COBRApy Metabolic Modeling

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis. Part of the AlterLab Academic Skills suite.

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

Part of the AlterLab Academic Skills suite. Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

Design and simulate a minimal CPU from scratch: define an instruction set architecture (ISA), build the datapath (ALU, register file, program counter, memory interface), design the control unit (hardwired or microprogrammed), implement the fetch-decode-execute cycle, and verify by tracing a small program clock cycle by clock cycle. The capstone "computer inside a computer" exercise that composes combinational and sequential building blocks into a complete processor.

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.