Sunday, October 18, 2009

About Windows XP

Optimizing HD Space

We may partition for specific use:
  • XPPR (20 Gigs) on C:\ for WindowsXP Pro setting an environment variable ROOTDRIVE='C:'
  • APPS (20 Gigs) on D:\ for new programs setting an environment variable APPSDRIVE='D:'
  • HOME (5 Gigs) on E:\ for all Home directories setting an environment variable HOMEDRIVE='E:'
  • DATA (10 Gigs) on F:\ for all data setting an environment variable DATADRIVE='F:'
  • SHAR (2 Gigs) on G:\ for all shared data in FAT32 setting an environment variable SHARDRIVE='G:'
  • OPTS (10 Gigs) on F:\opt for all optional software setting an environment variable OPTSDRIVE='F:\opt'

Environment Variables

$HOME
app/
bin/
data/
distro/
doc/
ext/
generated/
ico/
lib/
messages/
modules/
obj/
pkg/
script/
sql/
temp/
test/

MS VisualStudio

We always read the manual.
You can have free stuff at DreamSpark


Cool Programs

We always for new cool programs to use.

We can use VirtualDub and download it.

We can use TheKMPlayer for DVDs.

We can use PS3MediaServer follow the blog nor the forum and don't forget the manual.

We ca use BoxeeTV follow the instruction in their website.

We can use TVersity follow the instuctions in their website.

Monday, October 12, 2009

About BioRuby

RTFM

We always read the documentation first.
There is an installation guide too.

Installation using gemThe gem installation is recommended.
On Windows:
> gem update --system
> gem install bio
> gem update bio
> gem install chemruby-1.1.9.gem
> gem update chemruby
On Linux:
&] sudo gem update --system ; sudo gem install bio ; sudo gem update bio

There is a sourceforge download if you want a gem file.

Installation from source for BioRuby and ChemRubyThere is an archive download.

&] sudo cp ~/Downloads/bioruby-1*tar.gz /opt ; cd /opt
&] sudo tar -zxf bioruby-1*tar.gz ; cd bioruby ; sudo chmod -R +x *
&] ruby setup.rb -help
&] sudo ruby setup.rb
&] ruby setup.rb config
&] ruby setup.rb setup
&] sudo ruby setup.rb install
&] ruby setup.rb test

&] sudo cp ~/Downloads/chemruby-1.0.0.tar.gz /opt ; cd /opt
&] sudo tar -zxf chemruby-1.0.0.tar.gz ; cd chemruby-1.0.0 ; sudo chmod -R +x *
&] ruby setup.rb --help
&] sudo ruby setup.rb
&] sudo ruby setup.rb config
&] ruby setup.rb setup
&] sudo ruby setup.rb install
&] ruby setup.rb test

Using downloaded gem:
&] sudo gem install chemruby-1.1.9.gem ; sudo gem update chemruby

Installation of optional requirements in RAA (Ruby Application Archive)The RAA setup
&] sudo cp ~/Downloads/setup-3.4.1.tar.gz /opt ; cd /opt
&] sudo tar -zxf setup-3.4.1.tar.gz ; cd setup-3.4.1 ; sudo chmod -R +x *


The OBDA (Open Bio Database Access) to obtain database entries, copy a sample configuration file in the BioRuby distribution
&] sudo cp bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini /etc/bioinformatics/seqdatabase.ini
&] cp bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini ~/.bioinformatics/seqdatabase.ini

The expat library dependency for RAA:xmlparser.
In Debian-like:
&] sudo apt-get -y install libexpat1
From source:
&] sudo cp ~/Downloads/expat-2.0.1.tar.gz /opt ; cd /opt
&] sudo tar -zxf expat-2.0.1.tar.gz ; cd expat ; sudo chmod -R +x *

The RAA:xmlparser for faster parsing of the BLAST XML output format.
&] sudo cp ~/Downloads/xmlparser-0.6.8.tar.gz /opt ; cd /opt
&] sudo tar -zxf xmlparser-0.6.8.tar.gz ; cd xmlparser ; sudo chmod -R +x *
&] sudo ruby extconf.rb --with-expat-lib=/usr/lib
&] sudo make
&] sudo make site-install

The RAA:bdb for creating faster flatfile index using Berkley DB (see documentation) :

The RAA:rmagick version1 and version2 (available thru gem) for outputting png and jpeg images.

The RAA:rake (available thru gem) for testing, developing ChemRuby.

Installation of optional librairies

Accessing BioSQL database created by other Open Bio* libraries.

The RubyForge:ActiveRecord available via gem
The RubyForge:MySQL/Ruby
The RubyForge:postgres-pr available via gem
The RubyForge:ActiveRecord Oracle enhanced adapter available via gem

For BioRuby 1.2.1+ (note that ruby-oci8 can only work with ruby-dbi 0.2.2).

The RubyForge:Ruby/DBI and at least one driver from MySQL/Ruby, postgres-pr, or RubyForge:ruby-oci8 .
The driver from MySQL/Ruby
The driver from postgres-pr
The RubyForge:ruby-oci8 (install Oracle or Oracle client first)

Thursday, October 8, 2009

About FTP

RTFM

We always read the manual first

Monday, October 5, 2009

FirefoxAddOns

Setting up Firefox

Installing Add-ons under UNIX, Linux, OSX and Windows
Follow the steps to complete plugin/add-on installation when you run it.

  1. AVG Safe Search
  2. Bandwith Meter and Diagnostics
  3. Broadband Speed Test and Diagnostics
  4. ChatZilla
  5. DownloadHelper
  6. DownThemAll!
  7. FlagFox
  8. Flash Killer
  9. Flash Video Resources Downloader
  10. Flashblock
  11. IE Tab
  12. Java Quick Starter
  13. LinkedIn Companion for Firefox
  14. NoScript
  15. Skype extension for Firefox
  16. User Agent Switcher
  17. Weave Sync
  18. Web Developer
  19. Xmarks
  20. MP4 YouTube Downloader
  21. YouTube Download
  22. YouTube to MP3
  23. Media Converter
And so on...

For Web Developer on desktop (WinXP):
  • half_ 1230 x 320
  • half| 615 x 800
For Web Developer on desktop (Linux):
  • half_ 1670 x 320
  • half| 820 x 825
For Web Developer on laptop (WinXP):
  • half_ 1250 x 400
  • half| 620 x 800
For Web Developer on laptop (Linux):
  • half_ 1270 x 350
  • half| 620 x 800

Thursday, October 1, 2009

Setting up Aptana

Installing Aptana on UNIX, Linux and OSX
Download AptanaStudio.
Follow the steps to complete plugin installation when you run it.
&] sudo cp ~/Downloads/Aptana_Studio_Setup_Linux_x86_1.5.1.zip /Applications/ ; cd /Applications/
&] sudo unzip Aptana_Studio_Setup_Linux_x86_1.5.1.zip
&] sudo ln -s Aptana\ Studio\ 1.5 AptanaStudio
&] sudo chmod -R +x AptanaStudio
&] sudo chown -R root:enrique Aptana*

Installing Aptana on Windows
Download AptanaStudio.
Follow the steps to complete plugin installation when you run it.

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