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References

Afgan, Enis, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Čech, John Chilton, et al. 2018. “The Galaxy Platform for Accessible, Reproducible and Collaborative Biomedical Analyses: 2018 Update.” Nucleic Acids Research 46 (W1): W537–44. https://doi.org/10.1093/nar/gky379.
Alexakis, Alex. n.d. “You’re Not Your User.” https://blog.prototypr.io/dear-product-managers-youre-not-your-users-e5739627cbc8.
Andrzej Oleś, Wolfgang Huber, and Martin Morgan. 2021. “Authoring r Markdown Vignettes.” https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html.
Babich, Nick. 2019. “The 4 Golden Rules of UI Design.” https://xd.adobe.com/ideas/process/ui-design/4-golden-rules-ui-design/.
———. n.d. “F-Shaped Pattern for Reading Content.” https://uxplanet.org/f-shaped-pattern-for-reading-content-80af79cd3394.
Bodner, Herbet. 2018. “10 Reasons Why Code Reviews Make Better Code and Better Teams.” https://simpleprogrammer.com/why-code-reviews-make-better-code-teams/.
Bolchini, Davide, Anthony Finkelstein, Vito Perrone, and Sylvia Nagl. 2008. “Better Bioinformatics Through Usability Analysis.” Bioinformatics 25 (3): 406–12. https://doi.org/10.1093/bioinformatics/btn633.
Bolyen, Evan, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, et al. 2019. “Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2.” Nature Biotechnology 37 (8): 852–57. https://doi.org/10.1038/s41587-019-0209-9.
Budd, Aidan, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, and Niklas Blomberg. 2015. “A Quick Guide for Building a Successful Bioinformatics Community.” Edited by Amarda Shehu. PLOS Computational Biology 11 (2): e1003972. https://doi.org/10.1371/journal.pcbi.1003972.
Cronin, Mike. 2019. “What Makes a Good Code Comment?” https://itnext.io/what-makes-a-good-code-comment-5267debd2c24.
Csontos, Anna-Zsófia. 2019. “All You Need to Know to Run Successful Usability Testing.” https://uxstudioteam.com/ux-blog/usability-testing/.
Duck, Geraint, Goran Nenadic, Michele Filannino, Andy Brass, David L. Robertson, and Robert Stevens. 2016. “A Survey of Bioinformatics Database and Software Usage Through Mining the Literature.” Edited by Shoba Ranganathan. PLOS ONE 11 (6): e0157989. https://doi.org/10.1371/journal.pone.0157989.
Frazee, Alyssa. 2014. “Some Internet Wisdom on r Documentation.” http://alyssafrazee.com/2014/04/20/rdocs.html.
GitLab. n.d. “Writing a Usability Testing Script.” https://about.gitlab.com/handbook/engineering/ux/ux-research-training/writing-usability-testing-script/.
Herothemes. 2020. “8 Best Knowledge Base Software Compared (Pros & Cons).” https://herothemes.com/blog/best-knowledge-base-software/.
HotJar. 2019. “How to Run Moderated Usability Testing.” https://www.hotjar.com/usability-testing/process-examples/.
Keeto, B. J. 2019. “How to Comment Your Code Like a Pro: Best Practices and Good Habits.” https://www.elegantthemes.com/blog/wordpress/how-to-comment-your-code-like-a-pro-best-practices-and-good-habits.
Krug, Steve. 2010. “Rocket Surgery Made Easy:the Do-It-Yourself Guide to Finding and Fixing Usability Problems.” https://sensible.com/downloads/things-a-therapist-would-say.pdf.
Love, Michael I, Wolfgang Huber, and Simon Anders. 2014. “Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2.” Genome Biology 15 (12). https://doi.org/10.1186/s13059-014-0550-8.
Mangul, Serghei, Lana S. Martin, Eleazar Eskin, and Ran Blekhman. 2019. “Improving the Usability and Archival Stability of Bioinformatics Software.” Genome Biology 20 (1). https://doi.org/10.1186/s13059-019-1649-8.
Mangul, Serghei, Thiago Mosqueiro, Richard J. Abdill, Dat Duong, Keith Mitchell, Varuni Sarwal, Brian Hill, et al. 2019. “Challenges and Recommendations to Improve the Installability and Archival Stability of Omics Computational Tools.” PLOS Biology 17 (6): e3000333. https://doi.org/10.1371/journal.pbio.3000333.
Matos, Paula de, Jennifer A Cham, Hong Cao, Rafael Alcántara, Francis Rowland, Rodrigo Lopez, and Christoph Steinbeck. 2013. “The Enzyme Portal: A Case Study in Applying User-Centred Design Methods in Bioinformatics.” BMC Bioinformatics 14 (1): 103. https://doi.org/10.1186/1471-2105-14-103.
Meza, Frank. 2018. “The Value of Code Documentation.” https://www.olioapps.com/blog/the-value-of-code-documentation/.
Molder, F, KP Jablonski, B Letcher, MB Hall, CH Tomkins-Tinch, V Sochat, J Forster, et al. 2021. “Sustainable Data Analysis with Snakemake [Version 1; Peer Review: 1 Approved, 1 Approved with Reservations].” F1000Research 10 (33). https://doi.org/10.12688/f1000research.29032.1.
Moon, Garrett. 2011. “10 Tips for Creating a Killer FAQ Page.” https://www.socialmediatoday.com/content/10-tips-creating-killer-faq-page.
Moran, Kate. 2019. “Usability Testing 101.” https://www.nngroup.com/articles/usability-testing-101/.
Mulder, Nicola, Russell Schwartz, Michelle D. Brazas, Cath Brooksbank, Bruno Gaeta, Sarah L. Morgan, Mark A. Pauley, et al. 2018. “The Development and Application of Bioinformatics Core Competencies to Improve Bioinformatics Training and Education.” Edited by Olga G. Troyanskaya. PLOS Computational Biology 14 (2): e1005772. https://doi.org/10.1371/journal.pcbi.1005772.
Pavelin, Katrina, Jennifer A. Cham, Paula de Matos, Cath Brooksbank, Graham Cameron, and Christoph Steinbeck. 2012. “Bioinformatics Meets User-Centred Design: A Perspective.” Edited by Philip E. Bourne. PLoS Computational Biology 8 (7): e1002554. https://doi.org/10.1371/journal.pcbi.1002554.
Porter, Joshua. n.d. “Principles of User Interface Design.” http://bokardo.com/principles-of-user-interface-design/.
Quinlan, Aaron R., and Ira M. Hall. 2010. BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features.” Bioinformatics 26 (6): 841–42. https://doi.org/10.1093/bioinformatics/btq033.
Rehan, Adnan. 2019. “Build Online Community and Forum with These 8 Best Software.” https://geekflare.com/online-community-software/.
RStudio Team. 2020. RStudio: Integrated Development Environment for r. Boston, MA: RStudio, PBC. http://www.rstudio.com/.
Simon, Justin. 2020. “The Ultimate Guide to Easily Make Instructional Videos.” https://www.techsmith.com/blog/instructional-videos/.
Soegaard, Mads. n.d. “Visual Hierarchy: Organizing Content to Follow Natural Eye Movement Patterns.” https://www.interaction-design.org/literature/article/visual-hierarchy-organizing-content-to-follow-natural-eye-movement-patterns.
Spertus, Ellen. n.d. “Best Practices for Writing Code Comments.” https://stackoverflow.blog/2021/07/05/best-practices-for-writing-code-comments/.
Spielman, Stephanie. n.d. “Introduction to r - CB2R Data Science Workshop, Summer 2020.” https://github.com/sjspielman/cb2r-ds-summer2020/blob/71cb11277e7383292bf727841ab5fa4ed43cfcbe/resources/introduction_to_R.Rmd#L92.
Studios, Outlook. 2020. “6 Tools to Find Broken Links on Your Website.” https://www.outlookstudios.com/tools-to-find-broken-links-on-your-website/.
Subramanian, Aravind, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, et al. 2005. “Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles.” Proceedings of the National Academy of Sciences 102 (43): 15545–50. https://doi.org/10.1073/pnas.0506580102.
team, Divio. 2024. “The Documentation System.” https://docs.divio.com/documentation-system/.
Tidwell, Jeniger. 2021. “Organizing the Page:layout of Page Elements.” https://www.oreilly.com/library/view/designing-interfaces/0596008031/ch04.html.
Trounce, David. 2019. “7 Great Tools for Creating Your Own Video Tutorials.” https://helpdeskgeek.com/free-tools-review/7-great-tools-for-creating-your-own-video-tutorials/.
Wilson, Lee. 2020. “25 of the Best Examples of Effective FAQ Pages.” https://www.searchenginejournal.com/best-faq-page-examples/267709/.
Wolf, Damian. 2016. “Why Developers Write Horrible Documentation and How to Solve It.” https://dzone.com/articles/why-developers-write-horrible-documentation-and-ho.