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simulation-orchestrator
Provide tools to manage multi-simulation campaigns: generate parameter sweeps, track job execution status, and aggregate results from completed runs. ...
simpy
SimPy is a process-based discrete-event simulation framework based on standard Python. Use SimPy to model systems where entities (customers, vehicles,...
organoid-drug-response-agent
The Organoid Drug Response Agent provides AI-driven analysis of patient-derived organoid (PDO) drug screening data for personalized treatment selectio...
bio-flow-cytometry-differential-analysis
Reference examples tested with: R stats (base), edgeR 4.0+, ggplot2 3.5+, limma 3.58+ Before using code patterns, verify installed versions match. If ...
cellfree-rna-agent
The Cell-Free RNA Analysis Agent provides comprehensive analysis of circulating cell-free RNA (cfRNA) from plasma and other biofluids for cancer detec...
bio-reporting-jupyter-reports
import papermill as pm pm.executenotebook( 'analysistemplate.ipynb', 'outputreport.ipynb', parameters={ 'inputfile': 'data/counts.csv', 'conditioncol'...
bio-genome-engineering-grna-design
Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <pac...
gene-panel-design-agent
The Gene Panel Design Agent provides AI-driven design of targeted sequencing panels for clinical diagnostics, cancer profiling, pharmacogenomics, and ...
bio-spatial-transcriptomics-spatial-statistics
Reference examples tested with: numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+, squidpy 1.3+ Before using code patterns, verify installed version...
chromosomal-instability-agent
The Chromosomal Instability Agent analyzes CIN signatures to predict cancer prognosis, immunotherapy response, and therapeutic vulnerabilities. It int...
pytorch-lightning
PyTorch Lightning is a deep learning framework that organizes PyTorch code to eliminate boilerplate while maintaining full flexibility. Automate train...
bio-workflows-merip-pipeline
FASTQ → QC → Align IP+Input → Peak calling → Annotation → Differential → Visualization fastp -i IPR1.fq.gz -I IPR2.fq.gz \ -o IPR1trimmed.fq.gz -O IPR...