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Resources

Everything BORA teaches with is free and openly licensed. If a resource costs money, it does not belong on this page.

Curated links, hosted nowhere. BORA does not re-host copyrighted material. We point to the original sources and add our own Markdown walkthroughs and Colab notebooks on GitHub.

Stage 0 — Foundations

  • GitVersion control, branching, and pull requests.
  • PythonSyntax, pandas, plotting.
  • Rtidyverse, ggplot2, and basic statistical testing.
  • ShellFilesystem navigation, piping, and command-line tools.
  • EthicsResearch integrity, authorship norms, data privacy, plagiarism.

Public data sources

  • NCBISRA, GenBank, BioProject, BioSample.
  • ENAEuropean Nucleotide Archive.
  • OpenAlexOpen bibliographic graph.
  • GISAIDViral genomic surveillance data, free registration.
  • BBSBangladesh Bureau of Statistics.

Analysis toolchain

  • ColabFree notebook compute.
  • CondaReproducible environments.
  • NextflowPipeline orchestration.
  • NextcladeViral genome QC and clade assignment.
  • QuartoReproducible reports.

Writing & publishing

  • StructureIMRaD and reusable methods sections.
  • ReportingSTROBE, PRISMA, ARRIVE.
  • RefsZotero; Vancouver and APA styles.
  • PreprintWhy to post early.
  • JournalsLegitimate OA venues and predatory-journal checks.
Predatory-journal warning. Students are taught to check a venue against DOAJ, COPE membership, and indexing before submitting anything. Paying to publish fast is the single most common way early-career researchers waste money and credibility.