Category: Misc.

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

It describes not only a way to speed up continual ortholog annotation in bacterial and archaeal genomes but also is linked to an ongoing open code development project.

Here is the abstract:

Among proteins, orthologs are defined as those that are derived by vertical descent from a single progenitor in the last common ancestor of their host organisms. Our goal is to compute a complete set of protein orthologs derived from all currently available complete bacterial and archaeal genomes. Traditional approaches typically rely on all-against-all BLAST searching which is prohibitively expensive in terms of hardware requirements or computational time (requiring an estimated 18 months or more on a typical server). Here, we present xBASE-Orth, a system for ongoing ortholog annotation, which applies a “divide and conquer” approach and adopts a pragmatic scheme that trades accuracy for speed. Starting at species level, xBASE-Orth carefully constructs and uses pan-genomes as proxies for the full collections of coding sequences at each level as it progressively climbs the taxonomic tree using the previously computed data. This leads to a significant decrease in the number of alignments that need to be performed, which translates into faster computation, making ortholog computation possible on a global scale. Using xBASE-Orth, we analyzed an NCBI collection of 1,288 bacterial and 94 archaeal complete genomes with more than 4 million coding sequences in 5 weeks and predicted more than 700 million ortholog pairs, clustered in 175,531 orthologous groups. We have also identified sets of highly conserved bacterial and archaeal orthologs and in so doing have highlighted anomalies in genome annotation and in the proposed composition of the minimal bacterial genome. In summary, our approach allows for scalable and efficient computation of the bacterial and archaeal ortholog annotations. In addition, due to its hierarchical nature, it is suitable for incorporating novel complete genomes and alternative genome annotations. The computed ortholog data and a continuously evolving set of applications based on it are integrated in the xBASE database, available at http://www.xbase.ac.uk/.

Definitely worth checking out.

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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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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. 

You may recall that in September 2011 I eliminated the office of Vice Chancellor of University Relations and shifted Communications, Government Relations, and Special Events to the Office of the Chancellor, reporting directly to me. Shortly thereafter, Cynthia Barbera was brought on to serve as the acting Executive Director of Strategic Communications pending the appointment of a permanent director. 
  
In meetings with various colleges and departments over the past three weeks as well as in other contexts, I heard many comments and clearly expressed concerns about the ability of Strategic Communications to meet our present needs. I share many of these concerns. 
  
Accordingly, I have asked Barry Shiller to serve as interim Executive Director of Strategic Communications. He will assume day-to-day management of the campus’s central communications activities, effective January 5, 2012. 
  
Barry brings to us an extensive background in strategic communications, diverse career experiences from the UC system and elsewhere, and – as a proud Aggie parent (Class of 2007) – particular appreciation for UC Davis’ distinctions and excellence. 
  
Most recently, Barry served for more than three years as the Associate Vice Chancellor for Communications & Marketing at the University of California, Santa Cruz (UCSC). There, he guided UCSC’s marketing and institutional communication efforts including media relations, branding and marketing, and campus communications. He closely collaborated with students, faculty, staff, foundation and alumni representatives, campus leadership and others on a comprehensive effort to highlight UCSC’s many distinctions in teaching, research and service. Under his leadership, UCSC achieved greater regional and national prominence. 
  
Barry previously served in a similar capacity for nearly five years at Saint Mary’s College of California. Prior to that, he held communications and public affairs leadership positions at a San Francisco public relations agency; an e-commerce start-up firm and the northern California affiliate of the American Automobile Association (AAA). Barry earned his bachelor’s degree from the University of San Francisco and completed advanced studies in insurance and risk management. 
  
I am confident that Barry will serve us extremely well as the interim leader of our central communications activities. I hope you will join me in warmly welcoming him to the UC Davis family. 
  
It is also essential that we launch and complete a comprehensive national search for the permanent director of our central communications unit. Many faculty and others have expressed an interest in helping to shape and inform the long-term direction of our campus communications activities. Community input will be critical to this search as well as the ongoing evolution of our strategic communications efforts. 
  
I have asked Jessie Ann Owens, Dean of Humanities, Arts and Cultural Studies, to chair the Recruitment and Selection Committee for this important position, and Dean Owens has graciously agreed. You may expect details early in the New Year about the search process and in particular how faculty, students, staff and other members of the campus community can contribute to this endeavor. 
  
I’ll continue to share updates as we work to improve our communications efforts. Your assistance is critical to our success. 
  
I wish each of you much peace as we enter the New Year. 
  
Sincerely, 
Linda P.B. Katehi 
Chancellor

——–
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.

——–

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:

Email from the responsible parties:
The UC Davis Genome Center holds an Omics Office Hour from 9:00-10:00am each month in Room 3209 of the Medical Education building in Sacramento. These drop-in sessions are open to anyone in the SOM community 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, January 6, 9:00 am in Room 3209 of Med Edu Bldg.

NOTE: THE DECEMBER 23, 2011 MEETING HAS BEEN CANCELED!!!!!

For more details, please link to:
http://www.genomecenter.ucdavis.edu/outreach-and-giving/omics-office-hour-2012

The schedule is also available as a Google Calendar called “‘Omics Office Hours”. For anyone who wants to subscribe to the calendar, here are instructions:

For Google Calendars:
1- go to Google Calendar
2 – under “Other calendars” click Add/Add by URL
3 – past the iCal link shown below into the box (https://www.google.com/calendar/ical/o6rt68uree1205hictul75m614%40group.calendar.google.com/public/basic.ics)
4 – click Add Calendar
5 – DONE

For iCal:
1- just click on the link below (might require some advanced Mac skills)
– or –
1- open iCAL
2- in the menu select Calendar/Subscribe
3 – past the iCal link shown below into the box (https://www.google.com/calendar/ical/o6rt68uree1205hictul75m614%40group.calendar.google.com/public/basic.ics)
4 – click Subscribe
5 – DONE


——–
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.

——–

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


 *original message*
Dear Colleagues,

During an emergency teleconference meeting, on November 20, 2011, the Davis Division Executive Council approved formation of a Special Committee to review the incident in which protestors were pepper sprayed on November 18, 2011. The Executive Council Special Committee on the November 18th Incident has been appointed.   The charge and membership are available on the Academic Senate website: http://academicsenate.ucdavis.edu/committees/exec-council-nov-18.cfm.  If you wish to provide the Special Committee information, please forward an e-mail message to: specialcommittee@ucdavis.edu.  I anticipate receipt of the report from this committee in February 2012.  

Sincerely,
Linda F. Bisson, Chair
Davis Division of the Academic Senate

——–
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.

——–

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
——–
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.

——–

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.

——–
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.

——–

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:

And more … fun for the whole family
——–
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.

——–

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 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.

——–

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.

2) Petition received on December 15, 2011, requests a vote regarding 1) condemnation of both the dispatch of police and use of excessive force in response to non-violent protests on November 18, 2011; 2) opposing violent police response to non-violent protests on campus; 3) demanding that police deployment against protestors be considered only after all reasonable efforts have been exhausted and with direct consultation with Academic Senate leadership; 4) acceptance of Chancellor Katehi’s apology; 5) expression of confidence in Chancellor Katehi’s leadership and efforts to place UC Davis among the top public universities in the nation.

Sincerely,
Ines Hernandez-Avila
Secretary, Davis Division of the Academic Senate
Chair, Native American Studies

——–
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.

——–

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)

2. Constructed a “total evidence” phylogeny for these taxa (using a few approaches) 
3. Use this phylogeny to reinterpret some general features of the evolution of plants 
4. Searched for gene ontology categories (in annotated genes from these organisms) that agreed with the phylogeny. In essence, this seems to be a search for shared-derived traits (i.e., synapomorphies) in particular clades. 
5. Generated hypothesis about functional evolution in particular clades.
Overall, there is a lot that is really fascinating in here and this approach seems very powerful (though I note – I think something akin to this though not as comprehensive or as careful has been done for other groups but not sure).  Check out the paper for more detail …
Lee EK, Cibrian-Jaramillo A, Kolokotronis S-O, Katari MS, Stamatakis A, et al. (2011) A Functional Phylogenomic View of the Seed Plants. PLoS Genet 7(12): e1002411. doi:10.1371/journal.pgen.1002411
——–
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.

——–