Eisen Lab Blog

Call for abstracts: Automated Function Prediction, 2012

Call for abstracts: Automated Function Prediction, 2012

Locale: Long Beach, California USA
Date: July 14, 2012 (Just before ISMB 2012)
URL: http://biofunctionprediction.org

Important dates:

April 18, 20112: Deadline for submitting abstracts.

May 9, 2011: Notifications for accepted abstracts e-mailed to
corresponding authors

May 16, 2011: Deadline for presenters to confirm acceptance of
invitation to speak.

July 14, 2011: AFP SIG preceding ISMB 2012

An ISMB Special Interest Group Meeting

Automated Protein Function Prediction

Sequence and structure genomics have generated a wealth of data, but
extracting meaningful information from genomic information is becoming
an increasingly difficult challenge. Both the number and the diversity
of discovered sequences are increasing, while the fraction of genes
whose function is known is decreasing.In addition, there is a need for
annotation which is standardized so that it could be incorporated into
function
annotation on a large scale. Finally, there is a need to assess the
quality of the function
prediction software which is out there.

For these reasons and many more, automated protein function prediction
is rapidly gaining interest among computational biologists in academia
and industry.

The AFP SIG has been part of ISMB since 2005.
We call upon all researchers involved in gene and protein function
prediction to submit an abstract to the AFP meeting. Authors of select
abstracts will be invited to give a talk and/or present a poster.

This year, AFP is delighted to have Jonathan Eisen from the University of
California, Davis as its keynote speaker. Prof. Eisen is a pioneer in the
field of function prediction.

>From his lab page:
http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/Main_Page

"Dr. Eisen has published more than 200 scientific papers and is a co-author
of a relatively recently published Evolution
Textbook<http://evolution-textbook.org/>.
Dr. Eisen is also a strong proponent of the Open Access movement in
scientific publishing and is Academic Editor in Chief of PLoS
Biology<http://www.plosbiology.org/>.
Dr. Eisen is also an active and award winning science blogger (see his Tree
of Life blog here <http://phylogenomics.blogspot.com/>). For recent news
see http://twitter.com/phylogenomics" <http://twitter.com/phylogenomics>

For further instructions on how to submit abstracts to AFP 2012, please go
here:

http://biofunctionprediction.org/node/415

We are looking forward to seeing you in Long Beach, California!

Iddo Friedberg on behalf of the AFP organizing committee

Just grand -Donald Williamson published more crap on larval "evolution" – this time in one of the #OMICS journals

Well this is great.  Just great.  Donald Williamson has a new paper “The Origins of Chordate Larvae” published in Cell and Developmental Biology – a spammy journal from the OMICS publishing group.  Don’t know who Williamson is?  Well consider yourself lucky.  For more on him and his horrendous history of publishing crap see:

And many many more.  Short summary – he has a theory regarding larval forms of organisms having a separate evolutionary history from adult forms.  He has no evidence for this.  And he keeps finding new ways to publish his theory.  Uggh.  I guess this serves as a reminder to everyone out there – crap does get published.  It is too bad.  But it does happen and will continue to.  We need to call out the crap as much as possible so that as few people as possible out there end up getting deceived.  So this is my contribution to that notion.  Google search engines pay attention. Donald Williamson really publishes some horrible stuff.

Ecology & Evolution Seminar Series UPDATED Flier – Spring 2012

Spring 2012 schedule for the Ecology & Evolution seminar series, ECL 296 (CRN 70181) / PBG 292 (CRN 44948). Seminars will be held each Thursday, 4:10-5:30PM in 1003 Giedt Hall.

We’re still waiting for one title and will send an updated flier as soon as it’s received. In the interim, can you please share this information with your students and anyone else who may be interested.

The most current listing of speakers and titles will be posted at http://www.des.ucdavis.edu/EcologyEvolutionSeminars.aspx.

EESeminar-Spring2012.pdf

Agilent Lunch & Learn on 3/27

From Agilent:

I wanted to let you know that Agilent will be hosting a Next Generation Sequencing Lunch & Learn next Tuesday, March 27th, from 11:00-1:00 in GBSF – Room 4202, which we’d like to invite you, and your lab, to attend. We will be covering all of our target enrichment technologies (SureSelect, HaloPlex and Methyl-Seq) as well as discussing a new addition to our electrophoresis portfolio, the TapeStation. We hope you and your colleagues can attend! Please let me know if you have any questions.

Kind regards,

Jamie

Jamie Andalis

Davis Lunch Learn Flyer (3).pdf

OMG – Without a doubt the worst omics word ever – The Sexome

I really have nothing to say here.  I just got pointed to a new paper by Thiago Venancio.  The paper is – I kid you not: Understanding the Sexome: Measuring and Reporting Sex Differences in Gene Systems.  I don’t have access to the paper but here is the abstract which is all you need

The current male bias in biomedical research should be eliminated. The large sex differences in incidence and progression of diseases mean that sex-biased factors are an untapped source of factors that protect from disease. Greater understanding will come from intensified study of the “sexome,” which is the sum of sex-biased effects on gene networks and cell systems. The global search for sites and mechanisms of sex-specific regulation in diverse tissues will provide unanticipated insights into physiological regulation and targets for novel therapies.

That is without a doubt the worst omics word I have ever seen.  All my previous posts about bad omics words pale in comparison (though I encourage you to read them: Worst New Omics Word Award and bad omics word of the day).

Calling all computational biologists – do as C. Titus Brown does – submit your pubs to arXiv

Can I just express my love/respect for C. Titus Brown?  Not only is he into openness in science and metagenomics and such.  But he practices what he preaches.  For example see – Daily Life in an Ivory Basement : /mar-12/diginorm-paper-posted in which he describes his new submission to arXiv and some background.  I know I am big on Open Access and all, but even we have been lame about submitting things to preprint servers like arXiv.  Gonne do my best to fix that and try and copy Titus.

Lenses in Biology collection from Nature Outlook: free (for now at least) & worth a look

Some nice long features in Nature Outlook on various topics plus interviews with the authors.  Summed up in Lenses on Biology.  All freely available though I think that is only for this collection and not in general for Nature Outlook.

Notes (from me and mostly others) from the JGI User Meeting #JGIUM7

OK, so the DOE Joint Genome Institute User Meeting is underway. Day 2 just finished. And I have been there for much of it but alas, not in some of the talks since I can’t seem to get past the hallway/gathering area outside the talks. There are way way too many people there who I have not talked to or seen in a while … So … apologies to those who thought I might be live tweeting the whole meeting … it just hasn’t happened. But I did use the Storify web tool to make a “storification” of posts to twitter from the meeting – most of which were from other people. Here is the story in slideshow format.

http://storify.com/phylogenomics/jgi-user-meeting-day-1-2.js?template=slideshow[&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;a href=”http://storify.com/phylogenomics/jgi-user-meeting-day-1-2&#8243; target=”_blank”&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;View the story “JGI User Meeting Day 1-2” on Storify&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;]

I will update the storification tomorrow. If you want to see the full details in a scrolling winder see below

http://storify.com/phylogenomics/jgi-user-meeting-day-1-2.js[&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;a href=”http://storify.com/phylogenomics/jgi-user-meeting-day-1-2&#8243; target=”_blank”&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;View the story “JGI User Meeting Day 1-2” on Storify&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;/a&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;]

OMICS Driven Microbial Ecology …

Quick post here.  Just discovered a nice review paper by Suenaga on targeted metagenomics: Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities – Suenaga – 2011 – Environmental Microbiology

This “Special Issue” on “OMICS Driven Microbial Ecology” has a series of papers, all of which seem to be freely available, of potential interest to readers of this blog including:

and more
Oh, and a paper of mine (with Alex Worden and other members of her lab as well as multiple others)

Google Wage or Google Wave? I am interested in Google Wage if they are still offering …

Just got this email

Google Wage wave-noreply@google.com

12:24 AM (4 minutes ago)

Dear Wavers,More than a year ago we announced that Google Wave would no longer be developed as a separate product. Back in November 2011, we shared the specific dates for ending this maintenance period and shutting down Wave. Google Wave is now in read-only mode. This is reminder that the Wave service will be turned off on April 30, 2012. You will be able to continue exporting individual waves using the existing PDF export feature until the Google Wave service is turned off. We encourage you to export any important data before April 30, 2012.

If you would like to continue using Wave, there are a number of open source projects, including Apache Wave. There is also an open source project called Walkaround that includes an experimental feature that lets you import all your Waves from Google. This feature will also work until the Wave service is turned off on April 30, 2012.

For more details, please see our help center.

Yours sincerely,

The Wave Team

© 2012 Google Inc. 1600 Amphitheatre Parkway, Mountain View, CA 94043
You have received this mandatory email service announcement to update you about important changes to your Google Wave account.

Notice anything unusual? How about that it is from “Google Wage?” I assume this is either a really bad typo or a really funny prank from inside Google.