Question: when is a GitHub repository not a GitHub repository?

Answer: when it doesn't contain any useful code.

Update 2015-10-02 08.58: this post was updated to reflect the addition of code the metaPORE repository.

A discussion on twitter today revealed something which I find very disappointing:

A new paper by Greninger et al. (Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis) has been published in the journal Genome Medicine. The Methods contains the following line:

We developed a custom bioinformatics pipeline for real-time pathogen identification and visualization from nanopore sequencing data (MetaPORE) (Fig. 1b), available under license from UCSF at [23].

Reference #23 takes you to the metaPORE GitHub repository. At the time I initially wrote this post — and as the screen grab below shows — it contained zero code. Thankfully this has been changed and a set of Python and shell scripts are now available.

Maybe this was just some sort of error in scheduling the release of the paper and the code. However, journals and authors should understand that if a paper (or a pre-print) appears online and points to a code repository (or any other website), the expectation is that people should be able to visit the site in question and download code.

A top 10 list of 'Useful Bioinformatics Skills'

The deadline for my competition to win a signed copy of Vince Buffalo's excellent Bioinformatics Data Skills book has now passed. There were 65 entries and later this week I will randomly choose a winner. For the competition I simply asked people to tweet an answer to the following question:

Name a useful bioinformatics skill

I thought I would share some of the entries that people tweeted. In reverse order, here are my ten favorite answers. It was difficult choosing which ones made the cut, and there were many other excellent answers. Thanks to everyone who took part! I hope to announce the winner later this week.

 

10

This skill may not be so easy to acquire…

 

9

Two people came up with this suggestion…

 

8

I think this answer also applies to 'scripts you wrote yourself several years ago'…

 

7

Clouded by the Dark Side, your code is.

 

6

If you ever come up with some useful code snippet, the chances are that you will want to reuse it at some point.

 

5

This was the most popular answer in the competition…

 

4

Yes, yes, a thousand times yes!

 

3

If you ever run into any sort of bioinformatics problem, you can probably assume that someone has suffered from the same problem as you, and that someone else has posted a useful answer online.

 

2

Two closely related answers, so they can both share the number two spot…

 

1

And my favorite answer was one by Bastien Chevreux (@BaCh_mira)…

 

In bioinformatics it can be good to have some healthy skepticism about the tools and data that you use. Not all genome assemblies are perfect (many are far from perfect), not all gene annotations are correct, and not all tools use defafult values that will work well with your data. Be skeptical!

Maybe one of these answers will be lucky enough to be chosen by the magical 'Perl-script-of-destiny' (that I still need to write). The winner will hopefully be announced in a day or two.

3 important digital things all scientists should have nowadays

Good advice from Michael Koontz (@_mikoontz):

The second item on the list is something which I wrote about recently.