Bangladesh Open Research Academy borabd.org
Learning hub

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 — the minimum needed to collaborate on an analysis.
  • PythonSyntax, pandas, plotting. Enough to clean a dataset and produce a figure.
  • Rtidyverse, ggplot2, and basic statistical testing.
  • ShellNavigating a filesystem, piping, and running command-line bioinformatics tools.
  • EthicsResearch integrity, authorship norms, data privacy, plagiarism.

Public data sources

  • NCBISequence Read Archive, GenBank, BioProject, BioSample.
  • ENAEuropean Nucleotide Archive — mirrors and complements NCBI.
  • OpenAlexOpen bibliographic graph for literature mining and bibliometrics.
  • GISAIDViral genomic surveillance data (registration required, free).
  • WHO/FAODisease burden, surveillance, and livestock statistics.
  • BBSBangladesh Bureau of Statistics — national production and demographic data.

Analysis toolchain

  • ColabFree notebook compute for tutorials and light analysis.
  • CondaReproducible environments for bioinformatics tooling.
  • NextflowPipeline orchestration for multi-step genomic workflows.
  • NextcladeClade assignment and quality control for viral genomes.
  • QuartoReproducible reports that mix code, output, and prose.

Writing & publishing

  • StructureIMRaD, how to write a methods section someone can actually re-run.
  • ReportingSTROBE, PRISMA, ARRIVE — which checklist applies to which design.
  • RefsZotero for reference management; Vancouver and APA styles.
  • PreprintHow to post to a preprint server and why to do it early.
  • JournalsChoosing a legitimate open-access venue and spotting predatory ones.
How the hub is built

Versioned, forkable, alumni-maintained

01

Markdown on GitHub

All learning content lives as versioned Markdown in a public repository. Anyone can read the history, fork it, or open a pull request.

02

Notebooks for practice

Each module ships with a Colab notebook so students run real code without installing anything or paying for compute.

03

Alumni keep it current

Stage 5 mentors are expected to fix and extend the modules they were taught with. The curriculum improves with every cohort.

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.