Fuzzier Logic » Software

Pretty equations in WordPress

Simon — Fri, 22 Oct 2010 08:20:22 +0000

We’ve spent a couple of months now on Knowledgeblog since JISC funded the project. My one day a week working on developing the tools and workflows for lightweight publishing has presented totally different challenges to the majority of my work, and I’m really enjoying it so far. Hopefully we’re engaged in building something that a lot of people will find useful in the long run.

Part of what will make the project useful to as many people as possible is the incremental goals that we will be combining into the whole platform, but that will hopefully be useful to a lot of folks in their own right. The first of these milestones is MathJax-LaTeX, a plugin for WordPress that renders mathematical equations in as attractive a way as possible.

WP-LaTeX is the usual way to do this in WordPress. This plugin takes inline LaTeX code in blog posts, and converts it into PNG images. These images are pretty good, they look good at the default resolution and they do the job, but we thought there might be a better way. Images are not particularly accessible, and they don’t scale very well (as you zoom in on a page, they start to pixelate pretty badly). It also requires running LaTeX locally, or on a third-party server, which might be undesirable for some people.

I’m aware of MathJax because I used to listen to the Stack Overflow podcast, and Joel and Jeff talked about it in one episode in relation to the Math Overflow site, because it was being leveraged there to render the large quantity of equations that a site like that requires. MathJax is a Javascript library that interprets LaTeX and MathML, and renders it as scalable web fonts inline. The LaTeX that is interpreted remains in the source of the page, and the equations are not images, so they scale perfectly with the rest of the text on the page. So the question is, what’s the best way to use MathJax to render equations in blog posts?

The instructions on the MathJax page tell you to edit the header of your blog theme to introduce the Javascript library on every page of the blog. We thought that using a plugin to inject the Javascript only on the pages it is required would be more efficient (it’s a big library, and you don’t want to load it on every page if you don’t have to). It also allows us to stay compatible with WP-LaTeX, because we can leverage the shortcode API that is a brilliant part of the WordPress environment.

Well, the MathJax-LaTeX plugin was published this week, you can download it now, and there’s a page on knowledgeblog.org describing in full how it works. If you’ve used WP-LaTeX in the past, MathJax-LaTeX understands the same syntax, so you can replace one with the other, if you wish.

Here’s a few examples:

The probability of getting \(k\) heads when flipping \(n\) coins:

This is an inline equation: it should be rendered without affecting the text around it.

OK, one more, definition of \(e\):

If you want to keep tabs on how Knowledgeblog is developing, you can follow us on Twitter, watch our Google Code repository, and keep an eye on the site.

(Photo courtesy of bourgeoisbee on flickr.com)

While I was away…

Simon — Fri, 24 Sep 2010 19:57:22 +0000

I’ve just returned from a week away in North Yorkshire, and scanning through my RSS backlog and FriendFeed from while I was away, I notice a few interesting developments.

Zotero made a firm announcement of a standalone version of their excellent open-source reference management tool. I’ve been keen on Zotero for a while, but have moved away from FireFox as my browser lately (at present, Zotero is only available as a FireFox plugin). I’m looking forward to using it in earnest again, and trying to integrate it more fully into my workflow (which has been the main problem with other reference managers I’ve tried). No release date yet that I’ve found (sadly).
Nodalpoint, the bioinformatics blog of old, has been reincarnated as a podcast. I love podcasts, and listen to a whole bunch of them (to the point where I don’t have much of a chance to listen to music on my commute any more), but there’s not many around that are relevant to what I do with most of my time (apart from the excellent c2cbio podcast of course). I’m really looking forward to listening to episode one, and hope more follow in due course.
The people behind the ‘Science is Vital‘ lobby group, as well as organising a public rally, and a lobby of Parliament, have set up a petition, I urge everyone (in the UK) to go and sign it. If we don’t try to protect science in some degree in the forthcoming round of spending cuts, no one else will.

Google Acquires AppJet – are there any live, functional alternatives to Etherpad?

Simon — Fri, 04 Dec 2009 22:40:50 +0000

We are happy to announce that AppJet Inc. has been acquired by Google. The EtherPad team will continue its work on realtime collaboration by joining the Google Wave team.

[...]

The EtherPad site will stay online through March 2010 with some restrictions.

[...]

No new free public pads may be created. Your pads will no longer be accessible after March 31, 2010, at which time your pads and any associated personally identifiable information will be deleted.

[...]

via etherpad.com

Etherpad was a nice little tool, very effective at what it offered, I’m sure the guys who developed it will bring a lot to the Wave party. But seriously, Wave is nowhere near functional yet, it’s confusing, and glacially slow. So is there a decent alternative to Etherpad that is usable – right now?

Posted via web from Simon’s posterous

Randomness, statistics and understanding

Simon — Wed, 24 Jun 2009 14:25:35 +0000

So here I am, sitting in a statistics workshop, having finished all the exercises ahead of time, musing on how much easier all this stuff is once you understand where it all comes from. This made me think that I have found this workshop more understandable and simpler to tackle because I have pretty much finished reading a marvellous little book called ‘The Drunkard’s Walk’ by Leonard Mlodinow.

Photo from http://www.flickr.com/photos/sixmilliondollardan/3193613357/

Mlodinow aims to educate the reader about randomness and statistics, by way of history and illustrative example, and he succeeds admirably. The book is a walk through mathematics from the Greeks and Romans, by way of the renaissance, to Einstein and the modern day. Each important advance toward the modern day study of statistics is illustrated with excellent examples and anecdotes, many of them personal to the author. The Monty Hall problem, the anomoly of Jeanne Calment, who reverse-mortgaged her apartment to a 47 year old lawyer when she was 90, only to outlive him (and he died aged 77), even the author’s own (false) positive AIDS test makes for an intriguing case study, and illustrates the importance of understanding prior probabilities when reporting the results of a test.

The setting of all this stuff in context has really helped my brain with the basic concepts, and even without this current course, I feel like I’ve got a much better grip on statistics in general. A remarkable claim for a popular science book. I look forward to the remaining 30 or so pages.

Eee PC & Eeebuntu

Simon — Mon, 22 Jun 2009 21:38:58 +0000

I’ve been hankering after a netbook for a while. Not just new shiny gadget lust (though that is certainly part of it, I’m only human after all), but a small machine with good battery life would be ideal for on the road, and for all the chugging round campus (and beyond) to meetings I do on a weekly basis. I casually mentioned this fact to Phil recently, and a week later a nice new Asus EeePC 1000HE was sitting on my desk (thanks Phil!).

I got the 1000HE because of the promised battery life (9.5hrs). No other comparable netbook comes close, and it is every bit as good as promised. 6hrs real world use is no problem at all. 8hrs should be realistically achievable on a daily basis. Overall the machine is surprisingly nippy too. Its not going to break any speed records, but the Intel Atom N280 drives it along at a reasonable clip under normal usage. The extra 1GB of RAM I installed helps out with the speed some too, this is an ‘underpowered’ laptop that can fire up OpenOffice.org in around 10 seconds.

Since I just can’t get along with Windows as a primary OS these days, I installed Eeebunutu. This is a version of Ubuntu customised for use on Asus netbooks, and as such all the hardware works out of the box. Power management is very impressive, with the battery life holding up about as well as it does under Windows. The only glitch I’ve noticed so far is that the Wifi card doesn’t turn on and off properly with the keyboard shortcut, but its a low power device, I think I can live with that (and the Eeebuntu forums seem very good if I really want to find a fix).

Eeebuntu is certainly a pretty distro

The standard desktop is very good looking, better than the default Ubuntu look and feel, and the configuration makes the most of the (admittedly limited) screen real-estate. A few tweaks to Firefox to make the most of the available room, and I’m very happy to work on it all day. Considering I’m used to 20-24″ widescreens, that’s pretty impressive.

I’d recommend the Eee PC to anyone looking to make a netbook purchase, and since Asus are phasing the 1000HE out pretty soon, if you are looking, I’d grab one while you still can.

Experiments with MindMapping

Simon — Thu, 28 May 2009 17:00:26 +0000

I’ve been experimenting with various forms of note taking recently. I keep my daily diary on my wiki, but struggle to capture my every note there, because of the editing overhead, and requirement to be online (which I often am not during meetings, for example). So I have tried Evernote, which seems to work very nicely. The online requirement is gone, and I can take quick notes on my phone too (better for meetings). However, if I want to record these notes easily on the wiki, I have to adhere to wiki syntax in my note taking which can be a bit of a pain outside of that environment.

I’ve noticed a few people that I work with using Mind Mapping software recently, and the approach intrigued me. So I looked through FriendFeed for what different people were using (useful as a fast, informal survey of the tools available), and downloaded a couple to tinker with (FreeMind and XMind, for the record). Of these, XMind is the more polished tool, and allows you to share your maps once you have created them. I decided to give it a thorough test run at a workshop meeting in Manchester today. I’ve embedded the results below.

I’m quite impressed. It allows me to record detailed notes, and also to have a visual representation of how the various topics fit together. The XMind upload & share facility allows me to embed the final map in my wiki (or blog, obv.), and the outline view of the map is actually a good textual representation of the meeting too.

XMind is not going to be a solution for every situation. Often, pen & paper will still be used in meetings, and transcription to some electronic format will still be required. The fastest way of recording these types of notes will probably still be directly on the wiki. In the end, a mixture of tools seems the best approach overall, but for all day meetings/conference sitations, XMind seems like a very good tool.

Papers for iPhone, a brief review

Simon — Fri, 20 Feb 2009 12:52:52 +0000

Papers, from Mekentosj, is a literature management program for Mac. It organises pdfs into a searchable library, and stores the appropriate metadata associated with scientific articles (which it retrieves from public repositories such as PubMed, though in practise you can tag any document with any metadata).

I have been a Papers user since v1.0. I bought my license in April ’07 and have not looked back, it makes it so much easier to find that particular paper you are after, to organise papers by subject or project, and it even converted me to reading articles on the screen, rather than printing everything out.

I haven’t had an iPhone for very long, and it is safe to say it is by far the most impressive gadget I have ever owned. I am aware of its imperfections, but I don’t care, they are either in areas I don’t use anyway (I’ve never sent an MMS in my life), or they haven’t affected me yet (though I probably will curse the lack of Copy-Paste at some point). I have been thinking about the impending release of Papers for the iPhone ever since I got it, and wondering if it would (a) be any good and (b) add anything to the already high value of Papers for Mac.

The answer to both questions is a resounding yes so far. The app is lovely, very intuitive and smooth. Syncing my Papers library to my phone was a doddle, and my (not inconsiderable) library was copied across in less than 10 minutes. Now my article collection is quite literally at my fingertips. Searching PubMed on the phone and retrieving papers also works really well. Find the paper you want, click import, and you’re done. The viewer is good too, pdfs render quickly and clearly. My only criticism is that zooming in can be a little cumbersome, but I suspect this is a hardware, rather than software, limitation.

Although I have yet to spend a lot of time with it, I don’t regret my purchase of Papers for iPhone for a second (and £5.99 is a very reasonable price btw), I think that I will get so many more articles read now I can summon them at the press of a button on my bus ride home every evening. All I need now is the full range of my institution’s journal subscriptions available to me over my 3G connection.