Eisen Lab Blog

Humorous sciency signs #1: Please do not molest the spawning salmon

I am starting yet another thread here — my favorite humorous science related signs.  This one is from Alaska.  Not sure what Sarah Palin would think of this one, but that is another topic.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Davis Outdoor Art



I am planning to keep posting pics of Davis outdoor art whenever I can. Here are some pictures from the UC Davis Vet Hospital in an art display in honor of companion animals

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Drew Endy talking at Davis tomorrow ….

For those from UC Davis or the area who read the blog and have an interest in genetic engineering or synthetic biology or open science, you should come to this talk.

Genome Center Colloquium
Storer Life Sciences Endowment Presents

Drew Endy, PhD
Stanford University

“Post-Synthesis Genetics & Engineering Biological Simplicity”

Friday, September 26, 2008

10:00 a.m., 1005 GBSF Auditorium

For more on Drew Endy, well, use google of course or go here:

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Science Faux Pas #3: Editirs in Chief

The pictire seys it all.  Note – we think this was the restaurant’s fault.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Funny Davis Signs #1

Going to start a new section here … posting pictures of funny Davis
signs. This is one of my favorites.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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MapMyRun for Davis is a nice way to find new places to explore in town

I meant to post this a while ago but was in over my head with other things.  I found this cool site while googling for Davis MAPS and thought I would share —MapMyRun.com | Find Runs and Running Routes in Davis, CA
It has a diversity of routes for biking, walking and running in and around town.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Lance Armstrong Coming to Davis for the Tour of California

Get ready Davis.  Not only will Davis host a stage of the Tour of California this year, but new reports are today confirming the rumors – Lance Armstrong will apparently race in the Tour of California for the Astana team.  See for example

So Stage 2, February 15th, will be a big big Day for Davis.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Much ado about plants and blogs in PLoS Biology

Some good new articles in PLoS Biology in the last few weeks worth checking out.  There is definitely a theme there if you want to look for it.  So here are some of the papers connected to that theme and even one that covers both.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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What does privacy mean to you? Please complete this survey

ThePrivacyPlace.Org Privacy Survey is Underway!

Researchers at ThePrivacyPlace.Org are conducting an online survey about privacy policies and user values. The survey is supported by an NSF ITR grant (National Science Foundation Information Technology Research) and was first offered in 2002. We are offering the survey again in 2008 to reveal how user values have changed over the intervening years. The survey results will help organizations ensure their website privacy practices are aligned with current consumer values.

The URL is: http://theprivacyplace.org/currentsurvey

We need to attract several thousand respondents, and would be most appreciative if you would consider helping us get the word out about the survey, which takes about 5 to 10 minutes to complete. The results will be made available via our project website (http://www.theprivacyplace.org/).

Prizes include
$100 Amazon.com gift certificates sponsored by Intel Co.
and
IBM gifts

On behalf of the research staff at ThePrivacyPlace.Org, thank you!

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Fwd: MG-RAST User Newsletter No.2 — MG-RAST paper available // NEW version released // 2nd User Workshop planned

Out sick so email updates will have to do
Got this by email
Subject: MG-RAST User Newsletter No.2 — MG-RAST paper available // NEW version released // 2nd User Workshop planned



Dear MG-RAST users,

The MG-RAST team has some news we would like to share:

1) MG-RAST manuscript published
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The manuscript for MG-RAST has been accepted in BMC Bioinformatics and is available under the following URL:

http://www.biomedcentral.com/1471-2105/9/386/abstract

Please cite:
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The metagenomics RAST server F. Meyer, et al
BMC Bioinformatics 2008, 9:386


2) New version of the server software available
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After a lot of testing (Thanks again to all beta testers), we have released a new version of our MG-RAST server software. You will notice improvements in nearly all aspects of the MG-RAST platform and user experience.

Here is a  summary of changes and additions:
– added overview page with statistical summary
– ability to download arbitrary subsets of fragments as fasta
– user can change parameters for metabolic reconstruction and phylogenetic reconstruction on the fly
– ditto comparison/heatmaps
– recruitment plot
– metabolic comparison tool using KEGG pathway maps
– updated databases in background (NR no longer from 2006, Silva RNA database included)
– detailed sequence information and alignments
– support for groups and inviting friends to look at data
– much faster user interface
– ability to see/download fragments and see blast alignments
– added Silva rRNA database (from: http://www.arb-silva.de/)
– many small detailed fixes


3) MG-RAST workshop planned for winter 2008/2009
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In addition to the tutorial at Metagenomics 2008 in San Diego (see: http://metagenomics.calit2.net/) we are inviting participant registration for our second MG-RAST workshop. Please send an email to mg-rast@mcs.anl.gov if you are interested in participating.


— from the MG-RAST team
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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