As you may know, the Australian Federal Government is attempting to censor the Internet within Australia by forcing ISPs to block a list of websites. This proposed internet filter will not be optional; it will effect all Australians, and the blocklist will compiled by a small group of people. The list of blocked sites will remain secret, so the Australian public will find it difficult to determine if this power is being abused. It will not prevent the spread of illegal material, which is typically shared via peer-to-peer networks that will not be blocked by the internet filter. If it is not already self evident why this approach to internet censorship is both an ineffective, a waste of resources and a potential threat to the freedom of information flow required for a healthy democracy, you can read more at the Great Australian Internet Blackout site and the Electronic Frontiers Australia site.

The Great Australian Internet Blackout is a combined online and offline demonstration against this imposed online censorship. For one week – January 25-29th – Aussie websites will “black out” to inform an even wider audience about the threat of imposed censorship.

This is what it looks like right now. I'm guessing that on January 25th something exciting (or educational) will appear inside that popup box !

I’ve created a simple Wordpress plugin that makes it a little easier to participate in the demonstration and spread the word. It uses the ‘blackout.js’ script written by John Ferlito to display a popup box that tells the user about the Great Australian Internet Blackout, while “blacking out” (significantly darkening) your website in the background. Once the user closes the box things go back to normal – it uses cookies so they only see the popup once.

Download the Internet Blackout Wordpress Plugin

(version 0.9, md5: 16522abb4d492f445a4c5ffccd845c73 )

{{{

git rm path-of-file-to-kill

}}

Install it as you would any other simple Wordpress plugin – eg, unzip the archive in your wp-content/plugins/ directory on the server. Also, online demonstrations are all well and good, but that shouldn’t be where it ends. Finish the installation by Contacting your Member of Parliament.

This is my first Wordpress plugin, so it may be sub-optimal (or even contain bugs !). I’ve put the Internet Blackout plugin  source on Github so that programmer-types can fix it, if need be.

Like many of my online friends, I blame FriendFeed. I find commenting on a FriendFeed post a much more productive way of having a conversation around some new development sweeping the web than writing a dedicated blog post. Still, despite this being my “year of FriendFeed”, I started writing a few blog posts / articles / essays this year which never made it out of the Drafts folder. There is a positive side to unpublished drafts – they serve to nicely organize some thoughts, even if they are ultimately never shared. Anyhow, it’s time to clean them out and move on – and as part of that process – here are the highlights of my posts that never were.

“Why biohacking cannot come of age”

I wrote quite a long essay around the time that synthetic biology was getting lots of press, and just before DIYbio appeared on the scene (as a side note: the name “DIYbio” is PR genius  – taking the ‘hacking’ out of biohacking to help avoid misinterpretation by the mass media was a smart move). The opening of this defunct post pretty much sums up it’s contention:

“A healthy biohacking ecosystem requires the participation of hobbyists, and will fail to flourish in the same way ‘Information Technology’ and ‘The Internet’ have flourished if participants remain confined to academic and commercial labs.”.

The old Silicon Valley example (myth?) of the two guys, both called Steve, launching technology from their garage was cited. I then went on to state the obvious – current regulatory frameworks surrounding recombinant DNA and genetic modification make most serious pursuits by hobbyists acting alone legally dubious. Ultimately, I chickened out and decided it was better left unpublished, but a highly modified version my emerge one day. Key links:

• The case of Professor Steven Kurtz
• “The bio-security framework is going to collapse. — Drew Endy“
• Good chemistry kits are hard to buy these days
• The “precautionary principle”

IceCondor – continuous location tracking

Around the end of 2008 when I was momentarily in employment limbo, I began to write an Android mobile geolocation app and started playing with Don Park’s IceCondor. I decided to highlight it with a blog post, but never got around to ultimately publishing it. Essentially, IceCondor is/was a location sharing app, but unlike BrightKite, FireEagle, Google Latitude, Foursquare (& Twitter, these days), IceCondor does continuous location tracking. eg, your GPS location can be shared every 30 seconds via 3G on your Android device (although high frequency updates eat the battery quickly, so lower frequency updates are more practical). IceConder (initially) didn’t include any privacy settings – all locations were openly shared online, with individuals identifiable via their OpenID. As far as I could tell, the only two individuals that gave it any significant use were Don Park, and myself. My main point for writing about IceCondor was to argue that wilfully sharing your location in realtime and opting out of some privacy may actually be safer that not sharing your location. I believe that for most people there is more chance of being randomly mugged than actively stalked, so letting people know where you are is a Good Thing(tm). Don has since changed the focus of IceCondor (at least in the version on the Android Market) to be a simple GeoRSS reader. I get the impression that he is working on other things these days, but the original software and it’s potential uses are pretty cool – it lives on at GitHub, and I notice he has been poking at it again recently.

(Re)-discovering Pymol

I get a little sad thinking about this particular post. I’d planned to write about some lesser known functions of Pymol that I had recently discovered (namely the -p, -R and -G commandline options), but never got round to investigating them thoroughly enough to warrant a blog post. Some time after starting the draft and then leaving it to languish, the author of Pymol, Warren DeLano, tragically passed away at the age of 37. I never met Warren, but I was a grateful user of his amazing software, and I wish his family well over what must have been a difficult festive season without him.

Protein sequence clustering tools

I planned to write an article comparing protein sequence clustering tools. I still might, but here is the unannotated list so far:

• CLANS
• Blastclust
• CD-HIT
• MCL / TribeMCL ( http://micans.org/mcl/ )
• an excellent list of sequence clustering tools on Wikipedia

Spam as an indicator of social network success ?

Surely there are already multiple essays on this topic by social media and internet culture enthusiasts. I’ve only searched briefly. The idea for this post was stimulated by some advertising that was sent to me via my delicious inbox (On an unrelated note: 2009 was the year I moved to Diigo for social bookmarking). This spam wasn’t as indiscriminant as the usual “enlarge your whatever” you expect by email, but some fairly niche advertising for cheminformatics software …  while probably not spam in the strictest sense, it was nonetheless “spammish” in nature since numerous others were also targeted (via delicious “for:” tags). Neil Saunders also noted that he had seen some spam on Slideshare. Key ideas:

• Is spam an indicator of social network self-sustainability, ‘viral growth’ or ‘critical mass’ ?
• or is it an indicator that ’stationary phase’, the slowing of growth, has begun ?
• Just as “the network interprets censorship as damage and routes around it“, does spam “interpret small networks as inviable, and avoid them” ?
• How does this relate to the cost / reward – ie. cost of spamming vs. potential audience – see Economics of Spam.

Synthetic biology 4.0: reflections on the state of play

This is one I’d totally forgotten about until now, from late 2008, written shortly after I’d attended the Synthetic Biology 4.0 conference in Hong Kong. It contained the picture below, along with lots of opinion.

Gartner’s hype cycle

On re-reading it, I’ve decided to make some final changes and retro-publish it anyway. It’s not the most coherent article I’ve ever written, and some of my opinions have probably changed in the last 12 months, but I couldn’t bring myself to just trash it.

More thoughts on Biopython from a non-contributing shoegazer

This post was a little bit of a rant/analysis that probably better belongs on the Biopython development mailing list. It was started by Chris Lasher lamenting that academic researchers are rarely encouraged to work on tools like Biopython, and continued summarizing various peoples ideas on why Bioperl still remains in dominant usage, over Biopython. My main conclusion (if there was one), was that the Biopython team over the years has tended to do a good job by maintaining a high standard of quality by deprecating unused, undocumented and unit test-less code … but sometimes perfect has been the enemy of good. Plus, Bioperl had a head start

The Golden ratio in molecular biology ?

This one has been sitting in Drafts since 2007. I really should just dump it, but the idea still appeals to me. The Golden ratio does appear in nature at the macroscopic level, so why not at the micro- or nano- scale ?

Here’s a choice quote from my notes that may explain why I haven’t yet finished this post:

I think one difficulty in searching for this type of stuff is that the Golden ratio is popular with those into “numerical mysticism”, so if PubMed gives you naught, you have to wade through a lot of kooky pseudoscience in the Google hits before you find the “real science”.

Maybe it will see the light of day in 2010, you never know.

Computation in a single cell … how many logic gates would fit ?

Well … you tell me

1. What is your blog about?

I often ask myself this question. Being a scientist, I always feel like it should be about science, and the various biological systems I work with. I reality, it is about programming, bioinformatics, the web with the tiniest bit of structural biology thrown in. I used to blog about Linux related things occasionally, but I split that off into another blog (which gets 10 times more traffic ).

2. What will you never write about?

I’d rather not rule anything out. I’ve avoided politics, largely because all my “blogging peers” also largely avoid it. Sometime I wonder why, but I think I’m beginning to understand; blogging about political issues may seem important, but eventually it just becomes a constant ‘rah rah rah‘. That would get boring. So I’m saving it for when it really matters (the proposed ‘filtering’ of internet connections at the ISP level by the Australian government is coming close. There, I did it ).

3. Have you ever considered leaving science?

Yes. But I did cheat and read Bora’s answer to this one (by accident).
I think it would be impossible to leave ’science’ unless I became permanently brain damaged or something. Leave research … sure, it crosses my mind from time to time.

4. What would you do instead?

I’d try my best to get a job in video game development, or web application development (or both … developing a web-based game !). I’d try to work my experience as a scientist into this endeavour. Not sure how successful I would be, but I’m trying to slowly build up a portfolio, just in case

5. What do you think will science blogging be like in 5 years?

I think research groups will be tied together more and more by their blogs. A bit like the way RRRosie Redfield runs things. Not necessarily blanket Open Notebook Science (give it 10 years), but certainly a greater level of open, public communication of ideas.

6. What is the most extraordinary thing that happened to you because of blogging?

It’s not that exciting, but it’s the best I’ve got; I was contacted by an real journalist with some questions about the role of cloud computing for academic research. I didn’t really feel qualified to comment a length, since it largely stemmed from a ‘what if’ type idea I blogged about. But I gave my perspective anyhow.

7. Did you write a blog post or comment you later regretted?

Yes, quite often. I have a tendancy to always be in a hurry when commenting, coupled with a desire to not be overly self-censoring. I’m never trying to sound like a kook, troll or A-hole … it just turns out that way sometimes. Personally I find it takes a long time to write a concise, clear comment, beyond “LOL”. The FriendFeed comment box is always too small for me, but that’s a good thing, since it forces me to summarise.

8. When did you first learn about science blogging?

Not exactly sure, but I think it was via nodalpoint.org the bioinformatics weblog. I wrote one or two posts for nodalpoint. Around the time I was writing my PhD thesis, a few netziens of nodalpoint started blogs (or I discovered that they had blogs outside of nodalpoint). The most influential for me were Neil Saunders’ “What You’re Doing is Rather Desparate”, and well as Pedro Beltrao’s “Public Rambling” and Duncan Hull’s “O’Really ?”. I thought, “I can do that”, so I started a Blogger blog. One year later I moved to a self-hosted Wordpress blog. But lets not get side tracked with a boring meta-discussion about blogging software.

9. What do your colleagues at work say about your blogging?

Mostly, they are unaware. Occasionally I have dropped a comment about “my blog”, but no one has really jumped on it. Which is fine, since I don’t really blog about anything that most of them have any interest in.

Well, that’s it. Now to read everyone else’s responses ……

(Originally via Blog Around the Clock [Bora Zivkovic], via FriendFeed)

New URL is:

http://blog.pansapiens.com/

Feed url is via FeedBurner at:

http://feeds.feedburner.com/YourBonesGotALittleMachine

(Don’t read on if you don’t like meta-discussion about blogging software …. I personally have become pretty bored with this type of post, but it has to be done once after changing URLs etc. The blogger who “Blogs about blogging” is akin to those hip-hop artists who only ever sing about hip-hop … sort of like eating your own … yeck !).

Why migrate away from Blogger, and why use Wordpress ?

In the time since I started using Blogging, I’ve become acquainted with the Wordpress software, through running a few other blogs on the sly, and became frustrated with the lack of flexibility of Blogger. If I wasn’t already buying hosting for other projects, I’d have shifted to paid hosting at Wordpress.com, but since I have the hosting space anyway, Wordpress.com missed out again this time. Plus, migrating away from Blogger proves I’m not a complete one-eyed Google fanboy (but I can’t lie; Google currently owns my soul in when it comes to almost every other web-app).

Wordpress is so widely used that there is a huge array of pre-made themes and plugins to aid customization – something Blogger just can’t match. My key gripe with Blogger was source code formatting and highlighting. Yes, it can be done with Blogger using <pre> tags and the SyntaxHighlighter javascript, but I had a little trouble getting that working and ultimately decided not to waste the effort. Wordpress plugins make it easier to highlight source code, as well as various other nice things.

How I moved posts from Blogger to the Wordpress software

I’ve migrated older posts from the Blogger blog to this blog using the Import feature built into Wordpress 2.3 … it was dead simple. It even imported my ‘draft’ posts from Blogger, and kept their status as ‘draft’ within Wordpress. Hopefully there aren’t to many kinks, since I haven’t checked every post carefully.

Tweaking

After a bit of hunting (and a brief period considering using Drupal instead), I settled on using the K2 theme. It’s clean, featureful and reasonably easy to customize.

For the Wordpress’ers out there, here’s a list of the plugins I currently use on this site:

• Google Code Prettify. I also trialled Dean’s Code Highlighter, but felt more confident with Google Code Prettify, by the same author. There are a bunch of code highlighting plugins out there, these are just the first two I tried. Works well enough for me.
• Akismet deals with comment spam.
• All in One SEO Pack seemed like a good idea. It can’t hurt … I hope.
• FeedBurner Feedsmith to serve feeds through FeedBurner.
• Google Sitemaps helps Google index my site. More SEO.
• jQuery Lightbox makes image display nicer. All AJAXie and such.
• Link Summarizer gives a list of links used in the post, at the end of the post. I always appreciate this feature in others blog posts and articles, so I’ve used it here too, even if the list sometimes is a little ugly, it’s very useful.
• reCaptcha is another handy tool in the never-ending battle against spam.
• Related Posts uses keywords to give a list of related posts. I haven’t assessed how well it really works, but I hope it will help readers follow posts along one topic.
• Share This helps users submit posts to various social sites (Digg, del.icio.us, etc, etc). There are lots of these types of plugins, and I’m not thrilled with this one … any suggestions to replace it would be appreciated.
• Subscribe to Comments … I haven’t set this up properly yet, but it’s a feature I really like on other blogs … really handy for keeping up with long back-and-forward discussions in the comments.
• Ultimate Google Analytics, because I love website statistics … even if the amount of traffic for this blog isn’t all that amazing (and due to the Google Analytics / Adwords / whatever terms of service, traffic stats must also remain a secret ).
• WordPress Mobile Edition simplifies the view if a small screen mobile device is detected. As a Nintendo Wii owner, I appreciate this type of thing, even though I rarely bother browsing the web on the Wii (precisely due to the fact that most sites are painful on small screen devices). I haven’t actually tested this plugin using the Wii Opera browser yet, but if it doesn’t work I’ll probably tweak it to do so.
• Wordpress Video Plugin make embedding videos from YouTube and various other video sites simple.

It’s a bad thing to change URLs … readers and feed subscribers will inevitably be lost. I’m sorry if I’ve made a little work for you, but please update your feed readers, aggregators and blogrolls. I’ll try to keep my half of the deal and produce some decent content.

I generally dislike this kind of ‘meta-blogging’, but this is the easiest way for me to let go of them and move on … here is a list of the posts that could have been, but never were:

• “Open Data in structural biology: share your structure factors and restraints” was a post spurred on by the Chang et al incident and a letter written by Alexander Wlodawer about the importance of sharing ‘raw data’ in structural biology, particularly to allow structures to be independently validated. I’m sure mandatory deposition of structure factors tied to publication will become the norm in the not too distant future. The post became a long essay which really went nowhere except to suggest that maybe there should be more incentive (and even enforcement) for sharing not only raw data, but also source code used to process data too.
• There was the seed of a post on “Patenting“, based around this link to Christopher Soghoians blog “slight paranoia”. I’m not against the patent system, but I’m not all for patenting anything and everything either. If I ever got time to flesh this post out, chances are it would have turned into a dumb Slashdot-style anti-patent rant anyway. No one wants to read that crap, so I canned it. I will say, however, that Christophers post reminds me alot of the situation of being a Postdoc in a fairly pro-patent Institute, and underscores why the incentive to patent often isn’t there at the grass-roots level.
• One potential post started as some scribblings about one of last years new hot topics, “Open notebook science“. I wanted to compare a public/private wiki system I was envisaging with the scheme presented on page 2 of this presentation by Jean-Claude Bradley which shows the continuum between Traditional Lab Notebook (unpublished science), through to Tradational and Open Access Journals and finally through to the Open Lab Notebook (full transparency). The whole thing never materialized.
• Then there was a quick post to highlight an article about a GM crop in Nature Biotechnology. I never got it out in a timely fashion, but essentially the article discussed how the Italian media and politicians were continuing their blanket crusade against all GM crops, while conveniently ignoring the independent academic trails showing that the MON810 corn strain had significantly lower levels of the fungal toxin fumonisin when compared with the non-GM equivalents. This was (and still is) a topical and often emotive issue for Australians, as two states (Victoria and New South Wales) have recently lifted moratoria on commercial release of GM crops. It’s nice to see that sometimes a well tested GM strain is often better for human health than an untested traditional strain that has only had the benefit of genetic modification by crossbreeding and selection rather than the new techniques of molecular biology.
• Another post was my attempt at being funny. “Australian Government department concerned about organisms from space: Quarantine assessment of an asteroid“. Actually, I appreciate that they take this type of thing seriously … I wouldn’t be laughing if we end up with an outbreak of some deadly alien virus or something (still not sure if I’m joking or not ….).

There are also a few beginnings of some posts I can’t quite let go of yet, and they may appear in the future. One, while getting a little dated now, is “Why are the still 1000 uncharacterised yeast genes ?“, discussing a 2007 paper by Lourdes Pena-Castillo and Timothy R. Hughes. Another is “Has structural genomics paid off ?” … this is still pretty fresh and in discussion in the November and December issues of Structure. In fact, these letters to Structure are such a treasure trove of practical and philosophical arguments about structural biology the topic probably warrants multiple posts. Finally, I planned to host the inaugural “Bioinformatics data-munging challenge: 2.0-style“, but never felt I had time to devise and run the challenge properly. We can still come up with some guidelines (aka rules) and try it out if anyone is interested.

It’s not a New Years resolution … but I hope that this year I can produce more short, frequent and high quality posts. We’ll see.

This version boasts numerous bug fixes, and an nice interface to the Magnatune music store. Magnatune is cool since the full length tracks are under a Creative Commons license and are free to listen to. If you decide to support an artist you enjoy, you can buy downloads and choose how much you wish to pay. The artist splits the profits 50:50 with Magnatune, and you get uncrippled MP3/FLAC/Ogg files, which can be re-downloaded at any time if you loose them somehow. Since Magnatune operates like an enlightened version of a traditional record label, meaning they only select “high quality” artists … they don’t push loads of dross from self promoting artists that suck like the old mp3.com (RIP) did. “Brad Sucks” is (non-exclusively) on the Magnatune label, but his music doesn’t suck.

Hopefully in the future Amarok will include some generic API to interface with other enlightened music stores and repositories of Creative Commons music, so that Magnatune doesn’t get accused of monopolising . For instance, I’d like to be able to add say, ccMixter and maybe IUMA in addition to Magnatune. An open web services API for music stores would make this possible, and while I haven’t looked “under the hood” of the new Amarok-Magnatune browsing feature yet, I suspect this is what they have already created.

Anyway, there doesn’t seem to be a backported version of Amarok 1.4.4 in the Ubuntu / Kubuntu Dapper in the repositories (yet). There are some Edgy Eft packages, but I don’t want to upgrade to Edgy at the moment.

Instead, I’ve compiled my own and have made some deb packages, using the official deb source packages. I haven’t tested this version heavily yet, but it seems to work. I had to override one dependency, since it complained that the Dapper “Common Debian Build System” (cdbs package) was not recent enough …. hopefully this was a safe thing to do.

You can download my packaged versions here:

amarok_1.4.4-0ubuntu1_i386.deb (link fixed .. Thanks victor !!)

amarok-xine_1.4.4-0ubuntu1_i386.deb

amarok-engines_1.4.4-0ubuntu1_i386.deb

Install them by typing:

$ sudo dpkg -i amarok_1.4.4-0ubuntu1_i386.deb amarok-xine_1.4.4-0ubuntu1_i386.deb amarok-engines_1.4.4-0ubuntu1_i386.deb

Yah, I should probably GPG sign these and try to get them included in Dapper backports or something …. but no time to do the job properly at the moment.

Update – if you have trouble with some missing dependencies, this may help:

$ sudo apt-get install ruby python-qt3 kdelibs4c2a libifp4 libnjb5 libpq4 libqt3-mt libtunepimp3 libvisual-0.4-0 libxine-main1

Hopefully that catches most of the dependencies that are likely to be missing, particularly for those running Ubuntu Dapper and not Kubuntu Dapper.

Let’s see if I can keep this up (and keep it interesting+useful).