UBIC Workshops

Materials used for 2024-2025 UBIC (Undergraduate Bioinformatics Club at UCSD) workshops.

Most workshops consisted of a short introduction lecture followed by an interactive notebook. Although workshops were designed to take 90 minutes and not require much previous knowledge, your experience going through these on your own may vary.

I don't plan on updating these, but figured it would worthwile to share the materials for anyone interested. Feel free to send me a message if you have any questions.

Workshop Folders

Fall Quarter Events

• Week 2, Introduction: Introduction to Python for bioinformatics and the workshop series as a whole, including core data types and notebook-based practice.
• Week 4, RNA Seq: RNA-seq analysis foundations with dataframe practice and dimensionality-reduction visualization (PCA, k-means, t-SNE, UMAP).
• Week 6, Population Genetics: Population genetics concepts with a supporting linear algebra review.
• Week 8, Genome Assembly: Genome assembly fundamentals using k-mers, graph-based assembly, and Eulerian path intuition.

Winter Quarter Events

• Week 2, Phylogenetics: Building and interpreting phylogenetic trees from sequence data (FASTA/alignment/parsimony concepts).
• Week 4 , Structural Biology: Structural bioinformatics with AlphaFold/ColabFold and protein structure exploration.
• Week 6, Cell Imaging: Cell imaging and spatial transcriptomics analysis (MERFISH-focused tutorial).
• Week 8, Population Genetics: Population genomics/GWAS workflow, including SNP association testing and heritability context.

Spring Quarter Events

• Week 2, Gene Regulation Networks: Gene regulation modeling with transcription factors, probability, and Bayesian networks.
• Week 4, Biomedical Informatics: Biomedical informatics and sepsis prediction using clinical time-series data.
• Week 6, Computational Neurobiology: Computational neurobiology using Hodgkin-Huxley neuron modeling.

Credits

Workshops were prepared by the workshop committee Willard Ford (@WillardFord), Annapurna Saladi (@asaladi), Megan Chen, and freshman reps Etasha Thareja (@etashathareja), and Harper Hipps(@hhipps) for educational use in the Undergraduate Bioinformatics Club at UCSD. Most sources are cited in the notebooks and slides themselves, but if you can't find what you're looking for feel free to open an issue.

Descriptions of workshops on this page were generated by codex-cli and edited by Willard. Everything else in this repo was generated by human authors before LLMs became popular.