Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
Select and apply numerical differentiation schemes for PDE and ODE discretization — generate finite-difference stencils at arbitrary order and accuracy, choose between central,…
Explore and optimize simulation parameters via design of experiments (DOE), sensitivity analysis, and optimizer selection — generate Latin Hypercube, quasi-random, or factorial…
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructi — from…
Select and configure time integration methods for ODE and PDE simulations — choose among explicit Runge-Kutta, BDF, Rosenbrock, and Adams families, set relative and absolute error…
Extract, analyze, and summarize simulation output data — pull spatial fields at specific timesteps, compute time-series trends and detect steady state, extract line profiles…
Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building…
Plan and evaluate mesh generation for numerical simulations — estimate grid resolution from physics scales (interface width, boundary layers, wavelengths), check aspect ratios and…
Handle mental health crisis situations in AI coaching safely. Use when implementing crisis detection, safety protocols, emergency escalation, or suicide prevention featur — from…
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIA — from…
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics.
Create publication-quality plots and visualizations using matplotlib and seaborn. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).