Friday, April 29, 2011

iEVOBIO Coming soon (6/20-21): Metagenomics, Biodiversity, Barcoding, Data Integration, and more

Last year, iEVOBIO was a fun, interesting meeting for many reasons (not the least of which is that I was the keynote speaker).  If you want to learn more about last years meeting check out my blog post: Summary of #iEVOBIO Day 1 #evolution #phylogenetics #informatics #opensource

But I note, that meeting was so, well, last year.  This year, the meeting is focusing on metagenomics, barcoding and biodiversity as well as data integration (see the meeting website for more information: iEvoBio: Home).  From the website:

Wednesday, April 27, 2011

Wanted: Sample collections for the Earth Microbiome Project (EMP); help make an open Field Guide to the Microbes

The Earth Microbiome Project (EMP) is "a systematic attempt to characterize the global microbial taxonomic and functional diversity".  A little more detail is provided on the project website:

The Earth Microbiome Project is a proposed massively multidisciplinary effort to analyze microbial communities across the globe. The general premise is to examine microbial communities from their own perspective. Hence we propose to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe. We will analyze 200,000 samples from these communities using metagenomics, metatranscriptomics and amplicon sequencing to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, approximately 500,000 reconstructed microbial genomes, a global metabolic model, and a data-analysis portal for visualization of all information.
This project is certainly incredibly ambitious.  But hey, why not aim high?  The project is being coordinated by Jack Gilbert, Folker Meyer, and Rick Stevens from Argonne National Lab and the University of Chicago as well as Janet Jansson from Lawrence Berkeley National Lab and Rob Knight from U. Colorado Boulder. 

I note I am not unbiased here as I am one of the members of the EMP Steering Committee (others on the Committee include Jed Fuhrman, Janet Jansson, and Rob Knight).  

If you want to learn a bit more about the origins of the project, read this paper which is a report from a meeting where the idea came together as well as a follow up paper

Anyway, the reason I am writing this post is that the EMP is looking for collaborators and participants.  In particular we are hoping to line up lots of large sample collections that could be included in future analyses.  Currently a pilot project is being done on ~10,000 samples.  These will be characterized in a variety of ways including collection of metadata and also generation of sequence information for DNA from the samples (including both rDNA and metagenomic sequencing).  But the EMP wants more - much more.  So the EMP is recruiting anyone who either currently has, or could possibly collect, large collections of samples for microbial characterization along with rich contextual data about the samples.  The contextual data would ideally include as much information about the physical, chemical and biological parameters found at the time of sampling as possible. These parameters include, but are not limited to, nutrient concentrations, temperature, salinity, porosity, moisture content, time of day, latitude and longitude, depth below surface, elevation, pH, etc.

Tuesday, April 26, 2011

Lawrence Lessig on Copyright "The architecture of access to scientific knowledge" #CERN

Not much to say other than that Lawrence Lessig is worth listening to.

The Architecture of Access to Scientific Knowledge from lessig on Vimeo.
Lecture at CERN, Geneva, Switzerland, 18 April 2011: A new talk about open access to academic or scientific information, with a bit of commentary about YouTube Copyright School.

Hat tip to Russell Neches for pointing this video out to me ...

Sunday, April 24, 2011

The @nytimes missed a great chance to suggest what astronauts can do as NASA changes: go deep, into the ocean that is

I just got home from a day in the East Bay with family and read with great interest the above the fold story in the New York Times about NASA Astronauts looking for something else to do these days: With Flights Winding Down, NASA Astronauts Seek New Opportunities. While I for one wish we would keep sending people into space (well, that is, if they want to go), I think if space trips are cut back for some time there is something that the astronauts could do in the meantime which would be really really valuable. They could work to explore more of Earth, especially the oceans. Having just come back from a trip to USC's Wrigley Marine Ctr on Catalina Island where I met Chris Welsh and Loretta Whitesides, who are involved in the Virgin Oceanic deep-sea exploration project, I find it surprising that the New York Times article did not mention at all the need for more people to explore the depths of the oceans. Sure, it may not be quite as glamorous as space travel, but it is both difficult and very interesting. I do not personally think that space exploration and ocean exploration are mutually exclusive - we need to do both. But if there is a lull in space exploration for some time and people are looking for something to do - I would suggest they look down. Deep down. And while I am at it - I think the government should greatly expand deep sea exploration programs so we can learn as much about the oceans as we know about space.

Saturday, April 23, 2011

A "work" trip to Catalina Island: USC, Wrigley, C-DEBI, dark energy biosphere, Virgin Oceanic, Deep Five, & more

Panorama of Catalina Island

Well, the last few days have been completely eye opening for me. I have been on a little trip to the USC Wrigley Marine Science Center near the town of Two Harbors on Santa Catalina Island. Alas, this has not been a vacation. This has been work trip. I was invited a bit ago to come to a workshop here by Bill Nelson, a friend and colleague of mine I used to work with at The Institute for Genomic Research (TIGR). Bill is part of a project called the Center for Dark Energy Biosphere Investigations (C-DEBI). The workshop he invited me to was to discuss evolutionary studies as part of this project.

I note this is a general post about the trip - I will post more about the individual science topics including C-DEBI and Virgin Oceanic later.

As is usual, I did not fully commit to going to the workshop immediately and I dragged out committing for a very long time (driving Bill I am crazy I am sure).  But eventually I accepted and then kept flip-flopping on exactly when I would go, but eventually settled on dates too.

What is C-DEBI:

When Bill first invited me to this workshop, I had no clue what this C-DEBI project was.  And Bill must have assumed I knew because he did not provide any detail about what C-DEBI was.  So of course, that is what that Google thing is for.  And what I found was quite intriguing:

A simple description comes from their web site:
Welcome to the Center for Dark Energy Biosphere Investigations (C-DEBI), a National Science Foundation (NSF)-funded Science and Technology Center on the deep biosphere. Our mission is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins. We are a multi-institutional distributed center establishing the intellectual, educational, technological, cyber-infrastructural and collaborative framework needed for transformative experimental and exploratory research on the subseafloor biosphere.

Compilation of links about my brother Michael's story on Amazon's $23million book about flies

Since I think it is pretty cool, I am compiling links to news stories and blog posts about my brother's recent posting on his "It is not junk" blog about Amazon’s $23,698,655.93 book about flies.  Basically, he tracked some sort of automated computer pricing feedback loop between Amazon and another site that led eventually to a very very very very high price for a book about Drosophila.

And the post has now been picked up by all sorts of places.  So I am compiling a list of some of the stories here.

Yolo Bypass area to reopen Saturday


The Sacramento Bee : Yolo Bypass area to reopen Saturday

Friday, April 22, 2011

Wanted - best/funniest/strangest Acknowledgements sections from papers

I was reading a paper recently which had an awkward acknowledgements sections and I thought it might be fun to make a collection of papers with unusual such sections. So I am putting out a call here - do people know any good examples of strange or funny or exceptionally long or otherwise interesting acknowledgement sections from papers? Please post them here or on twitter/friendfeed and I will eventually post a list

Amazon’s $23,698,655.93 book about flies

OK I realize I am not objective here since this is from my brother, Michael Eisen, but his post about a book on Drosophila that is for sale for > $23 million is fascinating. See
Amazon’s $23,698,655.93 book about flies.

Monday, April 18, 2011

Microbes do some strange things: splitting and permuting tRNAs

Figure 1 - Predicted secondary structures of trans-spliced and permuted precursor tRNAs
(a) Mature tRNAAsp(GUC) in A. pernix and T. aggregans are formed by joining the 5half and the 3half at position 37/38 after splicing at the bulge-helix-bulge (BHB) motif. (b) The 5half and the 3half of trans-spliced tRNALys(CUU) in S. hellenicus and S. marinus join at position 30/31, same as the previously identified split tRNALys(CUU) in N. equitans [5]. (c) Circularized permuted tRNAiMet(CAU) and tRNATyr(GUA) in T. pendens have the 3half located upstream of the 5half separated by intervening sequences represented in green. The two fragments join at position 59/60, same as the T-Ψ-C loop permuted tRNAs in the red alga C. merolae [9]. Pre-tRNAAla(UGC) in C. merolae is shown for comparison. 5half of tRNA transcripts are represented in blue, the 3halves in orange. Black arrows indicate positions of splicing. Anticodons are boxed in light blue.
I was woefully unaware of some of the tRNA shenanigans going on in microbes until reading this paper: Genome Biology | Abstract | Discovery of permuted and recently split transfer RNAs in Archaea from Patricia Chan, Aaron Cozen and Todd Lowe. Life is pretty weird and wacky sometimes, even in components of cells that are considered "core" parts of the machinery of life. Go figure. It is worth a read ...

Hospital acquired infections - NY Times raising level of attention w/ editorial

Just a quick one here.  The New York Times had an editorial Sunday on hospital acquired infections: Hospitals Shouldn't Make You Sicker.  I couldn't agree more.  The Times discussed some recent studies published in the New England Journal of Medicine as well as plans by the Obama Administration to fund some work in this area.  It would be good I note if some of the funding focused not on infections per se but on the microbial ecology of hospitals, which we know very little about.  Focusing just on hand washing and transmission of nasty pathogens is not enough. 

Sunday, April 17, 2011

Boston, Bioinformatics & Ben Franklin Award wrap up from #BioIT11

Photo by Mark Gabrenya
Well, just got back from Boston where I went to the BioIT World convention to pick up the "Benjamin Franklin Award" for contributions to Open Science from Bioinformatics.Org.  A quick round up of the trip:

Interesting PLoS One paper on local assembly from short reads by "tagging" DNA via restriction enzymes

Quick one here. Interesting paper from Paul Etter et al. from Eric Johnson's lab at U. Oregon in PLoS ONE: PLoS ONE: Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

Here is the abstract:

"Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using paired-end sequencing of restriction-site associatedDNA (RAD-PE) fragments. We use this RAD-PE contig approach to identify single nucleotide polymorphisms (SNPs) and determine haplotype structure in threespine stickleback and to sequence E. coli and stickleback genomic DNA with overlapping contigs of several hundred nucleotides. We also demonstrate that adding a circularization step allows the local assembly of contigs up to 5 kilobases (kb) in length. The ease of assembly and accuracy of the individual contigs produced from each RAD site sequence suggests RAD-PE sequencing is a useful way to convert genome-wide short reads into individually-assembled sequences hundreds or thousands of nucleotides long."

Saturday, April 09, 2011

Hmm - How did I miss this paper discussing RFAM, Wikipedia & community annotation #cool

Edits for Wikipedia articles on RNA families. The cumulative number of edits since 1st January 2007 for the 733 Wikipedia articles that are associated with Rfam entries is shown in black. The total number of edits that were reverted or labeled as vandalism is shown in red. To mid-2010, there were just 106 of these. However, some reverted edits may have been well-intentioned but were deemed inappropriate for Wikipedia. From
Very interesting discussion in this paper on Rfam about community annotation: Rfam: Wikipedia, clans and the “decimal” release. In the paper the authors (inlcuding Alex Bateman, Sean Eddy, Paul Gardner and others) discuss the use of Wikipedia for Community Annotation of biological databases. They report:
Given our positive experiences, we can highly recommend other curation efforts turning to Wikipedia for their annotation
I am not sure how I missed this paper when it came out recently.  But it is definitely worth a look.  The last line hints at future developments
We look forward to working with the wider community to develop these new tools and techniques.
It seems that they have bought into the Wikipedia based annotation system as having enormous potential.  I generally agree though I am not sure how this is best done.   

Nice review/commentary on challenges in phylogenomic analysis in PLoS Bio by Philippe et al. #fb

This one is definitely worth a read for phylogeneticists and phylogenomicists (is that a word?) out there: PLoS Biology: Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough. Philippe et al. discuss some important issues in using genomes to infer phylogenies of species in this commentary/review paper.  They discuss in particular some recent studies of animal evolution but they cover a lot of useful ground here and include a good review of terminology and some of the basic issues at play.  I am personally going to have to read it in more detail to help deal with some of the issues in our recent study of novel sequences in metagenomic data.

Richard Branson getting into microbial diversity (a little bit)

Just a quick one here. For those interested in the deep-sea and microbial diversity you might want to check out this article: Richard Branson launches Virgin Oceanic: deep-sea exploring submarines - Boing Boing. It discusses how Branson will be working with Katrina Edwards, Doug Bartlett and others to study microbial diversity in the deep sea as a component of his project to make dives in his personal submarine.

Monday, April 04, 2011

Request for #UCDavis affiliates to help Japan from Chancellor Katehi

Just got this email from the Chancellor of UC Davis Linda Katehi and thought I would share

To the UC Davis Community,

The crisis and devastation in Japan following the March 11 earthquake and tsunami continue, and as with any natural disaster of this magnitude, healing will be neither simple nor immediate. Our thoughts and hearts are with the Japanese people and with their many loved ones who are teaching and learning on our campus and in our community.

Inevitably, the disaster will fall from the headlines, but the UC Davis community will not look away. We will continue to reach out in comfort and with assistance to honor those who are hurting and in respect for our deep connection to Japan. Nearly 200 Japanese residents are currently studying at UC Davis, and this year, we have more than 50 Japanese faculty members visiting our campus. Our students were also at five universities in Japan at the time of the disaster, including in areas with heavy damage, and we are grateful that all are safe.

There is still much to do, and you can help, too. Please see this link for a variety of charities aiding the Japanese people:

UC Davis has a compassionate spirit, and I thank you for proving that once again.

Linda P.B. Katehi

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