I am very happy with myself as, on saturday, I managed to complete the 64 mile Cyclone. The last time I managed this was 6 years ago [@url:www.russet.org.uk/blog/1697] There were other momentus events happening in my life that year [@url:www.russet.org.uk/blog/1846] which probably explain why I have not found the time to replicate the feat since then. My main change this year has been my training schedule; I knew that I was going to get there by cycling at the weekends --- it's not enough, and too irregular. So, instead, I have been using some cycle rollers that I bought ages ago but have not really just started to use. And what a difference they have made; I remember feeling tired after a 20 mile ride in April, so have got to 60 pretty quick. In fact, I managed to time close to my previou…

I have written about assess previously [@url:www.russet.org.uk/blog/3135] it is a tool which provides predicates, macros and functions to support testing for Emacs. It is actually agnostic to the test environment, although has specialised support for ERT. My new release of assess (v0.3.2) includes one significant change, and two new features. I have updated the call capture functionality --- the first version stored all the call data in a global variable, which was quick and easy, but clearly not a log term solution. It now uses closures instead which means that several functions can be captured at once. This also allows the first new feature, which is the ability to capture calls to hooks, with the function assess-call-capture-hook, which takes a hook and a lambda, and returns any calls t…

Assess is my new package supporting testing in Emacs. It has grown out of my frustration with the existing framework while building the lentic package [@url:www.russet.org.uk/blog/3071] For quite a while, the only testing framework in Emacs has been ERT (the Emacs Regression Testing tool) which is part of core. More recently, there have been a number of new ones arriving. For example, buttercup and ecukes both provide behaviour driven testing, rather like Jasmine or Cucumber respectively. Both worth looking at --- I've used Ecukes for testing Cask, and it's nicely implemented and very usable. Assess is rather less radical than this though. It focuses on providing a general set of tools for testing, mostly in terms of some macros and predicates that should be useful. For example, a recurren…

Over the years, a great deal has been written about the ontology of pizza [@url:robertdavidstevens.wordpress.com/2010/01/22/why-the-pizza-ontology-tutorial/] It's a good example, is easy to understand and works surprisingly well in a tutorial context. It is also comes up surprisingly commonly in the public sphere as it did last year on BBC News [@url:www.bbc.co.uk/news/magazine-33542392] The key point of which is this: the pizza maker argues that you can't have a marinara (tomato and garlic) with added mozzarella because a marinara is pizza rossa which can't have mozzarella; a margherita (tomato and mozzarella) with garlic is fine though. Ha, those crazy Italians. I paraphrase, of course. Of course, the right to comment first on this article rests with Robert Stevens, my colleague and worl…

My last blogpost was on logging [@url:www.russet.org.uk/blog/3112] with the SLF4J library, its inclusion in the OWL API, and its impact on Tawny-OWL. It raised quite a response, not least because it suggested that people ignore the advice of the authors of the library. Perhaps, unsurprisingly, the general feeling was against my position --- something that I expected given that this had already happened on the SLF4J mailing list. Now, of course, it does have to be said that there is a significant sampling bias here: anyone on the mailing list, or who reads and responds to a post about a logging API, is likely to be interested in logging rather than a passive user (or non-user) of such a library. None the less, I think it is worth reflecting on the reasons for the comments. Of course, I am a…

Shortly after the release of Tawny-OWL 1.5.0 [@url:www.russet.org.uk/blog/3110] I noticed a strange message being printed to screen, which looks like this: SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. What strangeness is this? I had never heard of SLF4J before, and could not see why this was happening; so I googled around, and found out. The reason is that I had switched versions of the OWL API [@url:dl.acm.org/citation.cfm?id=2019471] and this now uses the SLF4J API as a logging API. By default, it prints out this error message. Slightly irritated by this, I tweeted #slf4j I mean, who decided to print a message to …

I am pleased to annouce the 1.5.0 release of Tawny-OWL, the fully programmatic ontology construction environment. As with the 1.4.0 release, there has been quite a long gap between releases. The main change for this release has been the move to the OWL API version 4. The next release of Tawny will include more extensions to the patterns. Tawny 1.5.0 is now available on Clojars.

I was entertained to see that Springer recently retracted a set of papers, having apparently detected a set of fake reviewers [@url:retractionwatch.com/2015/08/17/64-more-papers-retracted-for-fake-reviews-this-time-from-springer-journals] The game seems to be that authors suggest reviewers who are real people but with fake emails owned by the authors. Allyson Lister, a colleague of mine, was twice the victim of this form of identity theft [@url:themindwobbles.wordpress.com/2011/05/04/stolen-professional-identity/] [@url:themindwobbles.wordpress.com/2011/07/19/a-new-journal-a-new-bogus-review-again-the-culprits-are-banned/] a while back so I am perhaps less surprised to hear that this is happening than some in the scientific community. Now, of course, this is a form of fraud and is not some…

I have discussed the issue of peer-review before, and my frustration at being asked to review for journals with high submissions fees [@url:www.russet.org.uk/blog/2327] something for which we as academics gain very little credit for. I recently fell across by an economist who acts as an editor for a journal [@url:marcfbellemare.com/wordpress/10776] which has an interesting perspective. One comment he makes rings true. When you receive a request to review, please respond, and please respond as quickly as possible. I am always baffled by how many people fail to ever respond to requests to review. --- Marc F Bellemare I have always felt slightly guilty about this, although I do get a fairly large quantity of spam about reviewing, much of which is not particuarly directed at me and often wi…

I'm winding by way back from a busy month with both Bio-Ontologies and ICBO, but in general I think the experience has been really positive, even if interspersing holiday and work travel has rather exhausted me. But both were in Europe and Bio-Ontologies was right next door, so I did not want to waste the opportunity. I have a long history with Bio-Ontologies, having been a chair for many years and a informal helper before that. We steered it from an informal meeting, to having a proper programme committee, proceedings and much of the structure that it has now. I bumped into Steven Leard at the meeting, and was rather shocked to realise that the first meeting I helped out at was 14 years ago. Strangely, though, since my last time as a chair, five or six years ago, I've never been once. For…