New Job New Scope New blog

December 3, 2009 at 1:20 am (Uncategorized)

Hi Guys!!
I have switched jobs! still doing bioinformatics but for a service company providing next gen sequencing. Hence I think I shall move to a new blog address its here at http://kevin-gattaca.blogspot.com/ if its still relevant to you

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Macify my Ubuntu

September 16, 2009 at 2:39 am (Uncategorized)

installed gnome-do and avant-window-navigator

trying to figure compositing.. hmm good that metacity does compositing!

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Ubuntu 9.10 WM quirks

September 16, 2009 at 2:17 am (review, software, tips, ubuntu) (, , , )

The quirks of my spanking new Ubuntu install is driving me nuts..

I found solutions online that do not seem to work!

1) I have to alt-tab twice to change windows (the first just shows the popup)

tried

http://ubuntuforums.org/archive/index.php/t-490238.html

http://ubuntuforums.org/archive/index.php/t-570357.html

but it seems that using compositing or adding visual effects solves the problem!

2) Alt_R doesn’t work! its a special mod key but xmodmap doesn’t help!

Any solutions is appreciated!

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Moving to Ubuntu 9.04

September 2, 2009 at 9:39 am (ubuntu) (, , , )

Finally made the move!

My old version was no longer supported (read respository servers are gone!)

I needed a bit of house cleaing (read I have files which i have no use for and don’t know if i shld del)

so the move was needed.

I wanted to use LTS (long term support)

but by a twist of fate i ended up with 9.04 amd64 no less (to make use of the 16gb ram that i got)

I must say the upgrade IS an upgrade. the graphics are slicker and more imptly they are faster!

the migration went well. So far I didn’t have to recustomize most of my settings. Just copying the profiles sorted everything.

but have the usual hiccups of having to reinstalling

  1. sun java 6
  2. flock-browser (why can’t i just copy it over?? had to get the deb from http://www.getdeb.net/)
  3. gnome-vim (why doesn’t this ship with ubuntu as default?)
  4. 64bit flash player (hmm haven’t gotten down to this yet)

But I must say the advantages are

  1. better support for HP network printers (yeah! no more manual setups with IP addresses)
  2. Google-chrome works!
  3. did I mention again that its faster and slicker?

after looking at gOS I might even fiddle to get a Mac look just to be the envy of my less techy frens

so far I haven’t met a prob like nsaunders.. with upgraded packages but will keep a note for his method

Blogged with the Flock Browser

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Eisen summarises JGI user meeting

April 4, 2009 at 8:09 pm (Uncategorized) ()

Wished I could have been there.. would love to c what tools are lacking for next gen seq technologies. 

http://phylogenomics.blogspot.com/2009/03/lessons-learned-at-jgi-users-meeting.html

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Using your shell

February 25, 2009 at 10:06 am (Uncategorized)

Had to use bash to run a few one off jobs or edit my bash_profile for enviroment settings..

these are useful links!

http://www.linux.com/feature/155903 — Patterns and string processing in shell scripts

http://www.linux.com/feature/147568 — Save time at the command line with shell aliases and functions

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prerelease version of the Adobe® Flash® Player 10 software for Solaris and 64-bit Linux platforms.

December 18, 2008 at 11:10 am (review, software, ubuntu) (, , , )

http://labs.adobe.com/downloads/flashplayer10.html

Get it while its hot! :)

will post experiences on an Ubuntu box later

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python script to inventorise your ab1 files with md5sums

November 7, 2008 at 11:35 am (opensource, tips) (, , , , )

The problem that needed solving this time was having a list of filenames of my ab1 files, location( directory path) and a md5sum so i know if duplicate filenames are the same file or just a result of misnaming.

managed to come up with this after copying from two different scripts

one that was used to make an inventory of  a directory of ogg songs and the other a python equivalent of md5sum check in linux.

Have fun!

#!/usr/bin/python
#===============================================================================
#
#         FILE:  inventory-abi.py
#
#        USAGE:  ./inventory-abi.py
#
#  DESCRIPTION:  Lists all the files of extension .ab1 with the directory and its md5sum
#  adapated from code from http://pthree.org/2007/08/09/recursion-in-python/ and
#  used md5sum code from http://code.activestate.com/recipes/266486/
#      OPTIONS:  ---
# REQUIREMENTS:  ---
#         BUGS:  will execute md5 on directory as well
#                current method to get CWD is not OS independent
#        NOTES:  ---
#       AUTHOR:  Kevin ,
#      VERSION:  1.0
#      CREATED:  11/07/2008 07:03:16 PM SGT
#     REVISION:  ---
#===============================================================================

import dircache, os, md5
counter = 0

def sumfile(fobj):
    '''Returns an md5 hash for an object with read() method.'''
    m = md5.new()
    while True:
        d = fobj.read(8096)
        if not d:
            break
        m.update(d)
    return m.hexdigest()

def md5sum(fname):
    '''Returns an md5 hash for file fname, or stdin if fname is "-".'''
    if fname == '-':
        ret = sumfile(sys.stdin)
    else:
        try:
            f = file(fname, 'rb')
        except:
            return 'Failed to open file'
        ret = sumfile(f)
        f.close()
    return ret

def PrintFiles(indent):
    global counter
    thisDir = os.getcwd()

    for file in dircache.listdir(thisDir):
        if (file.endswith('ab1') or os.path.isdir(file)) and not file.startswith('.'):
            if file.endswith('ab1'):
                counter += 1

            currdir = os.popen("pwd") #for output of cwd currently works for linux pending upgrade to OS independent
            md5 = md5sum(file) #calls the md5sum function, md5 lib ships with Python

            ab1File.write('%s%s\t%s\t%s\n' %(indent, file, currdir.readline()[:-1], md5))

            if os.path.isdir(file):
                os.chdir(file)
                PrintFiles(indent + '  ')
                os.chdir('../')

try:
    ab1File = open('ab1files.txt', 'w')
except IOError, e:
    print "Unable to open 'ab1files.txt' for writing: ", e
else:
    PrintFiles('')
    ab1File.write('\nCurrent number of ab1 files: %d\n\n' %(counter))
    ab1File.close()

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What has Bettas got to do with Programming?

October 30, 2008 at 10:34 am (review) (, , )

A programmer’s view of the Universe, part 1: The fish

I write a column for computer programmers called “Stevey’s Blog Rants.” It’s basically a magazine column — I publish to it about once a month. The average length of my articles is about 12 pages, although they can range anywhere from 4 to 40 pages, depending on how I’m feeling. But for precedent, don’t think blogs: think of Reader’s Digest. The blog format sets the wrong expectations.
Kevin: thought provoking blog post!

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Google DevFest D3vF3st now!

October 28, 2008 at 5:32 am (opensource) (, , )

Lolz writing now from the Google DevFest at Singapore… hmm sadly its not packed to the brim right now.. maybe cos its just after a long weekend. oh well, am pretty excited though.. will post relevant updates if any..

check out

http://code.google.com/events/apacdevfest/

my online notes as the event progresses

http://docs.google.com/Doc?id=dhj8xhdw_47djn633f6

Update: There’s going to be a SE Asia OpenSocial Application Contest

Check out details at http://code.google.com/events/apacdevfest/contest/

The Event website

http://www.e27.sg/2008/10/13/googles-1st-hackathon-in-southeast-asia-whos-coming/

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