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.

Description:

• 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.

Qualifications:

• 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

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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