「publication」の検索結果

Spring Modulith 2.0 implementation for bounded contexts in Spring Boot 4. Use when structuring application modules, implementing @ApplicationModuleListener for event-driven communication, testing with Scenario API, enforcing module boundaries, externalizing events to Kafka/AMQP, building a modular monolith, defining module dependencies, managing inter-module events, or organizing DDD modules as packages. Covers package-based module boundaries, named interfaces, event publication, and Scenario API testing. For architecture decisions, see domain-driven-design skill.

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Use when the user provides a Facebook URL or asks to read personal posts, comments, reactions, friends, timelines, profiles, stories, feeds, groups, events, or saved items, or to publish personal text posts, comments, and replies, or to discover public events happening near a place, nearby, or in a local area on a date, or to create, edit, publish, or delete their own Marketplace listings. To find, browse, or buy Marketplace listings, use shopping instead. Use pages commands for managed Facebook Page discovery, insights, native draft editing/deletion, same-draft publication, approved posts and native scheduling.

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Write recurring newsletter issues with a consistent format and POV using the Curiosity Gap (George Loewenstein) and David Perell's Online Writing framework. Different from one-off emails (use /content-writer or /email-nurture). Use when the user asks for a newsletter, weekly/monthly newsletter, "write this week's issue", recurring email, Substack issue, internal newsletter, or any periodic publication with subscribers. Reads brand voice and content library from knowledge/. For a nurture or lifecycle sequence, see email-nurture. For long-form thought leadership, see thought-leadership-writer. For the monthly plan, see social-calendar.

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Read and write beehiiv: list publications, subscribers, and posts; add subscribers. Trigger phrases: beehiiv, newsletter subscribers.

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Migrating Classic Knowledge (KnowledgeArticleVersion / Article Types) to Lightning Knowledge (Knowledge__kav with record types): article-type-to-record-type mapping, multi-language translation preservation, data category re-architecture, file attachment porting, version and publication-state retention, channel visibility translation, and downstream Case Feed / Community / Bot rewiring. NOT for new Lightning Knowledge setup or editorial publishing workflow design (use admin/knowledge-base-administration).

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Use when creating publication-grade scientific figure images or prompts, including graphical abstracts, mechanism diagrams, anatomy diagrams, surgical step figures, experimental workflows, pathology mechanisms, device principles, and structured paper illustrations. If the user asks to generate the image, use ChatGPT image generation.

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Develop an independent visual language and turn the human-chosen direction into a production-ready graphic, brand, campaign, publication, web, or product system. Use when originality and differentiation matter enough to escape generic AI and Big Tech aesthetics. Guides a minimum-evidence start, ten isolated typography-led HTML design directions made only from type, color, and space, visual-first human judgement, explicit commitment, and concrete Round 2 production. Do not use for routine UI fixes, small components, or applying an existing design system.

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Delegate implementation to Codex, grok, or cursor-agent, then review the diff, send it back to iterate, gate on the full test suite, and ship it as a PR. Use this whenever the user wants Codex, the grok 后端, or cursor-agent to write code, mentions handing off / delegating implementation to one of those backends, asks to work through a plan or spec unit-by-unit with an implementation backend doing the coding, or wants a review-and-merge loop wrapped around delegated output — and also when resuming such a loop ("keep going", "next unit", "继续下一个"). It encodes constraints that are expensive to rediscover: the implementer runs in the real environment behind backend-specific git and publication boundaries, must not be pointed at a full test suite by default, and its self-report is a claim rather than evidence. This loop expects an approved plan or an equivalently precise spec; settle an unsolved high-level goal into a plan first, using the engineering-mode skill when it is installed.

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Scope, preregister, execute, audit, normalize, and publish GEODE evaluations with research-question, reproduction, attempt-lineage, trajectory, verifier-receipt, and immutable artifact contracts. Use for benchmark runs or comparisons, eval-artifact and cache-accounting audits, GPT or subscription result normalization, research question or hypothesis framing, retry diagnosis, trajectory publication, DPO or reward-data readiness reviews, and requests involving MCPMark, tau2, BFCL, Agent-World, HAL, Terminal-Bench, or Toolathlon.

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Drafts a standalone API Acceptable Use Policy (AUP) for incorporation by reference into a master API license or terms-of-service agreement. Produces a publication-ready template with prohibited-use matrix, developer security checklist, graduated enforcement framework, AI/ML training restrictions, and versioning playbook. Trigger when a user needs to draft or update an API AUP, separate behavioral rules from core API terms, define prohibited API uses, add enforcement or change-management mechanics, or mentions acceptable use policy, developer security requirements, or API enforcement.

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Stage and verify Fusion exports, drawing PDFs, flat-pattern DXF, viewport images and local renders. Use for engineering deliverables, not automatic publication or release.

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Prepare a traceable local Fusion engineering review draft with source identities, artifacts and unresolved assurance gates. Not for sending, publication or release approval.

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Publication-quality statistical visualization with mandatory best practices. Use when creating plots, charts, figures, or any data visualization. Enforces accessibility, uncertainty display, proper labeling, and statistical accuracy.

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Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion estimation from DESeq2/edgeR. Covers the biological-versus-technical replication distinction (technical replicates do not add degrees of freedom for biological inference), replicate-number-versus-sequencing-depth budgeting, scRNA-seq sample-versus-cell allocation under a pseudobulk model, and the critique that "n=3" is a publication convention rather than a power calculation. Use when budgeting a sequencing experiment, writing the sample-size justification in a grant, estimating replicates from pilot data, allocating a fixed budget between samples and depth, or planning scRNA-seq cohort size. For clinical-trial sample size see clinical-biostatistics/power-and-sample-size; for the power-given-n direction see experimental-design/power-analysis.

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Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.

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Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Python) including shared axes/legends/guides collection, panel labels in Nature/Cell convention, and journal-spec sizing. Covers patchwork ≥1.2.0 axes='collect' feature, Type-42 font embedding, and the cairo_pdf save path. Use when composing 2+ subpanels into a single figure for journal submission.

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Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge bundling, community-based coloring, and reproducible seeds using NetworkX, PyVis, igraph, and Cytoscape automation. Use when rendering biological networks for static publication, interactive HTML exploration, or Cytoscape-format export.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Build genome-browser-style multi-track figures with pyGenomeTracks (config-driven), Gviz (R), and IGV batch screenshotting. Covers BigWig coverage tracks, BED/peak overlays, gene-model rendering, Hi-C matrix tracks, BedPE link arcs, spike-in-aware normalization, and the bamCoverage --normalizeUsing trap. Use when producing publication figures of genomic loci with stacked aligned tracks (coverage, peaks, genes, interactions) for ChIP-seq, ATAC-seq, RNA-seq, Hi-C, or generic locus visualization.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF calibration (BF >6 ≈ 90% posterior per Hart 2017; ~5% FDR by BAGEL convention). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.

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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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