Note @David_Dobbs @mbeisen had nice family PM yesterday watching wrapup of 2004 ALCS @David_Dobbs @mbeisen

Note @David_Dobbs @mbeisen had nice family PM yesterday watching wrapup of 2004 ALCS @David_Dobbs @mbeisen

Draft blog post cleanup #2: Metagenomics meets animals

OK - I am cleaning out my draft blog post list.  I start many posts and don't finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is #2:

Saw an interesting story on Genome Web: 'Denizens' of the Deep | The Daily Scan | GenomeWeb.  I have not been able to get the original article yet, but it seems that what they have done can basically be considered metagenomics for animals.  They collected sloughed off cells and other material from a lake and surveyed it for animal DNA.  This seems like a very cool derivative of metagenomic approaches and has enormous potential.  But alas, I never got down to getting access to the paper: Monitoring endangered freshwater biodiversity using environmental DNA so this will have to stay as a mini post.  Damn non open access journals ...

Draft blog post cleanup #1: Divide and Conquer to Find Orthologs

OK - I am cleaning out my draft blog post list.  I start many posts and don't finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is the first ---

Saw an interesting paper worth checking out:
PLoS ONE: Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach

UC Davis Chancellor putting increased emphasis on communications

Just got this email announcement and I thought I would share.  As many know, in the aftermath of the pepper spray incident, whether you support the UC Davis Chancellor or not, it was pretty clear that communications regarding the incident were, well, poor at best.  Hopefully this will improve things.  Of course, action is more important than communication --- but I am glad to see the Chancellor responding to communication issues ---

Dear Colleagues, 
  
I write to inform you about additional actions that I am taking immediately to strengthen Strategic Communications. These steps will help us address needs and challenges facing UC Davis today while preparing us to take advantage of opportunities that lie ahead. 

Top 10 Humorous Science Videos of the Year

I was starting to compile a Top 10 list of best humorous Science-related videos of the year.  And I got stuck on #1 because it is so so so good.  But I was able to find some others I liked (and listed them in no particular order)... so here goes.  If you know of other good ones please post/tweet ...

1. Bad Project video from the Zheng lab.  This is simply awesome.

2. Top 10 quirky science tricks for parties.  I found out about this from Twitter ... and it is very good.

If you subscribe to the NY Times - you might want to cancel to get their secret discount

Just got this email

Dear New York Times Reader, 


You may have received an e-mail today from The New York Times with the subject line “Important information regarding your subscription." 


This e-mail was sent by us in error. Please disregard the message. We apologize for any confusion this may have caused. 


Sincerely,


The New York Times

Which then caused me to go back to my trash and read the previous one:

Dear Potential Post Doc or PhD Student - top10 ways to get a position in my lab

Dear Candidate (for any type of position in my lab)

I thought I would write a letter to you to help guide you in how to apply for a position in my lab.  Here are some suggestions for things that really help out - based on real emails I note ...

1. Describe your interests by copying text from my web site.  This shows that you are not only able to read, but also able to either copy directly or retype what you have read.  It is very appealing.
2. Get my name or institution wrong in some way.  This shows that you are likely being industrious in applying for lots of jobs.
3. Include attachments that do not open on Macs. Screw Steve Jobs and all of his fans.
4. Send the same email multiple times - once to Prof. Eisen at UC Davis, once to Dr. Eisen at JGI, and once to Prof. Eisen from the "Genome Center at UC Davis."  Repetition is an important literary technique. 
5. Refer to the "reputation" of my group without saying anything specific about what interests you.  I love things based on reputation alone.
6. Describe your background as very relevant to our work and then say that you too have focused extensively on microarray based studies of gene expression (I love stealing candidates whose original goal was to work in my brother's lab).
7. Have no publications but a list of more than 10 as "in preparation".
8. Include viruses in attachments - as I am interested in evolution of microbes this is appealing.
9. Express an interest in biological weapons and biological defense and be from a terrorism sponsoring country.
10. Have the original email message be more than four pages long with dozens of questions for me about my institution and my open positions.

Some links worth checking out regarding suppressing publishing and bioterrorism

Just a quick one here with some links worth checking out regarding the recent discussion of suppressing some parts of a paper on engineering flu viruses

• Fearing Bioterrorism, Government Panel Asks: What Research Should Be Secret? | PBS NewsHour | Dec. 22, 2011 | PBS
• Stop the presses! H5N1 Frankenflu is going to kill us all! by Michael Eisen at "It is not junk"
• Strain Game by Carl Zimmer at Slate
• The Trouble with Scientific Secrets by Michael Spector at the New Yorker
• Seeing Terror Risk, US Asks Journals to Cut Flu Study Facts - NY Times
• AM Vitals: Figuring Out How to Handle Access to Bird-Flu Data by  Katherine Hobson

Reminder - Monthly Omics Office Hours at #UCDavis Genome Center - Schedule

For those at UC Davis interested in learning a bit about various omics issues - this may be of interest:

Omics Office Hour 2012 — UC Davis Genome Center

Email from the responsible parties:

Email regarding UC Davis Academic Senate Special Committee re: Pepper Spray

Posting for anyone interested (email from Linda Bisson - Chair of UC Davis Academic Senate)


Dear Colleagues:

There was an issue with the set up of the email address for the Special Committee that has now been corrected by IT. If you sent an email to the committee prior to Wednesday December 21st,  we request that you send it again. Sorry for the inconvenience.

Linda

A few tweets about open science for the non twitterati

Just posting a few tweets of mine regarding open science - for those who do not follow me on twitter. Each of the four stories linked to below are worth a look.

phylogenomics "A blogger's quest to replicate 'arsenic life' led to a remarkable experiment in open science." #ILOVEROSIE http://t.co/s1qBKpvW 12/22/11 6:37 AM

phylogenomics Open and Shut?: The Open Access Interviews: OMICS Publishing Group’s Srinu Babu Gedela http://t.co/AZyCqx4C #Wow 12/20/11 8:05 A

phylogenomics Must read of the week: Goodbye F1000, Hello Faculty of a Million from @caseybergman http://t.co/wwwO3061 12/19/11 9:02 AM

phylogenomics What does Creative Commons mean for science? (Wired UK) http://t.co/77wmWzv2 12/16/11 4:39 AM

The must have job of 2012: Faculty position in Evolution of Organismal Diversity at #UCDavis

The must have job of 2012 - a faculty position in my Department at UC Davis.  It is a GREAT department both scientifically (UC Davis is consistently ranked as having one of the best Evolution/Ecology programs in the country) and personally (the faculty, staff and students are great to be around).  See below for more information.  I am happy to give people any details of the Department, School, campus, etc if you are interested.

---

EVOLUTION OF ORGANISMAL DIVERSITY, UNIVERSITY OF CALIFORNIA, DAVIS 


The College of Biological Sciences, University of California, Davis invites applications and nominations for a tenure-track position in the Department of Evolution and Ecology at the ASSISTANT Professor level, with the possibility of ASSOCIATE appointment with tenure. Candidates must have a Ph.D. (or equivalent) in the biological sciences or related fields. 


They should have a strong record of integrative approaches to the evolution of organismal diversity. We seek candidates with expertise in the organismal biology/natural history of a multicellular group, and whose research uses genomic data in an explicitly phylogenetic context to address questions in macroevolution, ecology, behavior and/or development. The successful candidate will be expected to teach in the department's undergraduate program and in the Population Biology Graduate Group and should be committed to departmental service. 


Applicants should submit materials online at this site which contains additional information about the position. Materials required include: curriculum vitae, description of current and projected research, summary of teaching interests and experience, and up to five publications. Applicants should also provide the information requested for three referees. Once entered, referees will be prompted by email with upload instructions for their letters. 


Closing Date: Open until filled, but all application materials, including letters of recommendation, must be received by February 6, 2012, to assure full consideration. 


Administrative contact: Carla Munoz (camunoz@ucdavis.edu). 


Faculty contacts: Peter Wainwright, Michael Turelli, and Rick Grosberg. 


The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences.

PROMED-MAIL - Nice resource to keep up with stories on outbreaks of infectious disease

For those interested in outbreaks of infectious diseases (which I assume is actually everyone in the world) - there is a nice resource out there called PROMED-MAIL.  It comes from the International Society for Infectious Diseases and it catalogs some recent stories from around the world on outbreaks.  It is worth checking out.  And if you like it, they are trying to raise some funds to keep it going with an Internet-A-Thon so consider donating ...

Some recent stories I found there:

• Lassa fever - Ghana: (AH, EP) susp.
• Babesiosis - USA (02): nationwide survey, background
• Dengue/DHF update 2011 (50)
• Avian influenza, human (73): China, live poultry markets
• Hand, foot & mouth disease - Viet Nam (07): travel alert

And more ... fun for the whole family

Meeting of interest: 16th Evolutionary Biology Meeting at Marseilles

Just got an email about a meeting of potential interest and thought I would share:

It is my pleasure to announce that registration and abstract submission for the 16th Evolutionary Biology Meeting at Marseilles, September 18-21, 2012, is open. Please visit the web site of the meeting http://sites.univ-provence.fr/evol-cgr where you will find all relevant information. 

The following subjects will be discussed:

• - Evolutionary biology concepts and modelisations for biological annotation;
• - Biodiversity and Systematics;
• - Comparative genomics and post-genomics (at all taxonomic levels);
• - Functional phylogeny;
• - Environment and biological evolution;
• - Origin of Life and exobiology;
• - Non-adaptative versus adaptative evolution;
• - The « minor » phyla: their usefulness in evolutionary biology knowledge;
• - Convergent evolution

Looking forward to your participation.

This land is your land - inspired by Woody

p101.mov Watch on Posterous

Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively

In 2006 when I had just moved to UC Davis from TIGR, I was on a Southwest flight from Sacramento to (I think) Arizona. The person sitting next to me and I did the normal chit chat - what do you do? where are you going? etc. And the conversation became fascinating. The person sitting next to me was Mike Lagrone - a farrier (I forget people's names frequently ten minutes after meeting them - but his name I remember even today, so he clearly made an impression). He travelled around the West helping take care of people's horses. (I note - I think more information about him is here Mike Lagrone | EquiMed - Horse Health Matters).

Important paper on annotation standards for bacterial/archaeal genomes - readying for the "data deluge"

Interesting paper in the journal "Standards in Genomic Sciences" that is worth checking out for anyone interested in genome sequencing and annotation. The paper is "Solving the Problem: Genome Annotation Standards before the Data Deluge" by William (aka Bill) Klimke et al.

It discusses the development of international annotation standards at NCBI (The National Center for Biotechnology Information) in collaboration with others. Note - the paper is Open Access.

Their abstract:

The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries.

The paper refers extensively to workshops held by NCBI on genome annotation and gives a link to a page from NCBI with additional information about these workshops.

Now - never mind the extensive use of the term prokaryote in the paper ... the paper has got a wealth of information and tidbits worth checking out.

For example the paper has a nice table on annotation tools and databases and resources.

Among the other sections worth checking out
* Discussion of pseudogene annotation and identification
* Discussion of variation in structural annotation
* Evidence standards
* Functional annotation and naming guidelines

For anyone interested in annotating a genome - and more and more people are these days with the decrease in sequencing costs - this is a must read.

Arrived at Sacramento Airport to witness nice welcome for troops returning from Iraq

See the full gallery on Posterous

p94.mov Watch on Posterous

My brother Matthew, a UC Irvine grad. student in sound engineering, takes on the pepper spray issue

My younger brother Matt is a sound engineering student at UC Irvine. As I did with my post: Top 10 reasons to still consider attending #UCDavis #OccupyUCDavis he has tacked the UC crisis with humor ... Check out his radio spot:

Radio Spot by mattglenn

Two #UCDavis Academic Senate Ballot Initiatives related to #OccupyUCDavis Pepper Spray Incident

Just got this email and thought it would be of interest to some

Colleagues,

This message provides notice of two impending ballots, as required by Davis Division Bylaw 17:  http://academicsenate.ucdavis.edu/cerj/manual/dd_bylaws.cfm#17-.  You have received this notice as a voting member of the Davis Division of the Academic Senate.  The Davis Division received at least 50 valid signatures with each petition, requiring initiation of a formal notice and electronic ballot.  More information, including the method for gathering pro and con statements and the voting period, will be distributed on January 9, 2012.  The petitions are summarized below:

1) Petition received on December 6, 2011, requests a vote regarding a lack of confidence in the leadership of Chancellor Katehi, with the result of the vote to be communicated to the Board of Regents and UC President.

Butterfly exhibit at the Smithsonian Museum of Natural History

Some pics from the butterfly exhibit at the Smithsonian Museum of Natural History

 

Flash

Flash

Maybe the next thing is animal fecal transplant toys? #poop

OK - this is a bit gross - but whatever.  At the National Zoo the other day at the store my kids pointed out these "Pooping Animal Key Chains".  Wonder what is next?

IMG_0061.MOV Watch on Posterous

My twitter notes from the #NASOneHealth meeting via Storify

I am posting here a wrap up of my notes from the National Academy of Sciences Institute of Medicine Forum on Microbial Threats meeting on Improving Food Safety Through One Health I just attended. I made a little "story" via Storify and that is what I am embedding below. More comments to follow I hope but wanted to get this out there.

Very nice new #PLoSGenetics paper on "Functional Phylogenomics" of Seed Plants

Update2 - 12/22 - Data available here.  Thanks to the authors for clearing things up quickly.

---

Update1 -  12/19 - Data for this paper seems to be unavailable - not sure why - but looking into this after a TWEET from Karen Cranston. The paper says data is available at: http://nypg.bio.nyu.edu/main/ but I could not find any there.  Note - this is one reason that all data sets should be made available at the journal or third party sites.

---

Original post:

OK never mind that the terminology of "functional phylogenomics" is a tiny bit vexing to me (long story - some other time perhaps). The paper behind it - PLoS Genetics: A Functional Phylogenomic View of the Seed Plants is very cool.

Here's what the authors did (a very coarse summary)

1. Identified sets of orthologs between plant species using the OrthologID system (which has a phylogenetic underpinning) (the data input for this appeared to have mostly been Unigene EST clusters)

NSF Cyber-Enabled Discovery and Innovation declares success, terminates self

Just got this email.  On the one hand it is nice to see that NSF is not keeping around programs when they may no longer be needed.  On the other hand, this somehow seemed melancholy ...

Dear Colleague,

The Cyber-Enabled Discovery and Innovation program has demonstrated the value of interdisciplinary computational and data-enabled science and engineering.  Increasingly, this research approach is being integrated into new and continuing NSF programs and solicitations.  As of fiscal year 2012, proposals will no longer be accepted by the CDI program.

Me, as a Neanderthal

Went to the Smithsonian Museum of Natural History.  Did something there.  And got this email regarding it with a picture attached.  Explanation is below.  Though I think I probably should have taken off my glasses ...

Dear Visitor,

Congratulations! You have been transformed into a Homo neanderthalensis, one of the closest relatives of modern humans. Your picture is attached.

Fun with microbial diversity studies: SitePainter

Nice new tool out there: SitePainter: A tool for exploring biogeographical patterns by Antonio Gonzalez, Jesse Stombaugh, Christian L. Lauber, Noah Fierer and Rob Knight.

I saw the paper and figured I would see if I could get it up and running.

First I downloaded the software from source forge.

Then I uncompressed it and tried to run it.  When I opened the index.html file in Chrom I got a message saying it only worked in Firefox.  So then I opened it in Firefox and I got an error saying it only worked in newer versions of Firefox.  So I downloaded the latest version of Firefox and then finally the tool opened.  I then followed the simple tutorial they have provided and Voila I was up and running in a few minutes

Completely cool.  Going to definitely have to try this out with our own site-variable microbial data.

Art Meets Science at the Keck Center in DC

Some nice science-art on display at the Keck Center where I was for a NAS/IOM meeting today.  Here are some pics.

My kids learn about the center of mass

Movie_on_12-12-11_at_7.46_PM_#2.mov Watch on Posterous

Pluses and minuses if Wikipediafying your database

There is a really interesting article that just came out from Robert Finn, Paul Gardner and Alex Bateman: Making your database available through Wikipedia: the pros and cons.  The article is part of the Nucleic Acids Research Database Issue.

The abstract does a good job of summing up the article

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis.

Crosspost from http://microbe.net - fun stuff from Rob Dunn

I am cross-posting this from the microBEnet blog I co-write:

I am enjoying the posts to the Scientific American Blogs by Rob Dunn on his and other Citizen Science project(s) and I thought I would share here.

• Scientist Spots Missing Link in his Basement, but is too Sleepy to Catch it | Compound Eye, Scientific American Blog Network.
• The top 10 life-forms living on Lady Gaga (and you)
• Man discovers a new life-form at a South African truck stop

If you do not know about Rob Dunn's projects, well, you should.  I am particularly fascinated by "The Wild Life of Your Homes" which relate to the above posts.  He does some other fascinating projects too like "School of Ants" and "Wild Life of Your Body".  Completely brilliant stuff worth checking out.

Fact Sheet from #UCDavis Administration annotated by some skeptical faculty #OccupyUCDavis

Just got a pointer to this by email and thought some would be interested (not endorsing everything that is there but it is definitely worth a look - the Fact Sheet they are annotating rubbed me the wrong way too).

5 UCD faculty members prepared an annotated version of the "fact sheet" sent by the Chancellor's office last week: https://sites.google.com/site/realfactsheet/realfactsheet.pdf

This is designed not only to give more of the relevant facts, but also to analyze the quality of communications coming out of the Chancellor's office. The list of endorsers is at https://sites.google.com/site/realfactsheet/endorsers.pdf

Carl Zimmer on "Who Owns Your Microbes"?

There was an interesting piece by Carl Zimmer in the New York Times a few days ago: Our Microbiomes, Ourselves - NYTimes.com

In the piece Zimmer discusses the issue of who owns your microbiome. This can be considered an extension of the concept of "Who owns your cells?" such as has been discussed in the context of Rebecca Skloot's HELA book.

My favorite line(s):

Monitoring the bacteria flushed into the sewer system of a town, for instance, might reveal a lot about the entire town’s health. But a regulation requiring permission from every resident of the town would stop the study dead in its tracks

Personally I think none of us own our microbes - since we get them from the world around us and likely share them with millions of others. It would be akin to saying we own genes found in all humans. But there very well may be some person specific alleles in microbes that could in a way be akin to person specific cell lines. Not sure.

Anyway - I think I am going to name all my microbes as a first step in protecting my rights to them ...

Kids book of interest: Antarctic Adventure

http://www.artbookbindery.net/antarcticadventure.png

Just found out about this new kids book about Antarctica: Antarctic Adventure. Hat tip to Jeff Hoffman, a friend who has been on many many scientific field adventures.

From the book web site:

Antarctic Adventure is the story of author/scientist Mak Saito's research expedition to the Southern Continent. The book is targeted at children age 3 - 7. Simple text and stunning photographs highlight the adventure elements of fieldwork in the Antarctic (helicopters, snow storms, wildlife). Children learn where Antarctica is, what algae are, what glaciers look like, and the names of several different whales and penguins. More generally, they get a sense of what it means to do scientific fieldwork. A "Dear Reader" section at the end of the book goes into more detail about the expedition's research goals, which involve the importance of algae in global biogeochemical cycles.

I have just bought a copy ... will let people know more when I get it but I am guessing it is going to be good ...

Me and my girl Annapurna

See the full gallery on Posterous

The Rare Biosphere, 2011 report from American Academy of Microbiology

I had posted this to twitter a while ago but not here. There is a report that came out from the American Academy of Microbiology from a Workshop in which I participated. The report is on "The Rare Biosphere, 2011" and it discusses some of the issues associated with the long tail of rare organisms that might exist, especially microbes.  It is worth a look.

From their page:

The microbial world represents the last truly unexplored frontier in the diversity of life on Earth. New environmental sampling technologies have revealed a wealth of rare microbial species in the soil, ocean, even our own bodies that were effectively cloaked from previous sampling methods by more abundant species. Dubbed the rare biosphere, these microbial species, while individually rare, collectively account for more than 75% of the biomass of some microbial communities, yet little is known about them. This rare biosphere represents a treasure trove of genetic novelty that may possess numerous unique bioprocesses and biomaterials. These rare species may play keystone roles in microbial communities and act as a reservoir of genetic diversity. But how can scientists effectively study the rare biosphere? In April 2009 the American Academy of Microbiology convened a colloquium to explore this question. Based on that colloquium, this report analyzes the current state of study of the rare biosphere and identifies where gaps in knowledge exist. The report concludes that the Herculean task of studying the rare biosphere requires an international collaborative effort and additional environmental sampling, coupled with a focus on advancing sequencing and data analysis technologies. With less than 1% of microbial species able to be grown in the laboratory, the prospects of new discoveries in the rare biosphere seem as vast as microbial diversity itself.

You can get a PDF of the report here.

Yes, Colbert did indeed discuss Fecal Transplants #microbeRule

See Cheating Death - Chicken Pox Lollipops & Fecal Transplants - The Colbert Report - 2011-08-12 - Video Clip | Comedy Central

The Colbert Report	Mon - Thurs 11:30pm / 10:30c
Cheating Death - Chicken Pox Lollipops & Fecal Transplants
www.colbertnation.com
Flash Flash
Colbert Report Full Episodes Political Humor & Satire Blog Video Archive

Blast from the past: 1997 Walter J. Gores Teaching Awards at Stanford w/ Condoleezza Rice

Just got this digitized. One of my proudest moments. In 1997 I received the Walter J. Gores Award for excellence in teaching for my work on the "SME Core" at Stanford. The SME Core was a new way to teach Science, Math and Engineering for non science majors.

 

The SME Core was an initiative coordinated in part by then Stanford Provost Condoleezza Rice.  I worked with her office on and off for 3 years to help get the SME Core program up and running.  (I note - whatever you think of her now - at the time I really really liked her - she was great to interact with, brilliant, and I think inspired in pushing this SME program).

NPR Piece on Discovery of Hydrothermal Vent Oasis

Very nice to see this: The Deep-Sea Find That Changed Biology : NPR

It discusses the story of the discovery of the first hydrothermal vent oases back in 1977. I note this is near and dear to my heart. I worked as an undergraduate and then after graduating in Colleen Cavanaugh's lab at Harvard on chemosynthetic symbioses. And then amazingly I got to go on the 2002 deep sea cruise celebrating the 25th anniversary of the discovery of the vents. On that cruise Rosebud (mentioned in this article) was discovered.

Meeting of Faculty in College of Biological Sciences w/ Chancellor Katehi #UCDavis

A few days ago I got the following email:

Good Afternoon,

To all “Faculty Members Only” of the College of Biological Sciences:

Chancellor Katehi has requested a meeting with the faculty members of the College of Biological Sciences.  For this particular session, the invitation is extended to faculty members only.

This will be an opportunity to ask questions and to hear the Chancellors plans for moving forward.

Date:                     Thursday, December 8, 2011
Location:              Conference Room – Life Sciences Building / 1022
Time:                     1:00 pm – 2:30 pm

And today was the day.  It was a very hectic day for me.  AM kid related duties.  Then I dropped off two pairs of broken glasses to get soldered (one of which had broken on the day of the major post-pepper spray rally at UC Davis.  Then off to lab where I had only a short period of free time before lab meeting (alas, unlike last week, this meeting was indoors).  And then off to the meeting with the Chancellor.  Here are some notes from that meeting --- more of a stream of consciousness than detailed notes in many cases but hopefully this will give a gist of how the meeting went.

Meeting of Interest: DOE JGI "Genomics of Energy and Environment" 3/20-22

A meeting of interest: The Annual DOE JGI User Meeting.  Note - open to anyone - not just those funded by DOE.

Topics include

• Synthetic biology & biodesign
• Systems biology/transcriptional networks
• Application of single cell genomics in microbial ecology and bioprospecting
• Genomic analysis of biofuel traits in maize and switchgrass
• Cloud computing as a platform for large scale sequence analysis
• Ocean viruses: towards population genomics, understanding virus-host interactions, and accessing the uncultured
• Omics in the Arctic: Genome-enabled contributions to carbon cycle and biogeochemical research in high-latitude ecosystems
• Ancient DNA

Plus - Carl Zimmer.  Yes, I said Carl Zimmer.  

Twisted Tree of Life Award #12: Billion Year Old Smart Bacteria That Perfectly Treat Cancer

OMG - for crying out loud. In the following story Billion-year-old Bacteria Could be Medical Goldmine Fox News discusses studies of marine cyanobacteria at the University of Florida. It is so wrong in so many ways I do not know where to begin. Watch the video first for layers of trouble. Then, if you dare, read the article. Among the painful parts:

All cyanobacteria are basically lumped together into a single entity

Some new links/information regarding Pepper Spray incident and #UCDavis response

Not going to write much here but am posting some links for those interested:

• New letter to Davis Enterprise expressing lack of confidence in Chancellor Katehi
• Middle East/So. Asia Program calls for Resignation (via @AmyChamp on twitter)

More Davis Enterprise Stories

• Spotlight aimed at UCD police's use-of-force policies
• Yudof names members of pepper-spray task force
• Occupy UC Davis readies for 'long road' ahead
• Katehi op-ed: How do we learn from this?
• Katehi, faculty agree on message, not who can deliver it

Kroll Associates "fact finding" email re: #OccupyUCDavis #UCDavis

Just got this email and thought I should post it

from UC Davis Fact Finding Review ucdavisfactfindingreview@ucdavis.edu to UC Davis Campus Community date Wed, Dec 7, 2011 at 4:37 PM subject UC Davis Fact-Finding Review: November 18 Pepper-Spray Incident mailed-by ucdavis.edu

To the UC Davis Campus Community:

Have a bite while talking about bits & bytes #UCDavis

Just found out about this ...

Bits & Bites lunch club at UC Davis

"Bits & bites is a new lunch club that aims to meet once a week at UC Davis and talk about various aspects of sequence analysis. The idea is to gather together people in a very informal environment and share expertise on various subjects relating to bioinformatics and genomics."

More detail from the site:

The plan will be to meet on Thursdays between 12:00 and 1:00 at various venues on the UC Campus, possibly including the Genome Center, and Life Sciences Addition – as well as possible forays into Davis. Occasionally – maybe once a month – we would try to host an invited speaker to give deeper insights into a specific topic.

To find out more details please join the bits & bites mailing list (a low traffic list which will mostly be used to announce the venue and discussion topics each week).

Sounds good to me.

His fees are hella high - perspective from a #UCDavis student #OccupyUCDavis

Perspective from a UC Davis student

 

#UCDavis Genome Center Omics Office Hours

The UC Davis Genome Center will be holding an Omics Office Hour from 9:00-10:00am each month in Room 5206 GBSF on the Davis campus. These drop-in sessions are open to anyone with questions regarding Genomics, Epigenomics and Gene Expression, Proteomics, Metabolomics, Network Biology and Bioinformatics.

The mission of the Genome Center is to facilitate your "omics" research at UC Davis. Genome Center staff and faculty will be on hand for consultation in a friendly, informal setting. If you have ideas that you would like to explore, we would be happy to discuss it as well as the possibility of pilot grants.

The next session will be Friday, December 9.

#badomics word for the week: nascentome

Here is a #badomics word to ponder - the nascentome

From this paper PLoS ONE: Nascentome Analysis Uncovers Futile Protein Synthesis in Escherichia coli

It was called to my attention via twitter:

ayrrisbio ayrrisBIO - Appistry 

Awe MT @aaron_best But it's so new. Give nascentome a chance. RT @WvSchaik: #badomics word: The 'nascentome':goo.gl/o3E8t

8 hours ago 

aaron_best Aaron Best 

But it's so fresh and new. Give nascentome a chance. RT@WvSchaik: #badomics word: The 'nascentome': goo.gl/o3E8t@phylogenomics

14 hours ago 

m_m_campbell Malcolm M. Campbell 

Worthy candidate for #badomics word of the year: 'nascentome'. Blech. goo.gl/o3E8t via @phylogenomics

16 hours ago 

WvSchaik WvSchaik 

#badomics word: The 'nascentome': goo.gl/o3E8t @phylogenomics

18 hours ago 

It is a really bad omits word.  So we are giving it an award.  Not sure which one yet.  But one of these:

• bad omics word of the day
• Worst New Omics Word Award