Mini-review: Bibus, an open source bibliographic managment tool

After converting from Ubuntu linux about a year ago, I found that there were only two tasks that required me to boot into my Windows installation: syncing my iPod touch with iTunes, and writing documents that required heavy scientific referencing with EndNote. The first task may very soon have a viable linux alternative with the imminent release of PwnPlayer. When I recently set to work on a lengthy literature review, I decided to go and find a viable alternative for referencing too. After testing a few options, I came across Bibus. It’s not perfect, but it does competently replace all the functions of EndNote – and, of course, it’s totally free and open source.

Bibus performs all the basic referencing functions: it imports citations from files or manual input, stores and organises them in a simple database, inserts in-text citations into OpenOffice documents (MS Word is apparently also supported), and updates a formatted reference list at the end of the document. It was exceptionally stable, with not a single crash, and installation, database creation and integration into OpenOffice was streamlined and easy. There were a number of little usability hitches, however, which still require some polishing:

• Importing from Google Scholar, where I get the majority of my references, is not very streamlined. I found the best way was to open an ‘Import text window’ in Bibus, and set my Scholar preferences to offer a text-only BibTeX citation for each reference in the search results. I then had to copy and paste the citation into the inport window and hit ‘import’ and drag it from the import buffer into the reference list proper. The need for this buffer was not obvious and it felt like a totally unnessecarilay extra step.
• Inserting the reference into OpenOffice was also a little awkward. EndNote adds a toolbar which lets you insert an in-text citation from inside a MS Word window. Bibus makes you mark the spot in the OpenOffice document, change windows into Bibus and insert, then go back to OpenOffice to make sure it inserted correctly. This is a minor niggle, but can get tedious when you are inserting multiple citations for the same reference.
• The way Bibus imported the BibTeX data was a little haphazard, with it occasionally keeping curly brackets “{“, the BibTeX field delimiters, in the text of the reference itself. I couldn’t tell if this was an error on Bibus or Google Scholar’s side, but either way it meant I had to manually go though at the end and remove a number of stray curly braces from my references section.
• Formatting of the references was inconsistant, even when I repetedly applied a single ruleset to the entire list. Again, this could have been a problem on Scholar’s side.

Ubuntu 9.04 “Jaunty Jackalope” announced

Jaunty Jackalope? It may sound like furry porno but Mark Shuttleworth’s slightly eccentric announcement promises some interesting new directions for Ubuntu 9.04. First up is boot time, which has long been a pet peeve of mine in Gutsy and Hardy. There’s nothing that takes the shine off your favorite distro like watching it place a poor second against Windows in the startup event.

The Jackalope is known for being so fast that it’s extremely hard to catch, and breeds only when lightning flashes.

I’m a little confused about the significance of the second part, but the sentiment is good. Shuttleworth also mentions tailoring 9.04 for speed on specific devices. I’ll probably never see my dream of Ubuntu-based firmware for my old iPod touch; this more likely refers to subnotebooks shipped with customised versions of 9.04 as well as embedded devices.

Jaunty will also emphasise increased web integration into the desktop. Since “Jackalope” is apparently not sufficient to meet the awkward portmanteau quota, we are at this point introduced to the ugly “weblication”. This is a logical extension of the “pervasive internet access” slated for Intrepid Ibex. It’s going to be interesting to see what the developers come up with here, since this is the first application-centric major goal we’ve seen in a few releases. Google’s new Chrome browser has been stirring up a lot of talk about web based applications for no reason I can clearly discern: it’s certainly a great browser with a lot of potential, but beyond the improved Javascript handling and Gears integration it doesn’t offer anything particularly unique. I would be very surprised to see it become a part of Ubuntu any time soon, especially as there is still no linux port of the beta, although Google’s close ties with and support for Canonical could lead to some surprises.

More likely for Jaunty is a range of synchronisation services, some of which will be tethered to Google’s cloud. Given the increasing staleness of OpenOffice, we might even see Google Docs become the default office suite in 9.04. A revamp of web-integrated Gnome screenlets to be enabled by default is also a possibility, although this would be a fairly minor improvement. What excites me more is the possibility that entirely new weblication (ugh) systems will be dreamed up and implemented by the developers. This would be a boon in so many ways: it would lend some substance to the vaporous “web OS” paradigm; it would establish a hallmark feature to set Ubuntu clearly apart within the linux world and attract new users from without, something that has been sorely missing from the distro so far; and it would force web developers to take notice of the linux user base and push the spread of web standards. All good things.

Why you can’t trust even yourself with your own private data

A couple of months ago, I read Cory Doctorow’s excellent nerd-action novel, Little Brother, released free online. Among the many things this book instilled in me was a brief paranoiac obsession with computer security and privacy. I turned into an encrypting, password protecting, default denying machine. I began treating every scrap of information I released over the intertubes like a letter from the front lines, carefully redacting the non-essential and the potentially revealing. I got myself a PGP key and encrypted anything that stood still long enough to be expressed in bits. I started putting regex wrappers to prevent malicious input into even the most banal of PERL scripts that would only ever be run once, by me, locally.

There was a fatal flaw in all this. I’m a biologist, and I don’t really know much about computer security. This was brought home hard today when I decided to jump on the bandwagon and test Google’s new uberbrowser, Chrome. While playing around with this very impressive bit of software, I stumbled across a comment on Digg lamenting the fact that Chrome had copied the commenter’s stored passwords straight out of Firefox upon installation. If it was this easy for Chrome to do it, what about malware? Were the passwords just sitting around in some unencrypted file, happily to hand out my access codes for dozens other online services to any comer?

This bothers me deeply. It’s not the Firefox flaw, if you can even call it that; it actually seems quite reasonable that Firefox would store passwords in this way, as long as they can only be accessed by the correct user on the local system. It’s the fact that it didn’t even occur to me to wonder where and how the passwords were being stored. Why didn’t I make the connection between the gigabytes of extremely private and valuable data in my Gmail account, the password that protects it, and the fact that I so rarely actually have to type that password in? I run GNU/linux, and Firefox with NoScript, so it’s not that I’m in immediate danger of having the Russian mafia sneak some malicious code into my browser and steal my Facebook account. It’s the complete failure to question on my part that is so worrying.

I don’t have the security mindset, yet. Maybe I never will. Maybe it’s like Socrates said – if you think you’re wise, you’re not wise. Either way, I’ll think yet more carefully in the future about every step of securing my private data, not just the most obvious ones.

Commenters, do you have any stories about security holes, or even simple oversights like mine, that gave you pause?

Some good advice on converting friends (or enemies) to linux

Celettu offers some great ideas on attracting new comments to linux. I especially like his suggestion that you refuse to continue providing free Windows tech support – this has worked charmingly for my own family, if not for converting them then at least for showing that there is a reliable alternative when MSware goes sour. The only tip I would add is to take full advantage of all the shiny graphical customisation available in the linux world. I’ve had two friends approach me asking about Ubuntu purely on the basis of having seen somebody’s sleek desktop setup online.

Mnemosyne is one of the best open-source apps you’ve never heard of

Mnemosyne is da bomb. This is the closest thing humanity has ever had to sticking one of those Matrix cables into the back of your head and streaming info in on a broadband line. Sure, the GUI might not look quite that cyberpunk, but the functionality is all there.

The basic premise of Mnemosyne, according to its creators, is to combine a flashcard viewer with an algorithm that shows you exactly what you need to know at exactly the right time for it to get seared into your gray matter. True, the boilerplate about “spaced repetition” with its vague references to “memory research” and people with long European surnames sounds a little like pseudoscientific babble. Regardless, it seems to work, and damn well.

After viewing each card, Mnemosyne asks you to rate your recall on a scale of 0, “totally forgotten”, to 5, “remembered with ease”. If the card is a new one, it asks using you to rate how familiar it has become on the same scale. These ratings go into the magical black box of the algorithm, and cause the cards to pop up again after a certain period of time. A typical session might involve a good dose of cards you have learned recently but do not yet have entirely memorised, a sprinkling of older cards to keep them fresh in your mind, and five or so brand new cards which you will see several times during the session until you’re confident you have them for a few days. Learning ensues.

Mnemosyne has an interface to put a Spartan barracks to shame. Just below the surface, however, is a treasure trove of handy little features such as three-sided cards, easy categorisation, tweaks to the appearance of cards including a handy feature which blows up the size of foreign script, and more. Once you have used Mnemosyne for a while, you start to get the impression that the developers are heavy users of the program themselves: every time you think “gee, I wish there was a way to -”, you realise that a solution has already been implemented. If not, there’s a small family of plugins, and of course you can always write your own. Want to add a sound file for the pronunciation of some foreign vocab, or an image to identify? Easy. Import a tab separated or XML flashcards database from your old flashcards program? No problems. It also exports cards, which is handy for mobile card viewers like the iPhone’s iStudy.

The only real downside is that it takes a little while for your mind to ‘get’ working with Mnemosyne. If you’re dedicated to learning your content motivation should get over this hump easily. Otherwise, it is easy to see how somebody giving this app a 10-minute test run could dismiss it as a lightweight flash-card flasher and nothing more. It’s not.

Mnemosyne is downloadable for Linux, Windows and OSX. It’s also available in the Ubuntu universe repository.

Bleg: what do you use the tracker search tool for in Ubuntu Hardy?

One of the first things I do when configuring a fresh Ubuntu distro is disable all the tracking, indexing and search daemons I can find. I’ve simply never had a need for a search and indexing tool in any OS. Yet, they are enduringly popular and often trumpeted as killer features. What do people use them for? Is there some way of using them that I’m yet to get my head around, but which greatly improves usability and efficiency?

Slick Ubuntu Desktop

It’s very frustrating to see a picture or video online featuring a really gorgeous Ubuntu\Gnome desktop, and have absolutely no idea how to get the same thing for yourself. Purely out of the goodness of my heart, and perhaps just a tiny little bit out of a desire to peacock, here’s a breakdown of my own desktop.

Wallpaper: I was searching on flickr for some images of DNA when I stumbled across this shot of a sculpture in Munich. Apparently when you see the it from the right angle it resembles a double helix. I love how the dark glossy metal complements the black of the top Gnome panel, and the orange-blue contrast is fantastic too. Here’s another great shot of the same sculpture.

Icons: black-white 2 gloss. There are several variations in the black-white family but this one fits in best with the black-glossy theme. For linux n00bs like me who struggled to add new icons the first time round, type sudo nautilus /usr/share/icons/ into a terminal then drag in the uncompressed folder called black-white_2-gloss. The icons will then be available in System > Preferences > Appearance > (select a theme) Customise > Icons.

Theme: ColorBit 2. To install, open System > Preferences > Appearance then just drag the compressed file into the ‘Theme’ box. Go to Customise > Colours then tone down all the blues to white\grays – this took a bit of trial and error on my computer and it’s largely a matter of taste how dark or light you want to take it.

Compiz: I’d love to use alpha-blur behind the semi-transparent windows but my graphics card just can’t hack it. Set the following opacity settings in System > Preferences > Advanced Desktop Effects Settings > General Options > Opacity Settings (if you can’t see Advanced Desktop Effects Settings, you don’t have the compiz settings manager installed; sudo apt-get install compizconfig-settings-manager):

class=Gnome-panel; opacity 82

class=Nautilus; opacity 90

class=File-roller; opacity 80

Go back to the CompizConfig Settings Manager main window, and go into Animations (it’s under Effects). Change the close effect to Burn with a duration of 50, and open to Skewer with a duration of 200.

Panels: To save space, I removed the bottom panel and put all the necessary bits and pieces up along the top of the desktop. Right click on panel objects to move or remove them; if you can’t, just untick the ‘Lock to Panel’ box and try again. Get rid of the ‘Show Desktop’ button and the ‘Switch Desktop’ applet – if you want to switch desktops, just drag a window off the side of the screen, or use <Ctrl> + <Alt> + an arrow key. Move the window list from the bottom panel up onto the top panel, and slide it along until it’s taking up the maximum amount of real estate. Now you can delete the naked bottom panel entirely.

That’s it! Don’t forget…the point of free software is that it’s free, so take advantage of that and use your imagination rather than copying my set-up exactly.

8 Great Things and 8 Less-Than-Great Things About Ubuntu 7.10 Though the Eyes of a Linux Noob

Great Things

1. So, so, so much faster than Windows.
2. No blue screen of death, and very infrequent crashing.
3. Compiz-fusion. Oh the purty colours…
4. Installing and uninstalling all your apps from one simple interface.
5. Using the terminal makes you feel like a real 1337 hax0r.
6. New updates come out faster than you can download them.
7. Networking the way it’s meant to be: invisible and totally automatic.
8. The forums.

Less-Than-Great Things

1. Playing an encrypted DVD (read: any DVD) takes some solid tinkerin’.
2. Your webcam gathering dust on top of the monitor.
3. Regretting having ever bought an iPod.
4. Games. Yeah, yeah, I know…I mean REAL games.
5. Occasional inexplicable changes to icons, screen resolution, and pretty much everything else you don’t expect to change.
6. “You use LINUX? Nerd!” (Guilty as charged).
7. ‘Hibernate’ is buggy at best – not fun when you read hundreds of articles a day and like to be able to restart where you left off.
8. I honestly can’t think of an eighth thing. Yes, it’s that good. Get it.