None shall stare into the face of Medusa (or Medusa, or MeDUSA): more bioinformatics tools that use the same name

Following on from yesterday's post where I pointed out that there are three completely different bioinformatics tools that are all called 'Kraken', I bring you more news of the same. Scott Edmunds (@SCEdmunds on twitter) brought to my attention today that there is some bioinformatics software called Medusa that is either:

  1. A tool from 2005 for interaction graph analysis
  2. Some software published in 2011 that explores and clusters biological networks
  3. Or an acronym for a 2012 resource (MeDUSA) that can be used for methylome analysis

So if someone asks you to install Kraken and Medusa, it's good to know that there's only nine different combinations of tools that they might be referring to.

You wait ages for somebody to develop a bioinformatics tool called 'Kraken' and then three come along at once

I recently wrote about the growing problem of duplicated names for bioinformatics tools. A couple of weeks ago, Stephen Turner (@genetics_blog) pointed out another case:

So Kraken is either a universal genomic coordinate translator for comparative genomics, or a tool for ultrafast metagenomic sequence classification using exact alignments, or even a set of tools for quality control and analysis of high-throughput sequence data. The latter publication is from 2013, and the other two are from this year (2014).

I feel sorry for the poor Grad Student who is going to lose a day of their life trying to install one of these tools before realizing that they have been installing the wrong Kraken.

Which 'omics' assembly tools are currently the most popular?

I recently organized an online poll to find out which tools for genome, transcriptome, and metagenome assembly are currently the most popular with researchers. After a week or so of collecting results, I ended up with 116 responses that describe over 30 different assembly tools.

Thanks to everyone who took part. I've posted the results to Figshare as a PDF report, and have also embedded this below (I suggest downloading the PDF so that you can use all of the embedded hyperlinks in the report).

Impactstory: Publications are an important part of research…but they’re not the only part

I'm a great fan of the Impactstory service that makes it easy to aggregate all of your research output in one place, and then see how people are engaging with your research. I like it so much, that I signed up to be an Impactstory Advisor.

Today I'm giving a talk at UC Davis about Impactstory, and so that everyone can see why I like this service so much, I've made a video version of my presentation. 

Visit the Impactstory website to find out more or follow them on twitter (@Impactstory). For an example of the types of things that Impactstory can track, have a look at my own Impactstory page (impactstory.org/KeithBradnam) .