Bioconductor vs BioConductor
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Jim Hester ▴ 40
@jim-hester-7319
Last seen 11 months ago
United States

Is there a definitive resource for the proper spelling of the project? I am pretty sure it should always be spelled Bioconductor, with a lowercase C, as that is how it is everywhere at Bioconductor.org.

I regularly see people talking about 'BioConductor packages' and the 'BioC project', and it would be good to have somewhere definitive to point them to.

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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

Following up comments from Martin and Herve, I would view the refereed publications and the logo as definitive:

• Gentleman, R. C., Cary, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A. J., Sawitzki, G., Smith, C., Smyth, G. K., Tierney, L., Yang, J. Y. H., and Zhang, J. (2004). Bioconductor: a software development project. Genome Biology 5, R80.

• R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.) (2005). Bioinformatics and Computational Biology Solutions using R and Bioconductor, Springer, New York.

• Huber, W, Carey, VJ, Gentleman, R, Anders, S, Carlson, M, Carvalho, BS, Bravo, HC, Davis, S, Gatto, L, Girke, T, Gottardo, R, Hahne, F, Hansen, KD, Irizarry, RA, Lawrence, M, Love, MI, MacDonald, J, Obenchain, V, Oles, AK, Pagès, H, Reyes, A, Shannon, P, Smyth, GK, Tenenbaum, D, Waldron, L, Morgan, M (2015). Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12, 115-121.

While there are lots of Bioconductor publications by different authors, these are the only ones involving the whole leadership group.

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@martin-morgan-1513
Last seen 4 days ago
United States

No. ;)

I'm a fan of Bioconductor. The logo is pretty clear on that...

I think the original participants referred / refer to the project as BioConductor. The conference has always been BioC xxxx.

Some say <-, some say =. A few even say ->.

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The project was Bioconductor when I became part of the core group in 2003. A search of old emails going back to March 2002 doesn't bring up any usages of BioConductor, it was always either Bioconductor or just all lowercase.

The confusion in some quarters may arise from the conference name BioC XXXX wherein the "C" is playing a double role as the 4th letter of Bioconductor and the first letter of Conference. Or else just the temptation to convert to upper camel case.

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Plausible, although in early times the title "BioC YEAR Conference" was used, which would seem redundant if the "C" would stand for conference. Anyway, in the last 10 years this possible confusion seems to have been resolved because the term "conference" does not appear anymore in the title.

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You can see here my presention at the very first Bioconductor conference: http://bioinf.wehi.edu.au/marray/bioc2005/

You can argue whether "Conference" was an official part of the conference name or just optionally added for clarification on some of the web pages. It was certainly common to refer to "BioC2005" in correspondence at the time without needing to add "Conference". Anyway, it is my experience that Robert Gentleman always capitalized the "C" when it was just four letters (BioC) and never when it was part of the full word. You could ask him why.

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The 'BioC' repository was added to R_HOME/etc/respositories in February 2005, which predates my involvement in the project (so I took this as 'the beginning'). I'd always assumed that this was introduced by Robert Gentleman, but that's not correct.

The release from October 2004 lists 100 'BioConductor Packages - 1.5 Release'.

I think the Steve Wilhite of bio_conductoR is someone other than me!

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The uppercase R is cute.

I don't want to be the Steve Wilhite of BioconductoR either but I always considered the original Bioconductor paper from 2004 kind of the official birth announcement of the project. And since the paper uses the Bioconductor spelling I always considered this to be the one truly right spelling.

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I viewed the capitalization of "C" in the October 2004 announcement as just an inconsistency rather than the official/dominant usage of the time. The project wasn't always consistent in the early days!

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Yes! This was my perception too.

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You could offer a definitive statement and then we'll all ignore it a la Steve Wilhite and GIF

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I use <- in functions and = in brackets. Anything else makes me feel weird.

More importantly: ->? Heathens!