Forum:Crac: Funny And/Or Weird Names For Bioinformatics Tools

Question

[Istvan Albert]

The latest Article Alert from Genome Biology had a software tool that caught my attention

• CRAC: an integrated approach to the analysis of RNA-seq reads

I started imagining headlines of the sorts: CRAC Leads to Breakthroughs

What other weird or funny names for tools/methodologies are out there?

By the way here is a suggestion for a good bioinformatics tool name: YOLO

Or even better YORO meaning You can Only Run it Once

[Daniel]

It's not bioinformatics, but I'll never get over the fact that the Copper (Cu) Nanotubues (NT) paper got published without anyone googling the acronym once...

Source: http://pubs.rsc.org/en/content/articlepdf/2007/CC/B614147A

[Ram]

without anyone googling the acronym once

They knew. It was done on purpose or with a "fuck it"

[Pawel Szczesny]

You could also check funny names for biological entities. Have you checked if your proteins http://www.ncbi.nlm.nih.gov/protein?cmd=&term=will+die+slowly&go=Go

Answer 1

[SES]

One of the best I've seen is MethLAB. When combined with CRAC, you are guaranteed results.

[Cliff Beall]

Have some freebayes while you're at it.

Answer 2

[Sukhi Singh]

Homer drinks T-Coffee with new Tophat, shiny Cufflinks, a charming Bowtie and Tuxedo on, to BLAST some MUSCLE, when stressed, he detours to MethLAB for some CRAC!! :)

[Michael]

... just to find himself waking up in JAIL the next morning...

[Michael]

...wishing he had stuck to BACCardI in that BAR+...

[Sukhi Singh]

Realizing not a SMART decision, now, drenched in dirt, thinking SOAP would help, or asking DAVID for his SuperFamily to pull some STRING else life will turn from a SoftBerry to a 3D JigSaw ....

[komal.rathi]

Adding cummeRbund to what he is wearing!!

Answer 3

[Pierre Lindenbaum]

BioNOT is a searchable database of negated biomedical sentences.

[Michael]

Wow, this is maybe one of the most important biomedical text-mining applications (honestly)!

Answer 4

[BioApps]

Can I enlist myself here with my software?

Kitten Dereplicator

The idea was given by Pierre Lindenbaum in this post: Kitten - A DNA Sequence Dereplicator & Cluster Viewer (GUI)

Answer 5

[Jordan]

I liked the idea of Tuxedo (cufflinks, tophat and bowtie) in RNA Sequencing analysis. Makes one feel like a spy or something!!

Answer 6

[Daniel]

The recent addition of UPARSE to Robert Edgar's U* software (UCLUST, USEARCH, UCHIME) amuses me disproportionately to how funny it actually is.

(If you're missing the joke, this deconstruction may help: UP-ARSE)

Answer 7

[Pierre Lindenbaum]

ARYANA: Aligning Reads by Yet Another Approach

You have to admire the honesty of the name!

BMC Bioinformatics | ARYANA: Aligning Reads by Yet Another Approach http://t.co/7WqfKICbtY

— Keith Bradnam 📈 (@kbradnam) September 17, 2014

Answer 8

[Zev.Kronenberg]

SNVER MEME APE

And for the perverts:

BEDTOOLS

[Istvan Albert]

there was a situation where I was talking about bedtools and I happened to say bamtobed - someone in the first row started laughing, and it spread - I was puzzled at first eventually I got it

Answer 9

[David Quigley]

These aren't purely bioinformatics methods, but they require considerable bioinformatics expertise:

ChIA-PET (See also this important related supporting material)

Hi-C (With related material on how to replicate the groundbreaking but controversial Ecto-Cooler method )

Answer 10

[Fred]

A few funny bioinformatics tool names:

• SARUMAN : Semiglobal Alignment of short Reads Using CUDA and NeedleMAN-Wunsch http://bit.ly/e0tQry
• NORMA-Gene: A simple and robust method for qPCR normalization based on target gene data http://bit.ly/iS3lLC
• Sniper: improved SNP discovery by multiply mapping deep sequenced reads http://bit.ly/m5tSZw
• LinkinPath: From Sequence to Interconnected Pathway http://bit.ly/iqDepz

Answer 11

[Istvan Albert]

I keep misreading and recalling this as INSANE

NGSANE: a lightweight production informatics framework for high-throughput data analysis, Bioinformatics 2014

[Istvan Albert]

GAG - The Genome Annotation Generator

Answer 12

[rbagnall]

The CRAPome

a contaminant repository for affinity purification-mass spectrometry data.

http://www.ncbi.nlm.nih.gov/pubmed/23921808

Answer 13

[komal.rathi]

YASARA (*Yet Another Scientific Artificial Reality Application*)

[Mary]

Ha! I just saw almost that today on twitter:

You have to admire the honesty of the name! BMC Bioinformatics | ARYANA: Aligning Reads by Yet Another Approach http://t.co/7WqfKICbtY

— Keith Bradnam (@kbradnam) September 17, 2014

Answer 14

[Mary]

I thought this was doomed: G-nome Surfer.

[Istvan Albert]

plus they propose a multi-touch interface - I don't even know what to say

Answer 15

[ATpoint]

https://github.com/COMBINE-lab/simpleaf which actually stands for simple alevin-fry, and not simple as f*, but it took me longer to realize than I am willing to admit.

[zx8754]

I read it as "simp leaf", whatever this means.

Answer 16

[quentin.delettre]

Amber ?

[Ambu Vijayan]

This hits hard now... :D

Answer 17

[Devon Ryan]

The name will likely get changed at some point (I'm slowly putting together what will likely become "MethTools"), but I picked PileOMeth as a name to intentionally be somewhat funny. I like to picture Walter White when I type it...

Answer 18

[4galaxy77]

MethPipe always makes me laugh when I see it

http://smithlabresearch.org/downloads/methpipe-manual.pdf

Answer 19

[Istvan Albert]

A decade after this thread making fun of CRAC, Nature publishes CRAQ (Clipping information for Revealing Assembly Quality)

https://www.nature.com/articles/s41467-023-42336-w

The cycle continues.

Answer 20

[Pawel Szczesny]

My favourite has been Project HOPE (try to google it ;) ).

Also, there are two JANEs: http://biosemantics.org/jane and http://jane.bioapps.biozentrum.uni-wuerzburg.de Although they were not published in the same journal.

Answer 21

[Brice Sarver]

FUBAR, an improved method for detecting signatures of selection implemented within HyPhy.

http://mbe.oxfordjournals.org/content/early/2013/02/18/molbev.mst030.short

Answer 22

[Garan]

Probably abit of a UK specific one (http://www.urbandictionary.com/define.php?term=baps) but;

Bayesian Analysis of Population Structure (BAPS)

But since this was often linked with Nomenclature of Territorial Units for Statistics (Nomenclature des unités territoriales statistiques aka NUTS) presenting on the subject was a pain.

[Istvan Albert]

here is another "wordplay" on pooled population: PoPoolation https://code.google.com/p/popoolation/

Answer 23

[Cliff Beall]

I always thought Picard was a funny name. Were the authors Star Trek fans?

Answer 24

[jonathan.seguin]

Someone has been giving out awards to projects with silly accronyms.

http://www.acgt.me/blog?tag=jabba

Answer 25

[zx8754]

VODKA2 - Viral Opensource DVG Key Algorithm 2

VODKA2: An accurate method to detect copy-back and deletion viral genomes from next-generation sequencing data

• https://www.biorxiv.org/content/10.1101/2023.04.25.537842v1
• https://github.com/lopezlab-washu/VODKA2

Answer 26

[4galaxy77]

Oh and who could forget MasterBayes

https://jarrod.bio.ed.ac.uk/software.html

Answer 27

[Istvan Albert]

The Oxford Nanopore data storage format went from a design called FAST5 to SLOW5 and BLOW5

• Fast nanopore sequencing data analysis with SLOW5

Even the title above feels like a parody: Fast analysis with SLOW

... the Gods must be crazy ...

Answer 28

[Biojl]

I named my tool PALO. Which in Spanish mean wooden stick... and also when you feel lazy to do something in street language.

http://evolutionarygenomics.imim.es/josepl/codeigniter/index.php/pages/view/home