Materials & Downloads

All workshop files grouped by topic — also available on the USB backup.

⬇ Download Everything (ZIP)
Linux Basics  ·  Session 03
📊

Linux Basics

Slides (PDF)
📄

superman.md

Practice file
📄

attendants.docx

Hotel
📄

bato.docx

Hotel
📄

chef.docx

Hotel
📄

front-desk-agent.docx

Hotel
📄

housekeeper.docx

Hotel
📄

output.txt

Laboratory
📄

results-summary.txt

Laboratory
⚙️

check_data.sh

Laboratory / scripts
Database Setup & Schema  ·  Sessions 05, 06, 07
⚙️

install-db.sh

PostgreSQL 16 installer
🔄

restore.sh

DB creation & schema restore
🗃️

chado_dump.sql

Training database dump
📊

Ontology Concepts

Slides (PDF)
📊

Chado Schema Deep Dive

Slides (PDF)
📊

Chado Schema Deep Dive (ol1)

Slides variant (PDF)
Reference Genome Loading  ·  Session 08
🧬

11-feature-nipponbare.csv

Nipponbare reference features (pre-built CSV)
⚙️

loadReferenceGenome.sh

Reference genome loader from GFF
⚙️

loadReferenceGenomeWSeq.sh

Reference genome loader with explicit chromosome lengths
Dataset Loading  ·  Session 09
⚙️

uploadDataset.sh

Bulk dataset loader script
📄

sample_accessions.csv

Sample metadata file
📄

sample_list.txt

Stock/sample name list
📄

pos_500_per_chr.txt

SNP positions file
🗜️

demo.tar.gz

Hands-on demo archive
🗄️

load_template.sql

SQL template for bulk \COPY loading
VCF → HDF5 Pipeline  ·  Sessions 11, 12
📋

VCF v4.2 Spec

Format reference (PDF)
🔀

vcftomatrix.sh

VCF → genotype matrix
📦

make_HDF_dataset.sh

Matrix → HDF5 dataset
🧬

pipeline_vcf_to_hdf5.sh

Full pipeline wrapper
📋

Pipeline Run Lab

Lab worksheet (PDF)
📡 If Wi-Fi is unavailable: All slides, scripts, and workshop materials are also available on the distributed USB backup. Open index.html from the USB directly in your browser — all links work offline. (Note: Google Fonts requires an internet connection to display; the page will fall back to system fonts automatically.)