Is The Ipad Bioinformatics-Unfriendly?

Question

[Andra Waagmeester]

I have settled for an Apple Macbook as a personal computer and Ubuntu as a server platform. I have a dislike for Microsoft Windows. But I believe that the choice for a bioinformatician here is personal. For personal computers Bioinformatics is platform independent.

I was wondering how this is for the tablets. I am considering buying an iPad, but the salesperson advised me against it since Java is not well supported. I was advised to go for an Android based tablet. Since Java is widespread among bioinformatician can you say that the iPad is not suitable for a bioinformatician?

[Istvan Albert]

iPad is a consumer product that can only display Apple approved entertainment - it is very unlikely that you could be productive with it

[Michael Kuhn]

What kind of bioinformatic "things" do you want to do on (any) tablet?

Answer 1

[Michael]

This is just gadget. Or does it have:

• Java
• Perl
• Python
• R
• An IDE (eclipse)
• Emacs
• A c/c++ compiler (gcc)
• A terminal/shell ?

Still nice to have to read papers or make notes, maybe... Was thinking about buying one, for about 10 seconds.

[Michael]

Indeed, it could be a good entry point to an electornic lab-book or general LIMS system. It might yield better user acceptance among lab staff than a thick computer. It could scan barcode tags using the built in camera.

[Andra Waagmeester]

Indeed reading papers and making notes is primarily the thing you want to do with them. So is data entry at location. (Curating pathways at a conference for example)

[Istvan Albert]

though it has no builtin camera as of yet

[Joachim]

The iPad does not come with a built-in camera. Perhaps the next generation iPads will have a camera, but the current models certainly do not have one.

[Chris Evelo]

One day earlier and you would have been right. You still can't buy one for a few days but the Ipad2 will have 2 cameras. See: http://money.cnn.com/2011/03/02/technology/ipad_2_announcement/index.htm

[Joachim]

When I wrote that, the iPad 2 was not released then. They released it in the afternoon of the same day.

[Michael]

Take care though, some people were injured while trying to get it: http://www.globalpost.com/dispatch/news/regions/asia-pacific/china/110508/china-beijing-sanlitun-apple-ipad-2-store-brawl-fight

Maybe an Android tablet would be a safer choice?

Answer 2

[Joachim]

Despite of all the sneering and eye-rolling, I got myself an iPad to replace my lab-notebook almost a year ago. I do not regret this decision.

For managing your references, you can use the iPad version of the famous OSX application "Papers". You can either run it only on the iPad or sync it with your installation of Papers on your desktop machine. Now it also allows annotations, but I think they are only visible in Papers on the iPad and Papers on OSX.

I annotate my papers with comments and highlighting in iAnnotate, which niftily saves the modifications in the PDF itself. So, if you send the document to a friend or share it for a journal club, non-iPad and non-Apple users can benefit from that too.

Personally I am also a fan of "iSSH", which is an SSH- and VNC-client. A lot of people say it is not possible to type reasonably fast on the on-screen iPad keyboard, but I cannot agree to that. Most other iPad users I met also confirm that they can type almost as fast on the on-screen keyboard as on a normal keyboard. If you really write a lot, you can always get the bluetooth keyboard that goes with the iPad. I use it when I know that I will be scripting a lot via SSH.

In my previous lab, we used Google Docs a lot. You can use the app "Office2 HD" for accessing your Google Docs, which works fairly well with documents and spreadsheets. It can also open Word and Excel documents, so for me it was a no-brainer to get this app too.

Several apps exist for scribbling down notes, making sketches or layout mind-maps.

Remember the Milk is releasing an iPad version for their service soon too -- in case you need to manage your TODO-lists, notes and deadlines online. Right now, you have to use the iPhone version on the iPad, which works well but does not make use of the full-screen of the iPad.

Apart from that, I also have some biology books on it. This comes in handy when you need to look something up that is not covered in sufficient detail on Wikipedia. You can use Apple's iBooks and their book store, or alternatively, you use the Kindle-app and buy books in Amazon's on-line store.

I would say the iPad is a valuable tool and definitely a good replacement for a lab-notebook.

UPDATE Here is a listing of 10 mobile apps (most of them on iPad) that are relevant in bioinformatics: http://www.fiercebiotech.com/slideshows/10-mobile-apps-life-sciences?img=0

2nd UPDATE The Apple Store features iProteome (http://itunes.apple.com/ca/app/iproteome/id524883731) now, which is described as "[...] a mobile application to find information, tryptic peptide sequences and backbone fragmentation ions commonly found in mass spectrometry." (As seen by @attilacsordas on Twitter).

[Egon Willighagen]

I'm sorry, but this does not sound bioinformatics to me...

[Istvan Albert]

You are right, I did jump to conclusions (sneering that is) most likely because I find the closely controlled nature of Apple products (that now translate to even the software that you may run) disheartening. Hopefully web based applications will allow us to circumvent this control.

[Istvan Albert]

You are right, I did jump to conclusions (sneering that is) most likely because I find the closed and controlled nature of Apple products, that now translate to even the software that you may run, disheartening. Hopefully web based applications will allow us to circumvent this control.

[Michael]

Joachim, I still agree with Egon, none of the mobile apps you updated is bioinformatics (notwithstanding they might be very useful in a medical environment or for clinical study management). You have just fallen for the 'life-science' hype, but life-science != bioinformatics.

[Joachim]

Fair enough, Michael, I understand what you mean, but I think under such tough constraints the only conclusion can only be that any tablet is uninteresting to bioinformaticians. I would have at least rated the first app -- the genome browser -- as a bioinformatician's tool though.

[Michael]

I wouldn't say it's not interesting, I think you can do a lot of stuff remotely with it, and read web-sites, but is not specific, I could do that with my phone even, and still I wouldn't consider my phone 'bioinformatics' friendly or unfriendly. I think bioinformatician can make good use of a tablet, as they can make use of a phone, a car and a bottle of good whine.

Answer 3

[Scott Cain]

Obviously it depends on what you want to do with it. It is a tool/gadget. It has reasonably nice ssh terminals available, so if you plan on writing code on a remote server, you can do that. I've used Keynote for giving presentations from one. I've yet to miss Flash.

Also, I know that the most recent release of GBrowse works well on it :-)

Answer 4

[Mark Anthony Gibbins]

As this question is unanswered, I'd just like to state that I have started work on a few iOS development projects to keep me entertained while I finish off my degree that may be of interest to anyone using an iPad for their Bioinformatics work. At the moment I have the following planned:

1. A Bioinformatics "toolkit" that should be able to perform some basic tasks like BLAST queries against the online NCBI BLAST server, or your own. It should display graphics/formatted results in a nice, shiny Apple fashion. If you can think of any other tasks that would be useful then please let me know. This will be a free app of course.

2. I've also started some work on a small script editing app for the iPad which has syntax highlighting and the ability to edit in the "cloud", i.e. from a repository on your server or somewhere like GitHub. I know one of my lecturers would kill for this on his iPad.

3. A web service to translate any Flash video found online into HTML5, which the iOS devices love.

Any questions: ztac040 at live.rhul.ac.uk

[Michael]

Hi, nice idea!, but did you consider developing for android instead? I have the impression that android is more consistent with open-source, also I read that the Apple AppStore terms and conditions are incompatible with the GPL: http://www.fsf.org/blogs/licensing/more-about-the-app-store-gpl-enforcement

[Mark Anthony Gibbins]

Indeed I did consider the implications of GPL/Apple licensing, it is a sad state of affairs. I expect if demand was great enough, I would also create a version for Android devices with a separate code base and under a GPL license.