pipelines on the Latch platform using Python decorators, cloud data management, and GPU support.

Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface, covering loading, preprocessing, drift correction, spike sorting, quality metrics, and unit curation.

Integrate with Benchling's Python SDK and REST API to manage registry entities, inventory, ELN entries, workflows, and Data Warehouse queries for life sciences R&D automation.

Simulates a multi-perspective deliberation council to explore complex questions, decisions, or creative challenges from diverse thinking archetypes.

Formulate testable hypotheses from observations, design experiments, and generate predictions using a structured scientific method framework.

Write Opentrons Protocol API v2 protocols for Flex and OT-2 robots to automate liquid handling, control hardware modules, and manage labware configurations.

Create publication-quality scientific diagrams using AI generation with smart iterative refinement and quality review.

Access and manage LabArchives electronic lab notebooks programmatically via REST API. Create entries, upload attachments, backup notebooks, generate reports, and integrate with Protocols.io, Jupyter, REDCap, and other scientific tools.

Detects available CPU, GPU, memory, and disk resources and generates strategic recommendations for scientific computing tasks.

Guides statistical hypothesis testing with assumption checks, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting for research data.

Prepare ISO 13485:2016 certification documentation for medical device Quality Management Systems, including gap analysis, template-based document creation, and compliance checklists.

Generate comprehensive, professional-grade market research reports (50+ pages) with LaTeX formatting, strategic frameworks, and data-driven visualizations.

Integrates with the protocols.io API v3 to search, create, update, and publish scientific protocols, manage steps and materials, handle discussions, organize workspaces, and upload files.

Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corrupt an analysis. Use whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".

Creates scientific documentation using markdown with embedded Mermaid diagrams as the default format, enforcing a text-based diagram standard with style guides, 24 diagram type references, and document templates.

Generate novel research ideas through structured, conversational brainstorming that explores interdisciplinary connections, challenges assumptions, and identifies research gaps.

Create publication-ready scientific figures with multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and journal-specific formatting using matplotlib, seaborn, and plotly.

Predict 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. Six tasks over a REST API and a hosted MCP server (keyless public demo): promoter regions, splice donor/acceptor sites, enhancer activity, chromatin state, sequence-to-expression (log TPM), and de-novo gene annotation, plus a composite find-genes-then-predict-expression workflow. Use when the user has a gene symbol, a genomic region, or a DNA/FASTA sequence and wants any of these predictions, mentions Genomic Intelligence, genomicintelligence.ai, api.genomicintelligence.ai, or mcp.genomicintelligence.ai.

Generate professional clinical decision support documents for pharmaceutical and clinical research, including biomarker-stratified cohort analyses and evidence-based treatment recommendation reports with GRADE grading, statistical analysis, and publication-ready LaTeX/PDF output.

Automatically detect and analyze scientific data files across 200+ formats, generating detailed markdown reports with quality metrics and analysis recommendations.

Evaluate scientific claims and evidence quality by assessing experimental design, identifying biases and confounders, and applying evidence grading frameworks like GRADE and Cochrane Risk of Bias.

Track physical units and propagate measurement uncertainty in scientific calculations using pint and uncertainties. Use for unit conversion and dimensional checking, GUM uncertainty budgets, Type A and Type B evaluation, coverage factors and expanded uncertainty, Monte Carlo propagation, significant-figure and plus-minus reporting, error propagation through curve fits, CODATA constants, auditing Python code for stripped units or broken uncertainty propagation, and order-of-magnitude plausibility checks using dimensionless groups (Reynolds, Peclet, Damkohler, Knudsen, Biot, Womersley), characteristic scales such as diffusion time or Debye length, and observed magnitude ranges. Trigger on "is this number physically reasonable", "sanity check these units", "what regime is this flow in", or a result that looks off by orders of magnitude.

Prepares and structurally reviews readiness evidence for ISO management-system and laboratory-competence standards - ISO 13485 medical device QMS, ISO 14971 device risk management, ISO/IEC 17025 testing and calibration laboratories, and ISO 15189 medical laboratories. Use when organizing declared scope, controlled documents, risk-management files, scope of accreditation, traceability, CAPA, external-provider controls, or bounded local evidence manifests, and when separating ISO certification from laboratory accreditation, FDA QMSR inspection, CLIA certification, MDSAP, and EU MDR/IVDR evidence boundaries. Not for legal applicability, compliance, certification, or accreditation decisions; contains no clause text.

Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). Use whenever an ontology identifier must be produced or checked - annotating tissue, cell type, disease, phenotype, assay, chemical, organism, sex, or developmental stage fields; preparing metadata for GEO, ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or mapping between ontologies. Triggers include "ontology term", "ontology ID", "CURIE", "controlled vocabulary", "UBERON", "CL:", "MONDO", "HPO", "EFO", "ChEBI", "NCBITaxon", "GO term", "PATO", "annotate this tissue/cell type/disease", and any request to emit or verify an identifier shaped like PREFIX:0001234.

Multivariate severity assessment and humane endpoint prediction for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast forecasting. Use when combining welfare readouts — body weight or weight loss, body temperature, clinical or nesting scores, biomarkers, activity, heart rate, burrowing, wheel running — into one severity score per animal per day, when asking which animals are at risk of reaching a humane endpoint or when one will be reached, when defining attention/danger zones or thresholds on a severity scale by kernel density estimation, or when reporting severity for a 3Rs, refinement, animal-welfare, or EU Directive 2010/63/EU severity-assessment context. Covers directionality ("turned" variables), baseline normalization, reference sets, RELSA weights, ARIMA prediction intervals, and RMSE/PICP/MPIW evaluation.

Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include "method validation", "analytical method validation", "AMV", "validation protocol", "acceptance criteria", "linearity", "reportable range", "accuracy and precision", "repeatability", "intermediate precision", "recovery", "LOD", "LOQ", "detection limit", "quantitation limit", "specificity", "robustness", "method transfer", "method comparison", "Deming", "Passing-Bablok", "Bland-Altman", "equivalence testing", "OOS investigation", "ICH Q2", "Q2(R2)", "Q14", "USP 1225", "ICH M10", "incurred sample reanalysis", "ISR", "CLSI EP", and any request to show that an assay works.

Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry. Use whenever a question depends on the current state of a pathogen population rather than on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence has moved week to week. Triggers include "variant surveillance", "genomic surveillance", "what variant is circulating", "dominant variant", "Pango lineage", "lineage prevalence", "growth advantage", "SARS-CoV-2 variant", "XFG", "clade 2.3.4.4b", "H5N1 genotype", "influenza clade", "RSV/mpox/measles/dengue lineage", "CoV-Spectrum", "LAPIS", "Nextclade", "pango-designation", and any request to report what a pathogen population looks like today.