Software

Here’s a list of some of the publicly available web applications I’ve written. Some of them remain at the ‘perpetual beta stage’.

science

inmembrane

Bosco Ho an I wrote an analysis pipeline for helping predict surface membrane proteins in proteomes in gram-positive and gram-negative bacteria. It’s Python commandline software that relies on a number of subcellular localizaton and membrane topology predictors to determine segments of peptide sequence likely to be exposed to the extracellular milieu (or periplasmic space, in the case of gram-negative bacteria).

seguid-engine

An experiment in using Google App Engine for mapping SEGUID sequence “hashes” to database identifiers, with a nice RESTful interface (eg http://seguid-engine.appspot.com/seguid/7P65lsNr3DqnqDYPw8AIyhSKSOw ).

mPartsRegistry

mPartsRegistry (source) is a simple interface to the Registry of Standard Biological Parts aimed at mobile smartphone browsers. It’s built using the Parts Registry APIJQuery MobileBeautifulSoup and Google App Engine. I wrote a blog post about it.

ResolveRef

ResolveRef is a Google App Engine application, written in Python. It is an attempt at making a RESTful and human readable URL identifier for any paper in PubMed. It is based on an earlier version written with the Turbogears framework (OpenRef resolver), which in turn was based on an idea by Noel O’Boyle. The ResolveRef source code is available here.

“non-science”

I have other interests, outside science (“What a well rounded individual”, I hear you say !). Here outlines of some past and present projects.

WiiRSS (retired)

 WiiRSS is was a news aggregator site for Nintendo Wii news sources. I can’t claim too much credit here, since it’s a customization of Gregarious (which I didn’t write), tweaked to work better on the Nintendo Wii Opera browser. Wiider (below) was written to ultimately supercede this application.

Wiider.com (retired)

Wiider is was a news feed reader optimized for the Nintendo Wii Internet Channel (Opera-powered). I learned a lot about RSS, ‘small screen devices’ and modern Python web development working on this project, but ultimately decided that the way the browser is implemented on the Wii is not conducive to the type of application I wanted it to be (mainly, the launch time from power-on to front page load was too long for me to find it useful for quickly reading the morning news over breakfast. Smartphones have since filled this niche). Since I couldn’t see myself using it, I decided to retire the project.

Android Apps

GrandMasterPixel

A fun little social pixel art game for Android, that a lot of users seem to enjoy. This started out as a ‘small’ weekend project and sort of got out of control.

WristTweets

A Twitter client plugin for the Sony LiveView microdisplay. Designed to be more reliable and featureful than the built-in Twitter client that Sony ships with the LiveView Manager.

A bunch of games …

BONUS: SLIGHTLY EMBARRASSING Older web apps

They still work … they are just look ugly.

Estimate protein secondary structure content from CD spectra, “Raussens et al” method.

This is a simple CGI application for estimating protein secondary structure content based on a circular dichroism (CD) spectrum, using the method of Raussens et al, 2003. The Raussens method isn’t as accurate as some competing methods, but it is extremely useful if you need secondary structure estimates but cannot accurately measure the protein concentration of your sample (eg, due to the prescence of detergents). It also makes a nice sanity check to compare against the results from the CDPro suite or Dichroweb.

Quickchange(tm) mutagenesis primer design helper, “Zhang et al” method

I wrote this when I was doing some mutagenesis. The output is a little ugly, but it works. It can help design primers based on the method of Zheng et al, 2004, which is claimed to be better than the method recommended by Stratagene. I wrote this before I discovered PrimerX.

Silly biotech company name generator

This one really needs to be prettied up, and could do with an update with some more recent buzzword prefixes and suffixes.

Leave a Reply

Your email address will not be published. Required fields are marked *