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Review papers, drafts, and research ideas with evidence-linked feedback focused on improvement. Audit low-stakes assessment rubrics, trace supporting evidence, and check rater agreement and uncertainty without ranking people or recommending consequential decisions.

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• Prepare evidence-linked feedback on a paper draft
• Review strengths and limitations of a research idea
• Check assessment criteria and evidence traceability

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.

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• Map funding-call requirements to proposal sections
• Review research aims against evaluation criteria
• Align budgets and timelines with the research plan

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.

한국어 요약은 준비 중입니다. 영어 요약을 표시하고 있습니다.

• Check whether a paper's conclusions match its evidence
• Review study design before collecting data
• Identify statistical problems and potential biases

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.

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• Design new PCR or RT-qPCR primer pairs
• Review existing primers for structure and unintended products
• Plan exon-junction or isoform-specific assays

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.

한국어 요약은 준비 중입니다. 영어 요약을 표시하고 있습니다.

• Simulating quantum dynamics with environmental dissipation
• Choosing a solver for a quantum model
• Checking numerical convergence and state validity

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.

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• Draft evidence-based comments on a scientific manuscript
• Check methods, statistics, and reproducibility reporting
• Choose reporting guidelines and identify missing information

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.

한국어 요약은 준비 중입니다. 영어 요약을 표시하고 있습니다.

• Predicting voltage changes during charge, discharge, and rest
• Comparing simulation results with measured cycling data
• Checking how numerical settings affect predictions

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.

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• Finding biomedical papers on a topic
• Comparing methods and results across papers
• Reviewing regulatory documents and clinical trials

Find and download public cancer imaging data from NCI Imaging Data Commons. Select CT, MR, PET, or pathology datasets using metadata, view images in a browser, and check licenses and citations before using the data.

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• Find cancer images by disease, modality, or anatomical site
• Download selected DICOM image series
• View radiology and pathology images in a browser

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.

한국어 요약은 준비 중입니다. 영어 요약을 표시하고 있습니다.

• Turn an observation into testable research hypotheses
• Compare competing explanations and distinguishing predictions
• Define measurements and review an analysis plan

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.

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• Screen compound libraries with drug-likeness rules
• Flag PAINS and other structures for review
• Combine property, structure, and complexity filters

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.

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• Calculate carbonate chemistry from paired seawater measurements
• Assess aragonite and calcite saturation
• Convert laboratory results to ocean temperature and pressure

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.

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• Prepare a literature review for a thesis or research paper
• Record reproducible searches across scholarly databases
• Track screening decisions and exclusion reasons

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.

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• Looking up gene details and sequences
• Exploring protein structures and residue annotations
• Comparing tissue expression and disease associations

Analyze candidate sites where sugars may attach to proteins, review experimental evidence, and prepare prediction or structural shielding workflows. Supports mutation planning, antibody glycan comparisons, and interpretation of site-specific measurements while distinguishing candidates from confirmed modifications.

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• Find candidate glycosylation sites in protein sequences
• Plan mutations and rescan altered sequences
• Compare antibody Fc glycoforms

Prepare experiments for Ginkgo Cloud Lab by choosing a protocol, organizing required inputs, checking configured pricing, and navigating browser ordering. Covers protein expression, RNA synthesis, stability assays, and setup of measurement methods.

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• Choosing a protein expression and purification protocol
• Preparing inputs for mRNA or circRNA synthesis
• Reviewing stability assays and measurement method setup

Look up biomedical relationships in ARAX using explicit entity types and tightly bounded paths. Inspect direct links or paths through one intermediate entity, along with returned publications and source records, to identify candidates for further research.

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• Checking recorded drug–gene relationships
• Exploring paths between a drug and a disease
• Inspecting publications and original data sources

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.

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• Draft liquid-transfer or serial-dilution protocols
• Review deck layout, volumes, and tip changes
• Update older protocols for supported API versions

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.

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• Collect PDFs and web sources in a research notebook
• Ask questions about selected sources with citations
• Apply custom summaries and text transformations

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.

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• Prepare sample sheets for matched tumor and normal samples
• Review generated launch files with a dry run
• Submit a Nextflow launcher to a computing cluster

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.

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• Find papers and preprints on a research topic
• Look up a paper by DOI, PMID, or arXiv ID
• Find openly available full text or PDFs

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.

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• Find participants carrying variants that match specified criteria
• Inspect genetic variants carried by selected participants
• Identify participants with two reference copies at a position

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.

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• Investigating protein stability after a mutation
• Measuring structural changes and flexibility
• Tracking protein–ligand contacts

Generate candidate positions and orientations for small molecules binding to proteins with DiffDock and DiffDock-L. Prepare single or batch docking runs, organize predicted poses by model confidence, and review validation needs without treating confidence as binding affinity.

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• Predicting binding poses for a protein and small molecule
• Preparing and validating batch docking inputs
• Comparing poses across receptor conformations