Odds of losing ur Lab notebook vs ur Enotebook

September 5, 2008 at 9:15 am (bioinformatics, review, tips) (, )

interesting cross discussions at Saunder’s blog about archiving your lab notebook here

and another person’s take on it which kinda reflects my own opinions .. my previous notebook was a word document it certainly is more helpful cos I dun have to flip pages but jus do a crtl-F

interestingly they both didn’t talk about the odds of having the information lost due to spilled reagents or gasp ur lab notebook catching fire. I don’t think a dog would wanna eat that dirty notebook though. But i think that in some sense an E-notebook is more liable to have data loss.

of course there are safeguards to have to prevent the data loss due to harddisk failures. But I think along the way from the bench to the computer, its likely that one forgets to insert some data..

hmm incoherent? sorry brain is abit scrambled trying to figure out ensembl annotation pipeline. anyway hope you all have a nice weekend! heh next weekend i be travelling down to Cambridge Hinxton for Ensembl User Meeting .. hopefully I get my answers!

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nsaunders does a tag cloud on journal feeds

August 25, 2008 at 2:42 am (bioinformatics, genome, tips) (, , )

Always found tag clouds useful when looking for interesting things on a blog.. but never thought of using wordle on journals to get a feel on what’s currently hot in a journal.. Nice one !

check his post here

going to try the same thing on journals i read frequently and update this post

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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!


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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Lincoln D. Stein’s new review paper

August 21, 2008 at 6:10 am (bioinformatics, review)

just saw this in my mailbox..

Nature Reviews Genetics 9, 678-688 (September 2008) | doi:10.1038/nrg2414

Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

Lincoln D. Stein

there’s even a companion wiki page for an article in Nature Reviews Genetics by Lincoln Stein:

Cool part is that it’s free to read for a month for logged in nature.com users (you can use your Nature Network credentials).

I think he definitely hit it on the nail when he said “Much of the data is ‘out there’, but it can be difficult to find and challenging to use effectively once found.”

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Lest you think annotation is easy

April 17, 2008 at 9:53 am (bioinformatics, genome, review) ()

Fungal Genomes and Comparative GenomicsLest you think annotation is easyApr 13
I love the title of this post. And I totally agree.. gene annotation is anything but easy..
keeping track of which prediction programs and the rationale behind the annotation (manual or automated) is one thing the author didn’t mention.

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Bioinformaticians needed!

April 9, 2008 at 5:06 am (bioinformatics, genome) (, )

Chanced upon an ad by the Rubin’s lab. at newscientist link

the job scope is largely similar to what I am doing now. Currently where i am, bioinformaticians are moving away from the industry. Sad but true.

perhaps if we need more directors here like

‘Director David C. Page likens the Institute to an artists’ colony. “What we do here at Whitehead is attract the best possible intellectual capital and empower maximally creative—really wildly creative—individuals to realize their dreams within these walls”.’

I love reading job descriptions in my field. They let u in on the developing areas where talent is needed, so you know where to improve yourself. I am surprised though they didn’t mention python.


• Develop and implement existing and new computational methods and tools for high-throughput analysis of diverse data.
• Integrate multiple types of data and analytical methods in creative ways to exploit genomic information such as gene expression profiles and large-scale genome sequence data
• Manage data handling and analysis pipeline for Solexa sequencing platform – use software and databases to assemble and analyze genome sequence data
• Assist with the design and development of major bioinformatics-related programming projects.
• Conduct independent research projects, including primary responsibility for authoring manuscripts for publication in biology and bioinformatics journals.
• Write custom scripts to access databases and analyze sequence data.
• Collaborate with and support lab personnel in the area of bioinformatics analysis.


• M.S./Ph.D. or equivalent in bioinformatics / computational biology disciplines with emphasis on biology.
• Minimum of one year of related experience.
• Proven experience using bioinformatics to solve biologically important questions.
• Experience with microarray data analysis, familiarity with online bioinformatics tools and databases, and pathway analysis.
• Experience with genome sequence alignments, large scale sequence data analysis
• Excellent interpersonal, verbal, and written communication skills.
• Must demonstrate outstanding personal initiative and the ability to work effectively as part of a team
• Background in utility programming (C Shell, Perl, JAVA, or other languages) in a UNIX environment, preferred but not required.
• Familiarity with designing, developing, and programming databases (Oracle, MySQL), preferred but not required.

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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


to read the reviews and comments check out

O’Reilly Radar writeup



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.


consolidated links list from computational biology blog

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Supramap a tool to map evol trees onto a globe

March 3, 2008 at 9:44 am (bioinformatics, genome) (, , , )

interesting note to self should explore this one day..

http://supramap.osu.edu/supramap/index.php?page=theory — Geographic mapping of evolutionary trees projected into a virtual globe allows users to analyze the spread of the organismal lineages into areas of interest. When all these data are integrated, we can visualize patterns in or to develop and test hypotheses. For example, we have used supramap to combine phylogenetic and virtual globe technologies to pinpoint which strains of a virus are infecting which hosts in specific areas (Janies et al., 2007). Finally, because phylogenetic analysis groups like strains into lineages, information drawn from limited experimentation on one strain in a lineage can be used to predict the properties of another strain in the lineage. This transitive property of phylogenetic inference will help us predict which strains are capable of infecting humans, are pathogenic, and/or are resistant to drugs. These capabilities are valuable to the public health community to make informed decisions on where and how to allocate resources to prepare for emerging diseases.

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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.log — contains this line “No. words: 509136; after pruning: 497472”
test.fasta.screen.contigs.qual — quality file for test.fasta.screen.contigs
test.fasta.screen.ace.1 — ace file for consed to read
test.contigs — fasta seq of all the contigs
test.contigs.log — contains this line “No. words: 169360; after pruning: 166242”

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