September 1, 2006

Software as a Black Box….

Filed under: Bioinformatics, Science — cupton @ 12:58 pm

Why Biologists Should Not Treat Software as a Black Box….

On a similar theme to the last post.
Check out this link for a discussion by Dr. Joelle Thonnard.


EMBL-EBI’s Macromolecular Structure Database

Filed under: Bioinformatics, Science — cupton @ 12:57 pm

Somehow I managed to get signed up for the electronic version of:
OBBeC® Life Science Computing & Bioinformatics Magazine

I’m not really a big fan of electronic books and mags, but I thought I’d give it a try (beats getting a paper copy in the mail).

There’s a nice 4 page review of EMBL-EBI’s Macromolecular Structure Database (issue 12 p24).
It was easy to read on screen, and could quickly print off the review to hand around the lab.

You can subscribe to the mag here!

The issue also has a review of Leopard (the next version of OS X) and the new Apple X server smile.gif

August 13, 2006

Sequence alignments

Filed under: Bioinformatics, Science — cupton @ 7:53 am

Have you ever wanted to make a small diagram to show a conserved motif or a sequence aligment?
And then pulled your hair out while trying to get it to look JUST THE WAY YOU WANT?
There’s a few programs to help, but most don’t quite have the flexibility or resolution.
I always used to use SeqVu, back in the pre OS X days.

Well, finally we (Cristalle Watson) made a stencil in OmniGraffle to easily build these diagrams. Attached Image

Yes, Omnigraffle costs $$.
Yes, it’s a manual process and may not be useful for big alignments.
BUT, it works!!

You can find our stencils at: Graffletopia – Science category!

August 12, 2006

Competition for EndNote?

Filed under: Science — cupton @ 11:07 pm

I’ve used Reference Manager and EndNote over the years and have the latest version of EndNote (9 for Mac).
Can’t say they’re not useful, but I came across an Ad for SENTE (Mac only), which said:
“It’s like iTunes for academic literature”

Couldn’t resist! We tried the demo and like it enough to shell out a few $$ for a single license (3 machines).
So far the reports from the bench are very favorable.

One very cool feature is that you can DRAG a file (called 1471-2105-5-96.pdf) that you downloaded from a journal onto the SENTE entry for the article and SENTE will RENAME it something sensible like author name or title, e.g. Base-By-Base single nucleotide-level analysis of whole viral genome alignments.pdf
and then file it away for you.

SENTE seems to be under very active development. There’s nice HELP docs and a forum to ask questions.

Oh… and SENTE integrates into Microsoft Word and can import EndNote databases etc.

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