Kblog has been compromised

I have been pushing the idea of Kblogs --- scientific publishing using commodity software --- for a year or so know. Our main site, Knowledgeblog.org has got around 100 articles now, and has had about 50k page views (or about 4x the number of raw page hits) and has generated a certain presence on the internet. While this is generally good, the price of fame is that we have moved somewhat up the list of potential hack targets. Unfortunately, this has resulted in two compromises on the machine; they were probably not disconnected, although we have no evidence to link the two at the moment. The first was through the timthumb zero day vulnerability. It involved a code injection into a Wordpress installation using a thumb nail generator with a dodgy bit of PhP in it. We cleaned the system up as…

Oslo

My first visit to Oslo was in 2006. That time, it was for work and we were some distance away from town. I remember the flight in gave a dramatic impression, and I remember sitting in the conference centre, looking over the hill side, breathing in the thick scent of pine watching the sun slowing crawl toward the horizon at about 11pm. I only got into town the once, on the last night, and saw little of it which I was disappointed about. My second visit to Norway was to Trondheim and I enjoyed that as well. So I was looking forward to visiting Oslo again, for a few days, doing the tourist thing. But I am afraid that I have been disappointed again; this city has not really grabbed me. The architecture is impressive at points, but there is a random, thrown-together quality about the city overa…

The Naivete of Scientists

Although in some disciplines, it is relatively uncontentious, the rise of open access publishing has produced a lot of comment in others. In one of my two disciplines, computing science, this form of publication is still the minority, and still raises comment. For instance, Michel Beaudouin-Lafon has commented suggesting this scientists are highly naive about the costs of publishing. He argues that scientific publishing is intrinsically expensive, and that open access will have negative implication for science as a whole. Over the years, commercial STM publishing has become a cutthroat business with cutthroat practices and we, the scientific and academic community, are the naive lambs, blinded by the ideals of science for the public good-or simply in need of more publications to advance o…

Feedback on Webprints

Josh Brown from JISC has given his permission for me to reproduce the feedback from the peer-reivew of my last JISC grant which bounced. A shame, as it would have provided us with an opportunity to test out knowledgeblog on papers from the wild, while also producing an great demonstrator of the advantages of using the web to distribute papers with web technology rather than just dumping a link to a PDF. With luck, we can rejuvenate this work in another way. "One bid (Bid no 8: Newcastle University) was flagged by one of the markers as being out of scope, despite receiving good marks and positive comments from the other two markers. The original terms of the call specifically state that projects must add value to existing peer reviewed journals. Projects seeking solely to create new p…

Permalink Semantics

So, to start with a rant. I have reached a key and pivotal point in my life. I have decided that I never, ever, ever want to see permalinks with any semantics in them, ever again. And before any one gets clever, yes, I know that this post has semantics in its permalink. Recently I was looking through Knowledge Blog and realised that I have made a mistake with the permalink structure. When we created Ontogenesis I used semantic links --- that is permalinks with the title of the article in them, because I thought that they would be more popular with authors and easier to remember. However, I didn't want name clashes, land grabs or disambiguation of the sort that you get on Wikipedia(website). So I added in a date as well as a uniquish identifier. I realised quickly that I had manage to combi…

Wordpress for Authoring

In a typically thoughtful post, Peter Sefton discusses the advantages and disadvantages of Wordpress as an authoring environment. I though I would clarify my feelings on this a little. Previously, from our experience on Knowledge Blog suggests to us that the Wordpress environment is very poor for editing, something we have expressed in our process documentation. I should be clear that this is in the context of knowledgeblog. Academics have their own way of working, and normally are used to this. They use tools which fit with their lifes. For example, Google docs is a good tool but, basically, useless if you do most of your paper writing on an plane. The same will be true for tools such as Annotum if it ever appears. It is hard to beat Word and email (or frequently dropbox nowadays). Of cou…

Introducing Michael Bell's Blog

This is just a short introduction to Michael Bell, my PhD student. He's now in the second year of his PhD, and has been looking at annotation in biological databases. More specifically, we are trying to define quality measures for textual annotation, based around the bulk properties of these databases. It's related to, but distinct from my early work on semantic similarity. The question is whether we can judge the quality of sentences, words or records based on how they have been used previously, and how far they have spread. Michael has now started to blog his work, following on from my own knowledgeblog work, and our general commitment to open science. As part of his work, he is starting to build web delivered tools, as it is a useful way of navigating the complex knowledge space of biol…

Feedback on a failed JISC grant

Paola Marchionni of JISC has give her permission to reproduce the feedback from the peer-review of my last JISC grant which sadly failed. I want to publish it here, as part of my desire for open science rather that as an opportunity to reply which, perhaps unfortunately, the JISC process does not otherwise allow. I am a little surprised by some of the comments, to be honest. The main criticism was more expected though, which essentially says "it's not crowd-sourcing if you pay people to develop content". You have to try these things, but I did think that actually paying for content might be considered to be a little revolutionary. Ah, well, better luck next time. Markers felt the form of this proposal was "robust", however there wasn't enough clarity on the deliverable…

Greyhole and Scientific Data Handling

I was delighted recently to discover Greyhole. Essentially, it's a system that allows you to configure a Samba share at one end, and a bunch of disks at the other. The disks get the data shared between them, with a configurable level of duplication. It's aimed mainly at the home user, who wants a higher degree of data security than the single drive approach provides, but is not going to go the expensive and poorly scalable RAID approach. The implementation is fairly straight-forward and elegant. The Samba share is provided by a customised Samba virtual file system. This augments the standard process by logging to a spool region (one file per file operation). A daemon consumes these files, stuffing them into a database, then consumes the entries in the database. Essentially, if anything has…

Separating the Content from the Medium

I was entertained by a couple of articles recently, one from PLoS Blogs and one from Ed Yong both bemoaning the low social status of bloggers at least in some peoples minds. As the front page of the PLoS blog says: Blogging is just one of the outlets science journalists use. It's about time we separate the person from the medium. Of course, I agree with this. There is some excellent material floating around the blogosphere. But at the same time, there is a subtle irony in all of this. Both of these authors, I think make a similar confusion about the medium. For instance, my point is that the world of science blogging is populated with some of the best journalists I know. --- Deborah Blum PLoS Blogs At the moment, within science, blogging is still see as an appropriate place for Journa…