Research, academic papers, education, and exam prep (4.2K skills)
Run molecular property predictions, explore molecular shapes, and estimate how compounds bind to proteins through a cloud Python API. Process compound batches and connect modeling steps without maintaining local high-performance computing infrastructure.
Calculate equilibrium phases, their molar fractions, and compositions from a local thermodynamic database using pycalphad. Compare temperatures, check material balance and sampling stability, and export results with recorded conditions and database identifiers.
Simulate lithium-ion battery charging, discharging, and rest with PyBaMM. Track voltage and capacity, record parameter sources, check how numerical settings affect predictions, and compare simulated curves with measured cycling data.
Simulate quantum dynamics, steady states, and spectra with QuTiP 5. The skill guides solver selection and checks physical assumptions, units, state validity, and numerical convergence so local simulation results can be reviewed with their limitations.
Validate particle data and run RELION refinement for single-particle cryo-electron microscopy. Check independently refined half maps, calculate diagnostic map correlations, and perform soft-mask postprocessing while preserving execution logs and restart information.
Design and review laboratory automation with PyLabRobot, including equipment layouts and liquid transfers. Check planned volumes and tip capacities, draft protocols, and simulate operations in software before a trained operator reviews any physical run.
Prepare constructive review drafts for scientific manuscripts, protocols, preprints, and proposals. Organize checks of claims, evidence, methods, statistics, reproducibility, ethics, figures, and citations into specific comments that a responsible human reviewer can verify and revise.
Retrieve, validate, and export protocols.io experimental procedures while preserving version and attribution details. Check saved JSON offline, save protocol PDFs, or prepare reviewable plans for updates and publication; bundled scripts do not execute changes.
Assess scientific claims by examining study design, statistics, bias, and evidence quality. Use structured appraisal frameworks to identify supported conclusions, explain uncertainties, and propose practical improvements with concerns traced to specific evidence.
Prepare and review research funding proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Maps application requirements to draft sections, identifies gaps, and helps refine research aims, budgets, impact statements, and responses to reviewers.
Design and review PCR and RT-qPCR primers, short DNA sequences used to start amplification. Assess predicted structures and unintended products under explicit reaction conditions, with reports that track reference sequences, coordinates, and search limits.
Manage Zotero reference libraries through Python: search, create, update, and delete references, organize collections and tags, upload PDF attachments, and export citation data. Guidance covers both remote libraries and access through a running local Zotero app.
Organize research sources in self-hosted Open Notebook, then search them, ask questions with citations, create notes, transform text, or generate podcasts with multiple speakers. Supports REST API automation and configuration of local or cloud AI providers.
Prepare and run molecular dynamics simulations with OpenMM, then analyze molecular motion with MDAnalysis. Examine protein flexibility, structural changes, and protein–ligand contacts through calculations and plots of simulated trajectories.
Screen compound libraries for drug discovery using drug-likeness guidelines, structural alerts that flag patterns for review, and molecular complexity measures. Combine criteria to shortlist candidates and retain filtering results with reasons for further assessment.
Turn observations or preliminary findings into testable research plans. The skill separates candidate hypotheses from evidence, develops competing explanations and distinguishing predictions, and helps specify measurements and analysis plans for preregistration, a research plan recorded before testing.
Look up genes, sequences, protein structures, expression patterns, and disease associations across more than 20 bioinformatics resources using command-line tools or Python. Useful for interactive exploration, with results that can be saved for further analysis.
Plan and write literature reviews using multiple scholarly databases. Document searches, screen papers, synthesize findings, and check citations, then prepare Markdown or PDF reports with transparent selection counts, evidence limitations, and reproducible search records.
Search the 1000 Genomes Project’s 3,202 participants for genetic variants and their carriers. Filter by frequency or annotations, inspect variants in selected individuals, and check relatedness between two participants.
Prepare and launch nf-core/pacsomatic workflows for matched tumor and normal PacBio HiFi samples. Generate sample sheets and launch files from unaligned BAM inputs, run local checks, submit cluster launchers, and troubleshoot startup failures.
Finds papers, preprints, citation links, and openly available full text through 18 scholarly APIs. Selects databases for the task and returns relevant records with search parameters, identifiers, and access dates so the retrieval can be repeated.
Search biomedical papers, regulatory documents, clinical trials, and protein records through GXL Paperclip. Extract comparable information across documents, inspect figures, and organize findings with citations linked to the source lines that support them.
Calculate seawater carbonate chemistry from two independent measurements using PyCO2SYS. Produce pH, carbonate species, and mineral saturation results, convert laboratory conditions to ocean conditions, and propagate measurement uncertainty while recording calculation assumptions.
Create, review, migrate, and simulate Python liquid-handling protocols for Opentrons Flex and OT-2 robots. Covers deck layout, labware, pipettes, modules, volumes, and tip policies, with checks for Opentrons App analysis and operator review before physical runs.