The library

imaging-data-commons · Accessing large-scale radiology and pathology datasets for AI training without authentication

gnomad-variants · Filtering ENCODE regulatory variants by population rarity and assessing gene constraint before functional validation

skills-and-code-style-contribution · Formalizing code style conventions in a team repository through structured proposal workflows

conducty-execute · Orchestrating agentic work with tracer-first risk detection and calibrated review rigor matching task complexity

gtex-expression · Validating that genes near ENCODE regulatory elements are actually expressed in the matching tissue

conducty-improve · Closing the feedback loop so each plan produces measurable improvements to the next plan

iso-13485-certification · Understanding ISO 13485 requirements for medical device startups seeking certification

gwas-catalog · Finding GWAS variants that overlap ENCODE regulatory elements to identify disease-associated regulatory effects

conducty-obsidian · Centralizing Conducty plan state, lessons, and design decisions where they persist across sessions

labarchive-integration · Automating electronic lab notebook entry from instrument outputs to create audit trails

hic-aggregation · Comparing 3D genome structure across cell types by aggregating replicate Hi-C experiments

conducty-plan · Translating shaped work into a time-budgeted, risk-aware execution plan with clear milestones

lamindb · Building a lineage-tracked, versioned registry of biological datasets for reproducible analysis

histone-aggregation · Creating robust consensus histone modification profiles by aggregating multiple ChIP-seq replicates

conducty-review · Systematically extracting what worked, what failed, and why—before moving to the improvement phase

latchbio-integration · Running large-scale bioinformatics pipelines on managed cloud infrastructure without managing clusters

integrative-analysis · Creating a coherent multi-layer view of gene regulation by integrating ENCODE with expression, variation, and protein data

2224-editor-optimization_5342a688 · Teams debugging slow editor performance on weak hardware or large codebases.

conducty-shape · Medium/high-complexity goals where requirements are unclear and scope needs bounding before implementation.

jaspar-motifs · Confirming ChIP-seq specificity or discovering co-binding regulatory complexes when gold-standard target validation is required.

random-number · Quick random sampling in simple workflows when no statistical properties or reproducibility are needed.

conducty-ship · Pre-merge gates that must mechanically verify lint, tests, and secrets before human approval.

liteparse · Local parsing with spatial awareness when cloud APIs are forbidden or bounding boxes are required for RAG grounding.

liftover-coordinates · Integrating historical GWAS or legacy ENCODE data when assembly consistency is a silent correctness requirement.

05-ai-observability-and-reversibility · Pre-deployment review of AI-assisted features when customer trust and reversibility are non-negotiable.

conducty-system · Multi-plan projects where system-level learning (what worked, what failed, what changes) is valued over ad-hoc execution.

methylation-aggregation · Understanding tissue-specific regulatory chromatin state when aggregated epigenetic methylation landscape is the bottleneck.

conducty-tdd · Feature development where verification is continuous and acceptance criteria are unambiguous before coding starts.

markdown-mermaid-writing · Technical narratives where inline diagrams clarify concepts without external tool switching.

motif-analysis · Discovering unknown binding factors or validating ChIP-seq specificity when a prior motif is not available.

conducty-terse · Prompt engineering where every token spent must directly advance the acceptance criteria.

market-research-reports · Go/no-go decisions where market sizing and competitive threat assessment are the binding constraints.

multi-omics-integration · Systems understanding of gene regulation when no single modality captures the full biology.

structured-attack-campaign · Red-team validation when system robustness against coordinated attack is a non-negotiable requirement.

conducty-vault-graph · Maintenance sweeps when vault noise accumulates and signal-to-noise ratio drops.

markitdown · Bulk document ingestion for RAG when format diversity requires unified conversion.

peak-annotation · Functional interpretation of ChIP-seq experiments when gene-centric answers are needed quickly.

conducty-verify · Marking work complete only after running verification commands and reading output.

matchms · Identifying unknown compounds from mass spectra using spectral similarity.

pipeline-atacseq · Processing ATAC-seq FASTQ to peaks with proper Tn5 transposase offset correction.

conducty-worktrees · Parallel prompt execution targeting the same repo without merge conflicts.

matlab · Matrix operations and scientific computing with full visualization control.

pipeline-chipseq · Processing ChIP-seq data with treatment/control comparisons and IDR replicate analysis.

configuring-tauri-apps · Fine-tuning Tauri desktop app security, permissions, and platform behavior.

matplotlib · Creating publication-quality scientific plots with full customization control.

pipeline-cutandrun · Processing CUT&RUN epigenomic data with targeted chromatin profiling.

configuring-tauri-capabilities · Fine-tuning Tauri desktop app security, permissions, and platform behavior.

medchem · Designing drug molecules with integrated ADME and toxicity assessment.

eve-lab-topology-validation · Validating enzymatic reaction networks for synthetic biology feasibility.

configuring-tauri-csp · Fine-tuning Tauri desktop app security, permissions, and platform behavior.