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Biogang-related material.
The Biogang presents
An attempt to collate audio and video presentations by the Biogang and associates.
To do: replace links with embeds.
Video
Bill Hooker
Science 2.0...
Sample .ncbirc
[NCBI]
Data=/usr/share/ncbi/data
[BLAST]
BLASTDB=/usr/local/databases/blast
BLASTMAT=/usr/share/ncbi/data
formatdb e.g.:
formatdb -i pdbaa -o T
mv pdbaa.p*...
To get around to, one day.
Bioinformatics
Can we stop this introspection and just get on with it?
Wikipedia, abstracts, copyright
It's right and wrong
Ideas versus execution
Sometimes, the idea...
Database schema and associations
How many tables?
enzymes
properties
publications
units
uses
sources
Functionality
Add new enzyme
Add new property
CRUD
Search
Practical notes for conference attendance, as opposed to notes from conferences.
Travel planning - for meetings in Australia
Via the blog please, or through wikidot if you're a member.
Default Links
Copied from default start page.
Site Manager
side menu | top menu
Documentation
Themes
Creative Commons Attribution-Share Alike 2.5 License
Community
At present, prefer Rails over Django, but just in case.
Django Workflow
Create project using django-admin startproject project
Edit settings.py - database parameters, installed apps + anything...
FriendFeed - latest items
Issue using part_color and group_on
Steps to reproduce:
1. Start with file volvox4.gff3 from Gbrowse tutorial
2. Add the following lines:
# testing
ctgA example microarray_oligo 3301...
Issue using part_color and group_on
Steps to reproduce:
1. Start with file volvox4.gff3 from Gbrowse tutorial
2. Add the following lines:
# testing
ctgA example microarray_oligo 3301...
Git
Using Git + Github
Hobo tutorials index.
Aim of this page is a "cheat-sheet" for the Agility tutorial, with my modifications.
Generate a basic app using Hobo
sudo gem source -a http://gems.rubyforge.org
hobo MyApp;...
If you are allowed to edit pages in this Site, simply click on edit button at the bottom of the page. This will open an editor with a toolbar pallette with options.
To create a link to a new page,...
You can apply to join this wiki if I've given you the password:
I occasionally contribute answers to questions at the MadSci Network. This page is for notes to help compose those answers.
Notes for other people (code snippets etc.).
BLAST (from FriendFeed discussion)
Gbrowse configurations
Just testing.
module "feed/FeedModule" src%3D%22http%3A%2F%2Fnsaunders.wordpress.com%2Ffeed%2F%22%5D+limit%3D%223%22%5D%0A%5B%5B%2Fmodule
Flickr
In Jonathan's <a href="http://ttaxus.blogspot.com/2007/08/ismb-2007-vienna-part-i-keynotes.html">recent post on ISMB/ECCB 2007</a>, he touches on the lively topic of "organism...
Django
Django notes
Rails + BioSQL + bioruby + biographics
Summary of this excellent tutorial series by George Githinji, wrt Ubuntu and Rails 2.2.2.
Part 1
1. If rails, rake and rubygems were installed via apt-get,...
Via this tutorial.
A recommended workflow for creating Rails Application is as follows:
Use the rails command to create the basic skeleton of the application.
Create a database on the MySQL server...
Ideas for original research projects, as opposed to simply software.
Membrane protein loops: modelling and docking
Aims
Obtain protein sequences (fasta) from complete genomes of...
Rails
Rails workflow notes
Rails + BioSQL + bioruby + biographics
Hobo tutorial notes
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A place to list and work on skills that need improvement.
Version control
Seems like git + github is the way to go
Git for the lazy - excellent intro guide, but single user only
Web...
This page is my attempt to list all of the places where you can find me on the Web.
Professional networks
LinkedIn
Nature Network
Epernicus
OpenWetWare
Blog and...
Terse, bulleted notes on setup, configuration etc.
Ruby
Rails + BioSQL + bioruby + bio-graphics
Rails workflow
Python
Django notes
Intended to enable research, rather than being original research proposals.
Web front-end + database
Preferable to code these using a modern web framework: Django or Rails.
Laboratory Information...
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Conference Travel Notes
Getting to, from and around when attending conferences.
Brisbane
Canberra
Airport shuttle bus: airport info; timetable/pricing
National Convention Centre - really poor...
Getting started with git
1. Set up global config
git config --global user.name "USERNAME"
git config --global user.email user@mail.com
Can also do this per repository:
cd /path/to/repo
git...
You've reached the wikidot pages of Neil Saunders, a researcher in computational biology currently working in Sydney, Australia. The content here was formerly a series of private Google Notebooks;...
According to Wikipedia, the world largest wiki site:
A Wiki ([ˈwiː.kiː] <wee-kee> or [ˈwɪ.kiː] <wick-ey>) is a type of website that allows users to add, remove, or otherwise edit...
Great, concise sentences that sum up my work philosophy.
Wherever you work, most of the smart people are somewhere else
— Bill Joy
Data finds data, then people find people
— Jon Udell
It's not...
