cgeb2001's DokuWiki!

You've loaded an old revision of the document! If you save it, you will create a new version with this data.

**Do Bioinformaticians have naming regrets?**

Once a day, I was driving in front of the red light with an eye peeking on my iPhone UberEats driver app, that’s frequent manner for anyone hoping to earn extra after work. Suddenly, a vehicle’ plate on my right front drew my attention printed with the same word as my app’s name - UBEREATS. “Damn it, the plate name has been taken, I should have thought about it, it happens to be 8 characters as the maximum allowance in Ontario”. Many thoughts came into my mind, and finally I was reluctant to accept this is a smart competitor using the plate name I wanted.

I don’t know if you have encountered similar naming regrets in real life, but as a bioinformatician frequently requires naming a new tool, database or pipeline. I wish I could be smarter on it.

With the development of sequencing technology and computational analysis, more and more databases, tools and pipelines have been developed to prompt the biological data collecting, processing and managing. The naming routine for the earlier databases are short and unique, such as KEGG [#] and NCBI [#], which are short for Kyoto Encyclopedia of Genes and Genomes and National Center for Biotechnology Information, respectively. However, the abbreviation letters are not real word limiting the understanding and pronouncing. In comparison, another famous sequence alignment tool BLAST [#] can be easily pronounced and spread popularly, which is short for Basic Local Alignment Search Tool. Although it is hard to make the software name directly related to its purpose, an easy and spellable name is more user-friendly, such as FastTree [#] which is indeed a fast approximately-maximum-likelihood phylogenetic tree builder.

Although bioinformaticians have diversed ways to apply the capitalized letters or underlines on their tool names, such as RepeatMasker [#], Ori-Finder[#] and LTR_retriever[#], it does increase the difficult to read and write the name correctly, such as the tools’ name InterProScan[#], MaSuRCA[#] and NoBadWordsCombiner [#]. Let along some command-line running platforms are sensitive with upper cases and underlines. By the way, the last one is from our work and I regrated not thinking of a better name.

Although naming software is not as hard as naming baby, where you take into multiple considerations such as honoring certain family member or obeying certain tradition must including one descended word. There are some potential naming routines for bioinformaticians. For example, the database tools usually contain the letter ‘db’, such as OrthoDB [#] and RetrogeneDB[#]. The software tools usually have the letter ‘er’, such as OrthoFinder [#] and RepeatModeler [#]. Although there is no golden rule for the best names, the usefulness and practical of the software itself is more important, bioinformaticians better not forget to register the unique domain name in case of squatting by others. Recently, I read a database paper collecting the current extremophiles with an awesome name ExtremeDB which cannot be used even after publication on PLOS one. Because PLOS has received notice from McObject LLC that “ExtremeDB” is a registered trademark of McObject LLC. They had to send the correction and register a new domain name as declared: “The correct phrase in each instance in the paper should instead be “ExtremophileDB”, and the correct database link is http://extremophiledb.igib.res.in/ “. Although this is an extreme case for many bioinformaticians, which can be avoided by an earlier “Google search” or renaming the other, will it be more competitive with more bioinformatician in the field in the future? For example, in my recent project, there are two software designed for trimming the large phylogenetic datasets called TreeTrimmer [#] and Treemmer [#]. I don’t know if the author from later one regret naming later, but the word treetrimmer cannot be used again.

Suddenly, I am worried about my half-baked ideas such as a hypothetical protein database and a phylogenetic analysis booster. After a quick Google search, “Damn it, HypoDB and Phyloboost are already there” Will it worth trying “Hypotheticaldb or Phylobooster”? I don’t have answers, maybe let it go, the smart UberEats competitor.

Please fill all the letters into the box to prove you're human. O G Z D Q Please keep this field empty:

Edit summary

Note: By editing this page you agree to license your content under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International