Ubuntu For Biologists

BACKGROUND

This article is designed to expose you to alternatives for Windows and Mac operating systems, which let’s face it either perform poorly, or are prohibitively expensive respectively. This is not designed to solve all of your problems, but rather to make you aware of what Ubuntu is, and why you might be interested in using it. Keep in mind as you read this that I am an entry level user myself.

OKAY, I'M IN - HOW MUCH DOES IT COST?

Ubuntu is a free Linux based operating system that is available for anyone to download and install. It is a viable and frankly sexy alternative to Windows, or Mac operating systems. For relatively basic users like me you should have no problems getting it to perform for you.  

SO - WHY IS IT BETTER THAN WHAT I HAVE ALREADY?

The short answer is, it may not be. If you already own a Mac then I would say, good for you. They are known for being reliable and dependable computers. Since the early 2000’s Mac have built their software on the back of Linux based distributions, so they already have a lot of the benefits I will mention here, apart from the costs of their products. If you are considering getting a Mac then this article might be important for you. If you already own a Windows computer and you are finding it doesn’t really meet your current needs, this article is for you.

LOOK AND FEEL
Ubuntu looks pretty nice out of the box, but a few small teaks make it nicer to look at. But overall, things are in the right place. It looks much more like OS-X than Windows, and behaves more smoothly than Windows. The main task-bars are to the left or on the top, actually much more comfortable to see and use than the typical Windows placement of icons.

Desktop view of ubuntu after some modification to make the taskbars transparent.

Applications are launched via a single click on the icons, and new software is installed via the software center, which is a carefully maintained repository of software known to behave with Linux. It's routinely checked for spyware and viruses by the Linux development community, so the risk of installing something that will compromise your computer is limited.

SPEED AND SECURITY
Ubuntu is fast. There are applications you can use to measure how one computer behaves under different operating systems, but you won’t need to check. Installing Ubuntu will make it seem like you have a new computer. And the performance does not degrade over time. Ubuntu is not just fast to install or fast at opening applications, it is fast to work with because of how you find and store you files, how you launch applications, and how you utilize the desktop. One easy example is that of multiple/virtual desktops. This is a feature of every Linux distribution as standard, and is amazingly still not a feature in Windows unless you find and install additional software (read, time + risk of viruses)

This feature is the single biggest time saving  feature I use on a daily basis. It is arguably better than having four big monitors set up in front of you. As a scientific researcher it allows me to separate my work flow. Research papers and reference manager open on one screen, my current word document open on a second, my plots, images, and data on a third, music and email on a fourth. Skipping between screens is a simple combination of buttons, (Ctrl + Alt + Arrow). It just works well, and I miss it every time I have to use a Windows computer.

As for security, this is not a topic I know much about, but there is a lot of discussion on software forums. The consensus seems to be that every OS is susceptible to attack, and there is no bullet proof system you could use. However, the more people there are who use that OS the more likely it is to be a target. Simply put, why write a virus that will allow you to steal 100 peoples bank details when you could steal 100,000 peoples bank details. However, Ubuntu is not secure just because it is less popular. It is built to restrict access although not in an annoying way. For those who would like to see the debate, check this link, http://askubuntu.com/questions/1069/why-is-ubuntu-more-secure-than-windows-or-mac-os-x.

From my own experience, I am never worried that I will pick up something that will compromise my computer. I have yet to encounter something that has been a problem, and patches are very quick and simple to install. Only sometimes do they require a restart of the computer to take effect. It’s also worth noting that this means there is no need for anti-virus software for Ubuntu, although it does exist. This means you are not scanning your computer every week. Ever try to use your computer while Sophos is doing a scan? You may as well take a coffee break.

WHAT SOFTWARE DO YOU GET WITH UBUNTU?
Ubuntu comes preloaded with some useful applications, and in general you can do a lot more with the “out of the box" installation compared to Windows 7 which still doesn’t come bundled with office software. Everyone’s needs are different, but with Ubuntu you will find most of what you need, and the overwhelming majority of it will be available free of charge. Personally, I needed and wanted the following applications,  

OFFICE BASED APPLICATIONS:

• Office software
• Reference Management Software
• Dropbox
• Google Drive
• Image viewer
• Plotting Software (numerous, but Qtiplot is pretty useful and easy)

HOME APPLICATIONS:

• DVD player/DVD burner
• Audio conversion tool
• An AVI to DVD converter
• Music player
• e-book library manager.

OFFICE APPLICATIONS:
For office software, Ubuntu comes preloaded with Libre Office, an open source version of MS Office. This works fairly well, but actually I still use MS office thanks to a little piece of software called PlayOnLinux, which allows you to install Windows and Mac software to your Linux computer. If you can do this I would recommend it, it’s not really worth getting to know Libre Office, almost no-one else uses it, so you will spend your time converting files to MS Office readable formats. 

As for reference management software, Mendeley works perfectly well with Ubuntu, although only with Libre Office so far. This is the biggest problem I have encountered in my migration from Windows to date, but Word 2010 and above have in-built reference managers which can be exploited in the meantime. It’s not perfect, but putting pressure on Mendeley to fix this is a viable option. 

USEFUL APPLICATIONS:
Other handy applications for Windows work well with Ubuntu, including Dropbox, and Google Drive, although currently there is no desktop version of Google Drive, you still have access from your browser , again this is something that could be improved upon.

For viewing and manipulating images there are a number of good options, gThumb and RawTherapee for example are both good for basic fixes such as rotation, artificially colouring the image, sharpening, and cropping. For plotting graphs, Qtiplot is a pretty good application. It looks and behaves similar to the plotting software Prism. It does take some time to get used to, but after about 30 minutes I was able to generate nice looking linear and sigmoid plots altering details like the axis titles, plot colour and plot size. It is also easy to save/copy and paste the resulting plots into word documents.

As for the rest there are numerous music players, but I really like Amarok. It’s smart and easy to use, and allows you to set up podcast streams by simply adding the RSS feed url. Importing music is a simple as drag and drop, and it automatically scans for album art and metadata. For playing DVDs and almost every other format, download VLC player. It just works, there’s not much more to mention. For burning DVDs download an application called K3b. This is an excellent piece of software, simple to use and fast. A nice addition to have is an application called DeVeDe, capable of converting between AVI/mp4 and DVD file formats without fuss. As for audio conversion, an application called Sound Converter will convert a wide selection of audio files to mp3.  

HOW DO I GET MORE?
All Ubuntu software can be obtained immediately by opening simply accessing their software centre, using one click on the toolbar. From here you can search for key terms, for example, DVD player, or mp3 converter, and you will be presented with a list of options. Take your pick and the application will begin to automatically download and install. Once complete the application is automatically added to the launcher. 

The software centre view of ubuntu. Installation of new software is quick and easy.

CONCLUSION
Ubuntu is fast, and powerful in terms of the sheer number of applications that are readily available. It made a big difference to how I used my computer, and definitely increased my productivity once I could tear myself away from downloading every application that looked even remotely interesting. There are dozens of frankly cool little tools, from Brewtarget, an application to help you with your home brew, to Stellarium for those interested in the stars above them.

USEFUL LINKS
Potential users may find the following links helpful. Also, it is worth noting that you can even try Ubuntu without having to install the software, simply transfer your download to a usb key, or burn it to a DVD, and you can run it from the USB/DVD as though it were installed. It's impressively fast.

1. Getting the software Downloading Ubuntu

2. Getting Netflix working with Ubuntu,  Netflix for Ubuntu

3. Installing MS Office on Ubuntu, MS Office for Ubuntu

4. Controlling Ubuntu from your Android phone, Android and Ubuntu