Normally I stick to posts about science and technology on this blog. Like most Australians, I vote in elections, try to remain informed, but otherwise stay away from getting involved in politics. However, occasionally certain things become important enough issues that they need to be advertised more widely.
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 !
Continue reading ‘The Great Australian Internet Blackout Wordpress Plugin’
Those who have been watching may have noticed I quietly started developing an Android application in the last month or so. It’s still super-buggy and far from feature complete, but I thought it was time to announce it here (”release early, release often”). It’s not ready for real users yet, but developers may like to take a little look.
Continue reading ‘Occyd : tagging for locations’
Sometimes it’s nice to quickly check how many sequences are in a FASTA format sequence file.
It barely warrants it’s own blog post, but here we go anyhow: my one-liner shell script for counting the number of sequences in a FASTA “flat-file database”, based on the presence of the “>” header symbol.
#!/bin/sh
# ~/bin/countseqs
# Counts the number of sequences in a FASTA format file
grep ">" $1 | wc -l
Dead easy huh ? I put this in ~/bin/countseqs, make it executable (chmod +x ~/bin/countseqs) and use it in lots of situations, as a quick sanity check.
(oh, btw, this is not public domain and u can’t use it for commercial gain without paying me a license fee. academic users can fax me something for a free license. k thx bye).
Couldn’t help myself … everyone else is doing it 
I recently needed to make a simple, two dimensional figure of a beta-barrel membrane protein. I went hunting for programs that might take a sequence and/or structure and produce a pretty looking diagram to save me constructing everything by hand. Here are two I found and tried.
Continue reading ‘Software review: producing two dimensional diagrams of membrane proteins’
I updated ResolveRef last night and checked in the most current sourcecode to svn at Google Code.
New features include:
- Suggest/autocomplete for journal title field, using the journal title lists provided by PubMed.
- A “Verify” button. Allows a ResolveRef URL to be constructed with the web form and verified as working and valid without actually forwarding the user to the article.
- Some bugfixes (handled the case where there is no DOI in the PubMed record, handled network timeouts to PubMed)
- Refreshed visuals
- Disqus comments box for feedback
In the interest of just getting something working quickly, I implemented the suggest feature in the laziest, possibly most RAM and CPU hungry way possible (the “JQuery Suggest” code queries the web app with substrings as you type each character. At the server side, the app uses a regex to scan a ~1.5 Mb list of journal titles held in RAM). I’ve already noticed a few “This request used a high amount of CPU” warnings in the logs, with the threat “High CPU requests have a small quota, and if you exceed this quota, your app will be temporarily disabled“. If my nasty hack starts heating up Google’s datacentre too much, I might have to disable the ’suggest’ feature until I can implement it “properly”.
Continue reading ‘ResolveRef updated : now with auto-suggest and source code’
