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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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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Do you oovoo?

September 5, 2008 at 3:21 pm (review, software)

Was introduced to this video conferencing software by a friend. Its the first that I know of that can include up to 6 people in a video conference call. Definitely cool and possibly more environmentally friendly than flying overseas for just a meeting.

Cooler still its available for Win and Mac..but what’s uncool is that it isn’t avail for Linux (yet) help me pester them for a linux version will you?

Check it out!

http://www.oovoo.com/

ooVoo is the next evolution in online communication — a remarkably easy way to have a face-to-face video chat with friends, family or colleagues, no matter where they are in the world.

ooVoo Video Chat is remarkably easy to use: easy to download, easy to install, and best of all:
it’s FREE!

ooVoo…now you see!

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Save Toner when printing from Consed output!

August 22, 2008 at 2:49 am (bioinformatics, consed, software, tips)

finally found the answer here from this helpful site!

166) PRINTING CONSED WINDOWS

There is a free (or nearly free) program called “xv”. One web site is
http://www.trilon.com/xv It is written by one of those dying breed of
UNIX programmers who just *loved* UNIX and programming and sharing it.
His web site is enjoyable because some of his passion comes through.
With xv, you can make a postscript file from a Consed window. Then
you can print the postscript file on a color printer.

However, since some Consed windows are mostly black (Aligned Reads
Window and Traces Window), this uses up a lot of toner and is
difficult to read. So go to the Consed Main Window, pulldown the
‘Options’ menu and release on ‘General Preferences’. Scroll down to
“Make light background in Aligned Reads Window…” and click on “Do it
now”. Dismiss any Aligned Reads Windows or Traces Windows and then
bring them back up. You will notice the light background. A few
other things (traces colors and thickness) are also customized for
making color prints.

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Python script to split a text file by even or odd numbers

June 20, 2008 at 11:50 am (opensource, software, tips) (, , , , , , )

written a short script to split a file into even or odd line numbers 🙂

#!/usr/bin/python
## loop do something to each line of input file
## changed to write the even line numbers to a file
## and the odd line numbers to another
## note that even numbers start with line 0 (not 1!)
## usage: sort-even-odd.py inputfile
##  written by kevinl @ kevinl.wordpress.com

import sys

def isodd(n):
    return bool(n%2)

input=open(sys.argv[1], 'r')
L=input.readlines()
evenout=open('evenout', 'w')
oddout=open('oddout','w')

for linecount in range(len(L)):
    if isodd(linecount):
        oddout.write(L[linecount])
    else:
        evenout.write(L[linecount])
    #print "line number is " + str(linecount)

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1st to publish with Google apps?

April 8, 2008 at 3:47 pm (bioinformatics, opensource, software, tips) ()

Gosh down with flu yesterday and exciting news broke out

http://code.google.com/appengine/

to read the reviews and comments check out

O’Reilly Radar writeup

http://googleblog.blogspot.com/2008/04/developers-start-your-engines.html

http://nsaunders.wordpress.com/2008/04/08/googles-appengine/

I wonder who will be the first to develop an app host it there and publish a paper in a journal with it..

greasemonkey extensions have already been published. what’s stopping a bioinformatician with a lack of web resources to use google’s?

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7 bioinformatics secrets every biologist should know

March 28, 2008 at 5:26 pm (bioinformatics, opensource, review, software, tips)

see this lecture in youtube!

I am already using some of the stuff mentioned in here. I might even add a few more to the list..  but it seems like a cool lecture for biologists.

http://www.mozilla.org/
http://biobar.mozdev.org/
http://www.google.com/intl/en/options/
https://addons.mozilla.org/en-US/firefox/addon/748
http://www.ihop-net.org/UniPub/iHOP/
http://bioinfo.icapture.ubc.ca/iHOPerator/
http://gaggle.systemsbiology.org/docs/
http://apropos.mcw.edu/
http://string.embl.de/

consolidated links list from computational biology blog

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De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

March 17, 2008 at 6:51 am (genome, journal, sequencing, software) (, , )

 Chanced upon this interesting paper!

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Geneva University Hospitals;

Novel high-throughput DNA sequencing technologies allow researchers to characterize a bacterial genome during a single experiment and at a moderate cost. However, the increase in sequencing throughput that is allowed by using such platforms is obtained at the expense of individual sequence read length, which must be assembled into longer contigs to be exploitable. This study focuses on the Illumina sequencing platform that produces millions of very short sequences that are 35 bases in length. We propose a de novo assembler software that is dedicated to process such data. Based on a classical overlap graph representation and on the detection of potentially spurious reads, our software generates a set of accurate contigs of several kilobases that cover most of the bacterial genome. The assembly results were validated by comparing datasets that were obtained experimentally for Staphylococcus aureus strain MW2 and Helicobacter acinonychis strain Sheeba with that of their published genomes acquired by conventional sequencing of 1.5 – 3.0 kb fragments. We also provide indications that the broad coverage achieved by high throughput sequencing might allow for the detection of clonal polymorphisms in the set of DNA molecules being sequenced.

PMID: 18332092 [PubMed – as supplied by publisher]

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Rename Multiple Files Efficiently Using Excel or Google Docs

March 5, 2008 at 8:06 am (software, tips, winxp) (, , , , , )

link

batch renaming is what I picked up perl for in the first place. Then I found interesting software like 14arename (win only). I then also picked up abit of SED and AWK in linux.

I know about the batch rename feature in winxp but it didn’t occur to me I could do it in excel. Basically this page teaches you to use

“use SUBSTITUTE to change specific text in the filenames, use CONCATENATE() with DATE() if you want to add date to the filename, etc.” to create a column of rename commands in DOS. something like

ren  abcd.fa abcd.gbk

very old school i know but hey its a godsend in your colleagues windows box with no admin rights to install anything.

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Description of phredPhrap output files

February 18, 2008 at 7:28 am (bioinformatics, consed, phrap, phred, software) (, , , , , )

trying to figure out the output files in edit_dir.. this post will be a post in progress will update as and when i have new information

basically this is a list of files that I have when i run phredPhrap as a package where test is the default project/folder name.. the below files are created in top to bottom order

testNewChromats.fof — list of the chromatogram reads that are used in phredPhrap from the start.
test.fasta — suspect its fasta seq output from phd2fasta script from the phd files created by phred in phd_dir
test.fasta.screen.qual — suspect its quality file output from phd2fasta script from the phd files created by phred in phd_dir
test.fasta.screen
test.screen.out
test.fasta.log — contains this line “No. words: 509136; after pruning: 497472”
test.fasta.screen.singlets
test.fasta.screen.contigs
test.fasta.screen.view
test.fasta.screen.contigs.qual — quality file for test.fasta.screen.contigs
test.fasta.screen.ace.1 — ace file for consed to read
test.phrap.out
test.fasta.screen.log
test.fasta.screen.problems
test.fasta.screen.problems.qual
test.contigs — fasta seq of all the contigs
test_to_alu.cross
test.contigs.log — contains this line “No. words: 169360; after pruning: 166242”
test.newtags

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