bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

Collection of published “guides” for bioinformaticians

Recently there has been a proliferation of “guides” for bioinformaticians published in academic journals, so I wanted to start a list here.  If I have missed any, suggest them in the comments and I will add them.

  1. Loman N and Watson M (2013) So you want to be a computational biologist? Nature Biotech 31(11):996-998 [link]
  2. Corpas M, Fatumo S, Schneider R. (2012) How not to be a bioinformatician. Source Code Biol Med. 7(1):3. [link]
  3. Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, Guy RT, Haddock SHD, Huff K, Mitchell IM, Plumbley M, Waugh B, White EP, WIlson P (2013)  Best Practices for Scientific Computing.  arXiv http://arxiv.org/abs/1210.0530 [link]
  4. Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. [link]
  5. Bourne PE (2011) Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comput Biol 7(1): e1002001. [link]
  6. Oshlack A (2013) A 10-step guide to party conversation for bioinformaticians.  Genome Biology 14:104 [link]
  7. Via A, De Las Rivas J, Attwood TK, Landsman D, Brazas MD, et al. (2011) Ten Simple Rules for Developing a Short Bioinformatics Training Course. PLoS Comput Biol 7(10): e1002245. [link]
  8. Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las
    Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J,
    Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK. (2013) Best practices
    in bioinformatics training for life scientists. Brief Bioinform. 14(5):528-37. [link]
  9. Slonim DK, Yanai I (2009) Getting Started in Gene Expression Microarray Analysis. PLoS Comput Biol 5(10): e1000543. [link]
  10. Logan DW, Sandal M, Gardner PP, Manske M, Bateman A (2010) Ten Simple Rules for Editing Wikipedia. PLoS Comput Biol 6(9): e1000941. [link]
  11. Prlić A, Procter JB (2012) Ten Simple Rules for the Open Development of Scientific Software. PLoS Comput Biol 8(12): e1002802 [link]
  12. Bernard V, Michaut M (2013) Explain Bioinformatics to Your Grandmother! PLoS Comput Biol 9(10): e1003305. [link]
  13. Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424. [link]
  14. Kallioniemi O, Wessels L, Valencia A. (2011) On the organization of bioinformatics core services in biology-based research institutes. Bioinformatics. 27(10):1345. [link]
  15. Ouzounis CA, Valencia A. (2003) Early bioinformatics: the birth of a discipline–a personal view. Bioinformatics. 19(17):2176-90. [link]
  16. Valencia A. (2002) Bioinformatics: biology by other means. Bioinformatics. 18(12):1551-2. [link]
  17. Huttenhower C, Hofmann O (2010) A Quick Guide to Large-Scale Genomic Data Mining. PLoS Comput Biol 6(5): e1000779. [link]
  18. Dudley JT, Butte AJ (2009) A Quick Guide for Developing Effective Bioinformatics Programming Skills. PLoS Comput Biol 5(12): e1000589. [link]
  19. Bassi S (2007) A Primer on Python for Life Science Researchers. PLoS Comput Biol 3(11): e199. [link]
  20. Searls DB (2012) An Online Bioinformatics Curriculum. PLoS Comput Biol 8(9): e1002632 [link]
  21. Giddings MC (2008) On the Process of Becoming a Great Scientist. PLoS Comput Biol 4(2): e33. [link]
  22. Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. (2013) The anatomy of successful computational biology software. Nat Biotechnol. 31(10):894-7. [link]
  23. Nat. Biotech Editorial (2013) In need of an upgrade. Nat Biotechnol. 31(10):857. [link]
  24. Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV. (2013) The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. Brief Bioinform. 14(5):548-55. [link]
  25. Alexandrov T, Bourne PE (2013) Learning How to Run a Lab: Interviews with Principal Investigators. PLoS Comput Biol 9(11): e1003349 [link]
  26. Miller W (2009) 10 Steps to Success in Bioinformatics. ISCB Accomplishment by a Senior Scientist Award [link]
  27. Seemann T (2013) Ten recommendations for creating usable bioinformatics command line software. GigaScience 2:15 [link]
  28. Aerts J, Law A. (2009) An introduction to scripting in Ruby for biologists. BMC
    Bioinformatics. 10:221 [link]
  29. Gewaltig MO and Cannon R (2013) Current practice in software development for computational neuroscience and how to improve it. arXiv http://arxiv.org/abs/1205.3025 [link]

I am sure there are one or two more out there 😉


  1. “A Quick Guide to Organizing Computational Biology Projects” http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000424 and a more general article “On the Process of Becoming a Great Scientist” http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0040033

  2. Explain Bioinformatics to Your Grandmother @ploscompbio http://t.co/PTMsXT57aY

  3. Here, here! I 2nd these two. I’ve been advocating the 1st paper during all of the informatics classes that I’ve been teaching the previous years.

  4. One more:

    On the organization of bioinformatics core services in biology-based research institutes.
    Kallioniemi O, Wessels L, Valencia A.
    Bioinformatics. 2011 May 15;27(10):1345. doi: 10.1093/bioinformatics/btr125. Epub 2011 Mar 13. No abstract available.
    PMID: 21402560 [PubMed – indexed for MEDLINE] Free Article

  5. and one on the history of bioinformatics .. not exactly a “guide”
    Early bioinformatics: the birth of a discipline–a personal view.
    Ouzounis CA, Valencia A.
    Bioinformatics. 2003 Nov 22;19(17):2176-90. Review.
    PMID: 14630646 [PubMed – indexed for MEDLINE] Free Article
    Related citations

  6. My third one on different areas of bioinformatics (written quite some time ago but still largely valid … title used for some of the ISMB conferences. )

    Bioinformatics: biology by other means.
    Valencia A.
    Bioinformatics. 2002 Dec;18(12):1551-2. No abstract available.
    PMID: 12490437 [PubMed – indexed for MEDLINE] Free Article
    Related citations

  7. Reblogged this on Ghi chép vặt and commented:
    must read

  8. Reblogged this on SciPedia.

  9. RNA-seq guidelines

    24th April 2016 at 10:33 pm

    A survey of best practices for RNA-seq data analysis
    Genome Biology (2016) 17:13


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