Sources and credits
Everything this workshop builds on, and how to cite it
Where this course came from
This course began as BIOS259: The Art of Reproducible Science – A Hands-on Approach, a mini-course that Aziz Khan proposed and taught at Stanford Biosciences in Winter and Autumn of 2024. Much of the original material (slides, exercises, cheat sheets and setup instructions) is open in the bios259-w24 repository under CC BY 4.0.
The Stanford course was developed and taught with help from:
- Co-instructors: Clemens - Stanford University
- Teaching assistants: Alvina, Brennan - Stanford University
We thank them, and the students in that first and second cohort whose questions and feedback shaped the material.
This CBIO7501 version, taught at MBZUAI, is a rebuild rather than a copy. It adds Pixi as the main environment tool, the E. coli LTEE project as one running example, a Snakemake and Nextflow pipeline, and a Quarto site with tested tutorials.
This version is designed in a workshop-style and it reuses and adapts open material from many people. This page lists all of it, and every page links here from its footer. Each slide deck also ends with a Sources slide.
How we reuse (see LICENSES.md in the repository):
- Material under CC BY 4.0, CC0, MIT or BSD licenses is adapted, with changes, and credited on this page.
- Material under a non-commercial or share-alike license, or whose license we could not confirm, is linked, not copied.
- Third-party figures (journal pages, press photos, comics) are linked with a short description, not embedded.
1. Adapted material
NBIS: Tools for Reproducible Research
National Bioinformatics Infrastructure Sweden (NBIS). Main authors John Sundh, Erik Fasterius, Leif Väremo, Rasmus Ågren, Verena Kutschera, Mahesh Binzer-Panchal, Roy Francis and other contributors. Site https://nbisweden.github.io/workshop-reproducible-research/, repository https://github.com/NBISweden/workshop-reproducible-research. License: CC BY 4.0. Version used: commit 1bce220 (2026-10-23), read 2026-10-24.
The Carpentries Incubator: Introduction to Pixi
Matthew Feickert and contributors. https://carpentries-incubator.github.io/pixi-introduction/, repository https://github.com/carpentries-incubator/pixi-introduction. License: CC BY 4.0 (lesson template CC BY 4.0, The Carpentries). Version used: commit b88a073 (2026-10-05).
Amrei Binzer-Panchal: Reproducible Research course
https://amrei-bp.github.io/Reproducible_Research/, repository https://github.com/amrei-bp/Reproducible_Research. License: MIT, Copyright (c) 2026 Amrei. Version used: commit 015364a (2026-10-22).
The Carpentries Incubator: FAIR in (biological) practice
Tomasz Zieliński, Andrés Romanowski, Livia Scorza and contributors. https://carpentries-incubator.github.io/fair-bio-practice/, repository https://github.com/carpentries-incubator/fair-bio-practice. License: CC BY 4.0. Version used: commit 513e1d5 (2025-01-28). Cite as: Zieliński T, Romanowski A, et al., “FAIR in (biological) practice”, 2022.
Data Carpentry: Wrangling Genomics
Data Carpentry contributors; lesson editors include Erin Becker, Fotis Psomopoulos, Taylor Reiter, Jason Williams and Josh Herr. https://datacarpentry.github.io/wrangling-genomics/, repository https://github.com/datacarpentry/wrangling-genomics. License: CC BY 4.0, Copyright © The Carpentries. Version used: commit d965cc4 (2025-07-18).
Pixi documentation: container example (code)
The Dockerfile in the project template (containers/Dockerfile, used in 08 Containers) adapts the example in the Pixi documentation, Containerizing, https://pixi.prefix.dev/latest/deployment/container/. Copyright (c) 2023, prefix.dev GmbH, BSD 3-Clause License. Changes: the environment name is a build argument, PATH is set for Apptainer, and the project is mounted at run time instead of copied in.
2. Recommended resources
| Resource | License as we read it (2026-10-24) | Why we only link |
|---|---|---|
| Seqera training, Hello Nextflow, Nextflow Run, Nextflow for Science: Genomics, https://training.nextflow.io/ | CC BY-NC-SA 4.0 | Non-commercial and share-alike terms conflict with our CC BY 4.0 text |
nf-core pipelines and nf-core/demo, https://nf-co.re/ |
MIT (pipelines) | Used as-is in 10 Nextflow; not part of this repository |
| Pixi documentation, https://pixi.prefix.dev/latest/ | BSD-3-Clause (repository prefix-dev/pixi) |
Reference documentation; we explain in our own words |
| Snakemake documentation, https://snakemake.readthedocs.io/ | MIT (repository snakemake/snakemake) |
Reference documentation |
| Nextflow documentation, https://docs.seqera.io/nextflow/ | Apache-2.0 (repository nextflow-io/nextflow) |
Reference documentation |
| The Turing Way, https://book.the-turing-way.org/ | CC BY 4.0 text, MIT code | Reading list |
| conda-forge documentation, Contributing packages and noarch, https://conda-forge.org/docs/maintainer/adding_pkgs/ | BSD-3-Clause (repository conda-forge/conda-forge.github.io) |
Rules summarized in our own words in Package and share your tool |
| Bioconda, Guidelines for bioconda recipes, https://bioconda.github.io/contributor/guidelines.html | MIT (repository bioconda/bioconda-docs) |
Rules summarized in our own words in Package and share your tool |
| rattler-build, https://rattler.build/ | BSD-3-Clause | Tool documentation |
| Pixi build (preview), https://pixi.prefix.dev/latest/build/getting_started/ | BSD-3-Clause | Mentioned as an alternative in Package and share your tool |
| Zenodo GitHub integration, https://help.zenodo.org/docs/github/ | Steps in 12 written in our own words |
3. Data
LTEE sequencing reads (subset). Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE, Reiter T, Mizzi J, Psomopoulos F, Peek R, Williams J (2019). Data Carpentry Genomics Curriculum Example Data. figshare, dataset, version 3. https://doi.org/10.6084/m9.figshare.7726454.v3. License: CC0. We use the file sub.tar.gz (file 14418248): trimmed and subsampled reads (175,000 pairs each) of samples SRR2589044, SRR2584863 and SRR2584866.
The experiment behind the data. Tenaillon O, Barrick JE, Ribeck N, et al. (2016). Tempo and mode of genome evolution in a 50,000-generation experiment. Nature 536:165–170. https://doi.org/10.1038/nature18959. The three runs we use (SRR2589044, strain REL2181A; SRR2584863, REL7179B; SRR2584866, REL11365) are in NCBI BioProject PRJNA295606, part of the LTEE umbrella project PRJNA294072 that the figshare record cites (checked in NCBI on 2026-10-24).
Reference genome. Escherichia coli B str. REL606, complete genome, GenBank CP000819.1, assembly GCA_000017985.1 (ASM1798v1), NCBI. https://www.ncbi.nlm.nih.gov/nuccore/CP000819.1. Jeong H, Barbe V, Lee CH, et al. (2009). Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol 394:644–652. https://doi.org/10.1016/j.jmb.2009.09.052.
The Long-Term Evolution Experiment. Richard Lenski and colleagues, https://lenski.mmg.msu.edu/ecoli/.
4. Software
The exact versions are recorded in the lock files (pixi.lock in the repository root for the website, tutorials/ltee-project/pixi.lock for the example project). Main tools, with the versions we tested on 2026-10-24:
| Tool | Version | Citation or home page |
|---|---|---|
| Pixi | 0.83.0 | https://pixi.prefix.dev/ |
| Quarto | 1.9.38 | https://quarto.org/ |
| Python | 3.13 | https://www.python.org/ |
| FastQC | 0.13.0 | Andrews S. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| MultiQC | 1.35 | Ewels P et al. (2016) Bioinformatics 32:3047. https://doi.org/10.1093/bioinformatics/btw354 |
| BWA | 0.7.19 | Li H (2013) arXiv:1303.3997. https://arxiv.org/abs/1303.3997 |
| SAMtools, BCFtools | 1.24 | Danecek P et al. (2021) GigaScience 10:giab008. https://doi.org/10.1093/gigascience/giab008 |
| Snakemake | 9.27.1 | Mölder F et al. (2021) F1000Research 10:33. https://doi.org/10.12688/f1000research.29032.3 |
| Nextflow | 26.10.3 | Di Tommaso P et al. (2017) Nat Biotechnol 35:316. https://doi.org/10.1038/nbt.3820 |
| Cookiecutter | 2.7.1 | https://github.com/cookiecutter/cookiecutter |
| JupyterLab | 4.6.4 | https://jupyter.org/ |
| Graphviz | 14.1.2 | https://graphviz.org/ |
| snakefmt | 2.1.0 | https://github.com/snakemake/snakefmt |
| OpenJDK (for Nextflow and FastQC) | 25.0.2 | https://openjdk.org/ |
| micromamba (lesson 05b) | 2.9.0 | https://mamba.readthedocs.io/ |
| rattler-build (packaging extra) | 0.77.0 | https://rattler.build/ |
| conda-smithy (packaging extra, linter) | 2026.10.21 | https://github.com/conda-forge/conda-smithy |
| cffconvert (lessons 11, 12) | from conda-forge | https://github.com/citation-file-format/cffconvert |
| lychee (link checker) | 0.24.2 | https://github.com/lycheeverse/lychee |
| Bioconda | Grüning B et al. (2018) Nat Methods 15:475. https://doi.org/10.1038/s41592-018-0046-7 | |
| conda-forge | conda-forge community (2015). https://doi.org/10.5281/zenodo.4774216 |
5. Figures, images and fonts
- NBIS figures (CC BY 4.0): the seven listed under NBIS, stored in
assets/images/nbis/with a README of their sources. Each is shown with the line “Figure: NBIS, Tools for Reproducible Research, CC BY 4.0”. - Our own (CC BY 4.0): the diagrams of images and containers and of Nextflow channels and processes (
assets/images/diagrams/), the LTEE rule graph and the LTEE report screenshot, and every chart made from the LTEE data. - Linked, not embedded: third-party figures discussed in the slides (press photos, journal pages, comics, figures under other licenses) are described on the slide and linked in that deck’s Sources slide.
- Fonts, served from this site: Inter 4.1 (The Inter Project Authors) and JetBrains Mono 2.304 (The JetBrains Mono Project Authors), both under the SIL Open Font License 1.1 (
assets/fonts/, with the license texts).
6. Readings
Readings are listed in each lesson under Further reading. The core list:
- Noble WS (2009). A quick guide to organizing computational biology projects. PLoS Comput Biol 5:e1000424. https://doi.org/10.1371/journal.pcbi.1000424
- Wilson G, Bryan J, Cranston K, Kitzes J, Nederbragt L, Teal TK (2017). Good enough practices in scientific computing. PLoS Comput Biol 13:e1005510. https://doi.org/10.1371/journal.pcbi.1005510
- Wilkinson MD et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3:160018. https://doi.org/10.1038/sdata.2016.18
- Carroll SR et al. (2020). The CARE Principles for Indigenous Data Governance. Data Sci J 19:43. https://doi.org/10.5334/dsj-2020-043
- Ziemann M, Poulain P, Bora A (2023). The five pillars of computational reproducibility: bioinformatics and beyond. Brief Bioinform 24:bbad375. https://doi.org/10.1093/bib/bbad375
- The Turing Way Community. The Turing Way: a handbook for reproducible, ethical and collaborative research. Zenodo. https://doi.org/10.5281/zenodo.3233853
7. People
Workshop author: Aziz Khan (MBZUAI).
Thanks to the authors of every lesson listed above: this workshop would not exist without their open material.
8. How to cite and reuse this workshop
Cite the workshop with the information in CITATION.cff.
License: text and slides CC BY 4.0, code MIT. Adapted parts keep the license of their source, as listed above.