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What's in a name ?

Contents

The origins of the name EMBOSS

EMBOSS is the name of this package. EMBOSS is an acronym for "The European Molecular Biology Open Software Suite ".

Many suggestions were made during the planning stages of this package for a name that summed up the meaning of life, the Universe and Bioinformatics.

Many suggestions were never committed to paper and some should best be forgotten, but amongst them were:

HDH - (Pronounced Hi-De-Hi). If HAL is the acronym 'IBM' with each letter decreased by one in the alphabetic sequence, and Windows NT (WNT) is 'VMS' decreased by one, then HDH is ...

HDH is also the nucleotide ambiguity code for 'not-G' 'not-C' 'not-G'

EMBRYO - European Molecular Biology Roll Your Own

EMBOSS - European Molecular Biology Open Software Suite.

There have been some nice variants of EMBOSS. I liked the typo 'MEBOSS'.

Yes, but what does EMBOSS mean?

If you look it up in the Merriam-Webster online dictionary (http://www.m-w.com/), then the default definition is: 
 Function: transitive verb
 Etymology: Middle English embosen to become exhausted
            from being hunted, ultimately from Middle French bois woods
 Date: 14th century
 archaic : to drive (as a hunted animal) to bay or to exhaustion

The origins of the name AJAX

AJAX is the name of the EMBOSS major set of libraries.

The origins of this name are hidden in the mists of time and alcohol fumes, but legend has it that A.J. Bleasby was on his way home in a taxi while cogitating on the possible value of a set of library routines for bioinformatics. The name of the taxi company was AJAX.

The origins of the name NUCLEUS

NUCLEUS is the name of the EMBOSS minor set of program-specific library routines.

NUCLEUS is a code name invented jointly by Peter Rice and Rodrigo Lopez (then at EMBL and the Norwegian EMBnet node respectively) and saved until a really good use could be found. At one time it probably meant 'Norwegian...(something)'

The origins of some program names

chips

This program to implement Frank Wright's Nc statistic was originally in the EGCG package as "codfish" (codon usage for fission yeast). As Frank Wright is a vegan, we looked for a meat-free name for the EMBOSS version: "chips".

The official explanation is "Codon Heterozygosity (Inverse of) in a Protein-coding Sequence"

tfm

The unusual name of this program to display the help documentation on a program comes from the common computing science expression: RTFM. This acronym, as you probably already know, stands for Read The Fine* Manual; so this is The Fine* Manual.

* Insert the expletive of your choice here!

dan

This program finds the melting temperature of DNA.

'dan' is 'dna' melted. (It sounds better in the pub).

banana

This program predicts bending of a DNA double helix.

The consensus sequence for DNA bending is 5 As and 5 non-As alternating. "N" is an ambiguity code for any base, and "B" is the ambiguity code for "not A" so "BANANA" is itself a bent sequence.

splitter

Originally called 'splitseq' until it was pointed out that this was the name of one of the utilities in the Staden package. In looking for an alternative name for this program, we rejected names like 'shatter', 'shatseq' ...