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…
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…
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…
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…
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…
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…
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…
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…
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…
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…