The library

compare-biosamples · Comparing metadata and attributes across ENCODE biosamples.

computer-use-agents · Deploying AI agents to automate computer interactions and workflows.

gget · Querying genomic databases and retrieving sequence and annotation data.

cross-reference · Linking data across multiple heterogeneous sources with consistent identifiers.

conductor-core · Closing feedback loops across spec→resolve→orchestrate→enforce→review→ship in multi-organ systems where each phase owns a distinct gate.

ginkgo-cloud-lab · Validating protein expression or generating rapid fluorescent bioart when local infrastructure unavailable; 5–11 day turnaround beats lab overhead.

data-provenance · Publishing genomics workflows where 'we aligned with STAR' is too vague—lock down exact versions, genomes, parameters, and accessions for publication-ready methods.

luxury-frontend-design · Client-facing high-end e-commerce, SaaS landing pages, or luxury event sites where visual polish directly impacts conversion and brand perception.

conductor-orchestrator · Multi-organ builds where each task needs the right capability loadout (not generic) and visual work needs brand taste injected before code generation.

glycoengineering · Antibody Fc optimization (enhanced ADCC/CDC), therapeutic half-life engineering, or vaccine design where glycan patterns directly control immune recognition.

disease-research · Disease mechanism research where non-coding variants need interpretation, or identifying therapeutic targets from epigenomic evidence rather than coding-only databases.

conducty-bootstrap · First-time Conducty users who need muscle-memory of the full cycle (Plan→Execute→Verify→Improve) before running real multi-agent work.

gtars · Genomic interval analysis where performance matters (millions of regions) or tokenization for genomic ML models; orders of magnitude faster than bedtools in pure Python.

download-encode · Bulk download and organization of ENCODE files when local infrastructure needed; starts with dry_run preview to confirm scope before committing.

1481-receive-feedback_553c0e44 · Closing the learning loop in multi-agent systems where human feedback refines next-cycle decisions.

conducty-checkpoint · Enforcing independent evidence per task before multiplying work; prevents bad specs from cascading into later phases.

histolab · Cancer histopathology or tissue classification when patch-level features matter more than whole-slide; enables GPU-scale training on high-res scans.

ensembl-annotation · Genomics workflows where you need canonical gene structure, variant consequences, or cross-species orthologs; authoritative source (if on-date).

conducty-code-review · Pre-merge correctness gate enforcing 5-lens rigor; catches bugs, security issues, and missed simplifications before ship.

hugging-science · Rapid iteration on NLP/CV scientific tasks where pre-trained backbone beats training from scratch; HF Hub democratizes state-of-art.

epigenome-profiling · Cancer or developmental biology where multi-mark epigenome profiles reveal tumor states or differentiation trajectories better than single assay.

conducty-context · Bootstrapping Conducty: seeds the vault with project knowledge so next /plan reads architecture upfront.

hypogenic · Drug discovery when rational design beats screening; structure-guided SAR (structure-activity relationships) directly from sequences.

functional-screen-analysis · Functional genomics when you have CRISPR/RNAi data and need to rank candidates by statistical rigor; MAGeCK gold standard.

conducty-debug · Efficiently diagnosing where a prompt failed (plan/prompt/code level) rather than blindly retrying

geo-connector · Finding complementary expression datasets in GEO that validate or extend ENCODE regulatory findings

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.