mPartsRegistry : small update

I just made a small update to mPartsRegistry, the mobile interface I wrote to make browsing the Registry of Standard Biological Parts a little easier on smartphones.

This update adds a “Random Part” button – it’s mostly just so people who want to play with it without actually knowing a part ID can get some instant gratification. This is in addition to the quiet update I made a few months ago to replace jQTouch with JQuery Mobile, since jQTouch development stagnated for a while and never really properly supported most mobile browsers.

Wiider postmortem

I always intended to write this postmortem earlier … now three years after development ceased, I’m finally getting around to it. Warning – retrospective rambling ahead.

In mid 2007, Nintendo released the Opera-powered browser for their Wii gaming console which they called the Internet Channel. For many people, including myself, this was the first time they had been able to use “Internet on the TV”. Because of the typical viewing distance, low resolution for CRT-based televisions, and the unique navigation interface using the Wiimote, many web sites were functional but not particularly comfortable to use. Many sites targeted at desktop PCs were too complex and heavyweight for the Internet Channel, fonts were often too small such that cumbersome zooming and scrolling was required. I felt this was a good opportunity to write a Wii-browser specific app – in particular, I wanted a news reader that was comfortable to use in a lounge room setting, controlled via the Wiimote.

I started the Wiider project around Dec 2007, as the successor to a Wii-specific news aggregator service I had set up called WiiRSS. The last SVN commit for Wiider was in Dec 2008.

The goal of the Wiider project was to create a web-based news feed reader optimized for the Nintendo Wii Internet Channel. Features included:

  • Wii-friendly user interface – large TV friendly fonts, simple navigation
  • Cookie-less view-only access for a personal feed list (via ?key=xxx, bookmarked on the Wii once you’ve logged in)
  • Wiimote navigation controls, beyond what the browser provides
  • Painless image zooming (eg Lightbox)
  • RSS and ATOM feed support
  • Easy feed discovery using the Google Feed API
While I’ve since retired the project, I felt it would be good to document some of the insights I gained as a result of developing it.

The Great Australian Internet Blackout WordPress Plugin

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 will appear inside that popup box !

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 !

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Occyd : tagging for locations

Occyd Map View (search results)

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.

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Count the number of sequences in a FASTA format file: a Unix shell snippet

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 🙂