Radiolab on artificial life

Definitely worth listening to the RadioLab show episode “So-Called Life”. The second act describes some “bioengineering kids” who engineered sweet smelling E.coli. I’m sure some of them hang out at OWW. The BioEngineer’s song at the end of the 2nd act is definitely worth listening to, still trying to find a link. The third act talks with founder of Codon Devices, George Church, and Craig. They describe George Church “as Santa Clause as played by Clark Gable.”

who would have thought a pig’s trabecular meshwork could be so pretty?

 From Biotechniques email newsletter.  Winning images from IN Cell Analyzer Image Competition 2007.

Open data

Neil points out that the Science Commons has released a new standard for implementing open access data and also references Deepak’s nice summary of the important points. A standard like this will be an important step towards increasingly more open science and how data is made accessible.

The ISMB open data and open source BoF which never got around to discussing aspects of open data – it was mostly a discussion of different points of view on how obligated one should be to make code open source when it is necessary for a published manuscript. One thing I heard discussed was the idea that the software necessary to access the data needs to be made available, we don’t want to end up with unreadable data because the software doesn’t exist anymore.

Slideshare

Trying out Slideshare, there is apparently now wordpress plugin so that this can be embedded.

Phycomyces genome now available

The JGI has released the Phycomyces blakesleeanus genome. This represents the second Zygomycete genome sequence that has been released in addition to Rhizopus oryzae that was released by the Broad Institute last year. We are now getting a better look at the basal fungal genomes including the Chytrids and Zygomycetes. Much more on specifics of Phycomyces biology and history are on this site run by the group organizing the genome analysis.

I find one of the most interesting things about P. blakesleeanus is its phototropism. We know light sensins is controlled in part by the gene white-collar 1. A homolog of this gene in Neurospora crassa is involved as an oscillator circadian rhythm. Of course many more genes are involve in pathways for light sensing including some really old proteins like phytochromes.

There will be a lot of cool analyses to do with this genome beyond phototropism. I am looking forward to seeing what gene families are unique and expanded in this species relative to the other zygomycete. It also looks like it is quite intron rich much like the Basidiomycetes, further supporting the idea that fungi had intron rich ancestors.

visiting Vancouver

Had a great chance to unwind after the defense and visit Vancouver. I was invited to talk at the VanBug seminar series and got to meet with a lot of great people.

I also got to visit with some friends there and see downtown and Vancouver Island (where it seemed to rain less). Much fun was had, but much more to see.

Some pictures of Vancouver

Jim and Becky generously hosted me for a few days down in White Rock and showed me around during Easter weekend, including a trip to Vancouver Island.

Becky also convinced us to go to Butchart Gardens to see flowers and stuff, we protested but probably too loudly… It WAS fun so am glad we got to go.

tools to create a pretty thesis

Recipe for success….

• Emacs 21(+X11) installed from Fink on OSX
• LaTeX installed from fink.
• A Duke style latex class for dissertations.
• JabRef for biblio management.

• Direct download of references from PubMed

• Insert citations into emacs directly as long as you have gnuserv running. See notes about gnuserv starting.

BioPerl Graffiti

After halloween party from a few years ago there was a little more direction on who to ask for BioPerl help…