SAmageckK-Dense-AI-scientific-agent-skills#scientific-agent-skillsResearchbioinformaticsgenomicsscientific computingAnalyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and library QC, and produces gene hit...
SAmarine-carbonate-chemistryK-Dense-AI-scientific-agent-skills#scientific-agent-skillsResearchscientific computingchemical-oceanographycarbonate-systemSolves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired total alkalinity, dissolved...
SA13c-metabolic-fluxK-Dense-AI-scientific-agent-skills#scientific-agent-skillsResearchbioinformaticsscientific computingmetabolic-flux-analysisEstimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart...
SAcellprofilerK-Dense-AI-scientific-agent-skills#scientific-agent-skillsResearchbioinformaticsquality controlmicroscopyRuns reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/channel manifests, headless...
SAfolklore-variant-evidenceK-Dense-AI-scientific-agent-skills#scientific-agent-skillsResearchMCP integrationgenomicsliterature-retrievalRetrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one supported GRCh38 germline nuclear...
Nnav-deep-researchalekspetrov-navigator#navigatorv8.4.11Researchweb-researchknowledge graphcited-reportWeb deep research producing a cited report from fetched sources, adversarially reviewed and gate-checked, with conclusions ingested into the knowledge graph. Auto-invoke when user...
OMbio-sketchpradyumnasagar-open-research-skills#ors-metaResearchgrant writingNSFNIHUse when generating an NIH or NSF Biographical Sketch in SciENcv (current format): personal statement, contribution statements (new 2025 NIH format), positions and honors,...
OMbrainstormingpradyumnasagar-open-research-skills#ors-metaResearchideationresearch-planningscientific-thinkingCreative research ideation and exploration. Use for open-ended brainstorming, interdisciplinary connections, challenging assumptions, or identifying research gaps in early-stage...
OMcritical-thinkingpradyumnasagar-open-research-skills#ors-metaResearchbias-detectioncritical-appraisalevidence-gradingEvaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE,...
OMdarpa-baapradyumnasagar-open-research-skills#ors-metaResearchfundinggrant-proposalsdarpaUse when responding to a DARPA Broad Agency Announcement: white paper vs full proposal, Heilmeier Catechism framing, program manager engagement, BAA-specific formatting, cost...
OMercpradyumnasagar-open-research-skills#ors-metaResearchgrant writingerc-proposalsacademic-fundingUse when drafting or revising an ERC proposal: B1 Extended Synopsis (2 pp), B2 Full Proposal (≈7–8 pp), CV, Track Record, resources, ethics issues table, and host institution...
OMfailure-handlingpradyumnasagar-open-research-skills#ors-metaResearchreplicationscientific methodpreregistrationHandle negative results, failed experiments, preregistration violations, and replication failures. Use for reporting null findings, deciding when to revise vs. discard hypotheses,...
OMfoundation-grantspradyumnasagar-open-research-skills#ors-metaResearchgrant writingresearch proposalsbudgetingUse when applying for private foundation grants: Templeton, HHMI (Investigator, Freeman Hrabowski, Hanna Gray), Damon Runyon, Searle, Pew Scholars, McKnight, Packard, Keck....
OMgrant-reviewpradyumnasagar-open-research-skills#ors-metaResearchpeer reviewscientific writingfunding-agenciesReview a research grant proposal (NIH/NSF/ERC/private foundation): section-by-section criteria, panel process, criterion scoring, overall impact, reviewer etiquette, and a...
OMhypothesis-generationpradyumnasagar-open-research-skills#ors-metaResearchexperimental designscientific methodfalsifiabilityGenerate testable hypotheses from literature and observation. Use for converting research gaps, contradictory findings, cross-domain analogies, or clinical observations into...
OMmanuscript-reviewpradyumnasagar-open-research-skills#ors-metaResearchpeer reviewscientific-manuscriptsresearch-integrityConduct a formal peer review of a scientific manuscript for a journal: section-by-section evaluation, reporting-checklist compliance, major/minor comments, recommendation to...
OMnih-k-seriespradyumnasagar-open-research-skills#ors-metaResearchgrant writingproposal-draftingnih-fundingUse when planning or drafting an NIH mentored career-development award (K01, K08, K23, K99/R00, K25, K22, K07): Candidate Section, Mentorship Plan, Training Plan,...
OMnih-r01pradyumnasagar-open-research-skills#ors-metaResearchgrant writingacademic writingproposal-developmentUse when planning, drafting, or revising an NIH R01 (Research Project Grant) application: Specific Aims, Significance/Innovation/Approach, Authentication, Budget Justification,...
OMnsf-standardpradyumnasagar-open-research-skills#ors-metaResearchgrant-proposalsnsf-pappgresearch-fundingUse when planning, drafting, or revising an NSF Standard Research Proposal: Project Description (15 pp), Data Management Plan, Postdoc Mentoring Plan, Broader Impacts,...
OMperspective-tourpradyumnasagar-open-research-skills#ors-metaResearchproject scopingmulti-perspective analysisgrant writingMulti-perspective exploration of a research question using 5-7 expert lenses. Use for grant specific aims, manuscript framing, project scoping, or when a question benefits from...