Thoughts on biology, genomics, and the ongoing threat to humanity from the bogus use of bioinformatics acronyms, by Keith Bradnam
Today I received notification of a paper that cites some work I was involved in. The paper was a Word Document, that was inside a zip archive, that was on an FTP site of a very-famous-mutinational-software-company!
Read MoreEvery year I help teach a course[1] to grad students that hopefully leaves them with an understanding of how to use Unix and Perl to solve bioinformatics-related problems. We use a Mac-based computer lab because all Macs come with Unix and Perl installed. Many of our students are new to programming and many are new to Macs. Because of this, and because they need to use a code editor to write their Perl scripts, we have previously pointed them towards Fraise. Despite its age [2], this relatively lightweight editor has proved fine for the last few years that we have taught this course.
This year, however, Fraise proved problematic. The computer lab has now upgraded to OS X 10.8 which provides extra safeguards about what apps can be run. This Gatekeeper technology has been set up to only allow ‘signed’ apps[3]. The version of Fraise that we were using required administrator privileges for it to be opened (not possible in this computer lab).
My first thought was to direct students to download and install TextWrangler. This is an excellent, powerful, and well maintained code editor for Macs. Most importantly, it is free and also a signed app. However, it does try to install a helper app which caused a persistent dialog window to keep popping up during the installation. Clicking ‘cancel’ worked…but only after about 20 attempts[4]. I like TextWrangler as an app, but prefer the cleaner look of Fraise. So today I set out to find code editors for Macs that:
Here is what I came up with. These are all apps that seem to be under current development (updated at some point in 2013):
AppSize in MB Free? Notes
Komodo Edit301.1YesBig because it is part of a larger IDE tool which is not free[5]
Sublime Text 227.3sort of[6]Gaining in popularity (a version 3 beta is also available)
TextMate 230.3YesWhile this is technically an ‘alpha’[7] release, it seems very stable.
TextWrangler19.2YesVery robust and venerable app. Free since 2005
Tincta 25.6YesSmall app, similar to Fraise in appearance
If I had to suggest one, it would probably be Sublime Text 2 (though I will encourage students to buy this if they like it). TextMate 2 is a good second choice, particularly because it is also a very clean looking app. Of course, at some point we need to tell students about the joys of real text editors such as vi, vim, and emacs…but of course this might lead to hostilities![8]
This course material is available for free and became the basis for our much more expansive book on the same topic ↩
Fraise is itself a fork of Smultron which stopped development in 2009 but which reappeared as a paid app in the Mac App Store in 2011. ↩
Those apps that are approved by Apple, even if they are not in the Mac App Store. ↩
Seriously, it takes a lot of clicks to make this dialog box go away. It then produces more pop-up dialogs asking whether you want to register, or install command-line tools. ↩
Currently $332 for a single license ↩
This is a paid app, but can be used in trial mode indefinitely with occasional reminders. ↩
TextMate 2 has been in alpha status since 2009 ↩
Editor wars should be avoided if possible ↩
PhD students in our lab are mostly split between a couple of UC Davis's many graduate groups. A conversation with some of the students today about 'outreach' and 'social media' led me to wonder how well these graduate groups are communicating their presence to the outside world. The simplest ways of doing this would be:
I looked at 11 different graduate groups to see how well they ticked the above boxes. I might be missing some blogs, Facebook groups, and twitter accounts, but if I can't find the relevant details from a Google/Facebook/Twitter search, then I'm assuming that others won't discover them either. This is what I found:
Headline links take you to the home page for the respective graduate group.
Please let me know of any updates or additions that I can make to this list
So overall it is pretty poor. BMCDB outshines the others, though BME and Ecology also have a good presence on the web. In many ways, I think it looks worse to do these things badly than to not to them at all. Closed Facebook groups don't send out an inviting message, and having a 'news' page for your graduate group with items from 5 years ago, also sends out the wrong signals.
It takes time and effort to maintain a social media presence, but it doesn't take much effort to at least maintain a news page or simple twitter account (even posting just 1–2 times a week is better than nothing).
Furthermore, the ability to show that you can communicate your work to the wider world is of increasing relevance when applying for grants. It can also raise your profile with your peers and be a useful addition on a resume that helps you stand out from other applicants. Finally, starting a blog or twitter account also helps you hone your writing skills (the latter is great for making you think about how to condense complex thoughts into 'bite size' chunks).
I hope that some of UC Davis's graduate groups make more of an effort in this area (and of course the same can be said for many of UC Davis's departmental and lab websites).
Updated 26th September: Added details of some graduate groups that do have blogs and/or websites but which, unhelpfully, are not linked to from their official graduate group webpage.
JABBA is an acronym for Just Another Bogus Bioinformatics Acronym. I hand out JABBA awards to bioinformatics papers that reach just a little bit too far when trying to come up with acronyms (or intialisms). See details of previous winners here.
So without further delay, let's see who the new recipients are. As always, journals like Bioinformatics produce many strong candidates for JABBA awards. Here are three winners from the latest issue: