Eisen Lab Blog

Sequence/short read archive (SRA) back from the dead

Well, in February it seemed as though the Sequence/Short Read Archive was dead (see for example, End of Sequence Read Archive (SRA) – some quick notes and Though I generally love NCBI, the Sequence/Short Read Archive (SRA) seems to have issues; what do others think?)).

But now it seems as though there has been a resurrection of sorts (I guess I should have paid attention in March). See for example: SRA Home where it is stated that
“Recently, NCBI announced that due to budget constraints, it would be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. However, NIH has since committed interim funding for SRA in its current form until October 1, 2011. In addition, NCBI has been working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next generation sequencing data after October 1, 2011.
We now plan to continue handling sequencing data associated with:
RNA-Seq, ChIP-Seq, and epigenomic data that are submitted to GEO
Genomic and Transcriptomic assemblies that are submitted to GenBank
Genomic assemblies to GenBank/WGS
16S ribosomal RNA data associated with metagenomics that are submitted to GenBank
In addition, NCBI will continue to provide access to existing SRA and Trace Archive data for the foreseeable future. NCBI is also continuing to discuss with NIH Institutes approaches for handling other next-generation sequencing data associated with specific large-scale studies.”
Well I’ll be. I guess it is back at least for now.
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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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New #UCDavis Dean of the College of Biological Sciences: James E.K. Hildreth

Just announced a few minutes ago. The new Dean of the College of Biological Sciences at UC Davis is James Hildreth from Meharry Medical College.

Some tidbits about him:
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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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Selfish DNA, symbionts and parasites – some quick links

I was at a committee meeting yesterday for a great PhD student here at UC Davis, Michael Hornsby and the topic of selfish DNA came up.  After his meeting we sat down and looked for some new papers and review papers on the topic.  I just thought it might be of value to share some of these here:

We also discussed briefly the evolution of mutualists and parasites and here are a few papers that came up:

If anyone knows of any other good recent papers or blog posts about selfish DNA or mutualists vs. parasites please post them here.  Thanks
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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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NSF requests for "conflicts of interest" lists drive me batty and seem to penalize collaborative, interdisciplinary researchers

OK, time to bitch and moan a bit.

I am working on a few proposals to the National Science Foundation where NSF asks one to include “lists of institutions, project personnel, and collaborators with Conflicts of Interest”.

Seems simple I suppose.  But not when you get down to the details.  For example I found some guidance from the NSF about this where they ask one to list coauthors, collaborators, co-editors, students, advisors, advisees, friends, relatives, and many other affiliations.

To make a very long story short.  NSF wants you to make a list of anyone who possibly should not review your grant.  And if you are involved in many large collaborative projects or teach or train a lot of students.  Well, you are screwed.  For example, if they really want me to be thorough, I would probably have to list more than 500 people.  This would include a few hundred co-authors and hundreds of collaborators (e.g., on some projects I am working on with the Joint Genome Institute there are hundreds of people involved in some way).


Why does NSF ask for this?  Apparently, to help them select reviews for grant (I note, as far as I have seen, other granting agencies do not ask for this information).  If I were to do this as thoroughly as they ask, it would probably take me 2-3 full days of work – compiling the entire list of all who I collaborate with in some way on the many large projects on which I work.  I note – they don’t just ask for a list of names.  They ask for current organizational affiliations.  I published some papers four years ago with people who I have not met and have no frigging idea where they are now.  In some cases I might be able to figure this out with google but in others it might be impossible.  Even when easy it would take many minutes of searching per person to be sure.  So with some 500 people on my list (actually, probably more) it could take many many many hours just to figure out where people are now.

Anyone heavily involved in genome sequencing would probably have a massive list to go through.  Actually anyone involved in any large scale collaborative science project would have a pretty big list.  So, in a way, NSF is punishing people who do large scale projects like this by giving us extra work to do.  If you don’t collaborate with anyone or train anyone, well, you get a free pass and have no work to do here.

Do you get the feeling I am annoyed by this?  I used to compile a relatively full list.  But I have given up making it complete.  I now do my best to list major collaborators and coauthors but even that takes a long time.  And it all seems a bit inane.  Why can’t NSF just ask reviewers to declare their conflicts like other granting agencies?

Oh, and don’t even get me started on the fact that they ask for this as an Excel spreadsheet saved in csv format.

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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’s Lurking in Your (Work) Basement

Well, sad as it may be I finally made it into the basement in the building where I have worked for five + years – the Genome and Biomedical Sciences Facility (GBSF) at UC Davis (the Genome Center is in the same building).  There, down in the basement they were having an Open House for the CMGI – the Center for Molecular and Genomic Imaging.  I knew of some of the stuff they did but had never been down to see their facility and their, well, toys.  And it was really cool.

https://picasaweb.google.com/s/c/bin/slideshow.swf

They also had a nice food spread upstairs on the first floor of our building that I discovered later.  The best part of this spread were the animal chocolates and carvings:

Anyway – just a little post here.  Oh, and they do some pretty cool science at the CMGI, including some interesting uses of CT, PET, SPECT, MRI, and more.   You just never know what you will find in the basement …

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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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A good day for the Public Library of Science and science in general: #PLoS opens up search API

Well, thanks to @yokofakun (Pierre Lindenbaum) and #gepasi (Pedro Mendes) on twitter I found out about the announcement from the Public Library of Science (PLoS) yesterday that they have opened up a search application programming interface (API) to allow outside users better access to PLoS searching (see the PLoS blog: PLoS API). This is a great step for PLoS and should accelerate the ways that people access and search for content at PLoS. For more information see:

To use it you need to register for an PLoS API Key (I just got one, not that I will use it, but was just checking …). 
Looking forward to seeing what people do with this.
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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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Crosspost from microBEnet: Where is metagenomic analysis heading? Hopefully in directions suggested in this paper.

Figure 3 from Raes et al. Molecular Systems Biology 7 #473  doi:10.1038/msb.2011.6 

Just a quick post here.  I have been reading this paper: Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data by Jeroen Raes et al. in Molecular Systems Biology.  This integration they try to pull off in the paper is to me where we need to move as a field (i.e., microbial ecology) in order to make full use of metagenomic data.  The paper provides a nice overview of microbial biogeography too.  Definitely worth a read.

Am crossposting this from the microBEnet blog (microBEnet is the site for the microbiology of the built environment network that I am building):

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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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Microbiology for the public – Science at the Lesher in Walnut Creek Sponsored by DOE-JGI

Well, a month or so ago I asked people for help in planning a talk on microbes to a non sciency crowd.  I got some good suggestions and, well, I think it ended up OK.  The talk I gave was part of the JGI Science @ the Theater series in Walnut Creek.  The topic was “The Deal with Carbon: How the Earth’s Mighty Microbes Respond”  and my job was to introduce microbes to set up talks by Rachel Mackelprang (on permafrost melting) and Berkeley Lab’s Terry Hazen (on microbes and the gulf oil spill).  In the beginning, JGI debuted a short video about the carbon cycle and the Berkeley Lab Carbon Cycle 2.0 initiative, created in collaboration with Illumina Visual in Emeryville.

The best part of the whole thing was meeting John Fowler from KTVU TV.  He was great.  I have a ten minute chat with him before the talks started and he inspired and impressed me with his interest in both science and science communication (see his “Side Effects” blog here and his twitter feed here).  Another good part of this event was I got to meet Terry Hazen.  We have seen each other before at conferences but never really talked.  He is doing some very interesting work on bacteria and oil spills (see the video).  I note, I am not completely convinced by his conclusions regarding microbes being “primed” to degrade/eat the oil that was spilled into the gulf but his work is still fascinating and comprehensive.  I note – it is not just that he does interesting work.  I published a paper a few years ago with his daughter Tracy Hazen on plasmids from marine sediments and I always wanted to meet her dad.

Another good thing about the night was that some of my wife’s family came to the event.  That was inspiring in a way and kind of fun.  I think that was the first time they had seen me give a talk.

Anyway – I hope people like the talk I gave – it was my first real introduction to microbes and molecular studies of microbes to a non science audience.  So forgive me for some of the mistakes in there.

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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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Mina Bissell, another of my science heroes, returns to #UCDavis

Well, one of my favorite people Mina Bissell is coming to talk at UC Davis tomorrow “The Microenvironment and the Genome: How Do Tissue Architecture and Extracellular Matrix Inform Breast Cancer Therapy”. I first met Mina through my activities in something called the Defense Science Studies Group (DSSG) which I was a member of in 2004-2005.  DSSG was an amazing program that introduced me (and others) to the various science activities going on in the defense, intelligence, security and related agencies of the US Government.  I wish I had had a blog during much of this because it would have been fun to write about it (well, the parts that were not classified of course).  Among the amazing things in that program, I got to meet Mina Bissell who was one of the program advisors.  What an incredible woman.  See her lab page here: Bissell Lab and more about her on Wikipedia Mina Bissell – Wikipedia, the free encyclopedia or here in a New York Times article by Gina Kolata Forty Years’ War – Old Ideas Spur New Approaches in Cancer Fight .  Mina became a bit of an advisor to me when I was looking to move to California many years ago and every interaction with her is always rewarding.  So I am really looking forward to her coming to UC Davis tomorrow.  Hopefully I will not screw up like I did the last time she was here (see The Tree of Life: A eureka moment – but not of the good kind).

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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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Updated Again: Compilation of articles, news, blogs about the "arsenic bacteria" NASA study

Lots of new stuff on the arsenic-bacteria front.  For those interested I am compiling some of the more useful links here:

News stories:

Blogs:
  • A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
    • Felisa Wolfe-Simon, 
    • Jodi Switzer Blum, 
    • Thomas R. Kulp, 
    • Gwyneth W. Gordon, 
    • Shelley E. Hoeft,
    • Jennifer Pett-Ridge, 
    • John F. Stolz, 
    • Samuel M. Webb, 
    • Peter K. Weber, 
    • Paul C. W. Davies,
    • Ariel D. Anbar, 
    • and Ronald S. Oremland

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • James B. Cotner and

          •  

        • Edward K. Hall

        Science 27 May 2011: 1201943Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Rosemary J. Redfield

        Science 27 May 2011: 1201482Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • B. Schoepp-Cothenet, 
        • W. Nitschke, 
        • L. M. Barge, 
        • A. Ponce, 
        • M. J. Russell, 
        • and A. I. Tsapin

        Science 27 May 2011: 1201438Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • István Csabai and

          •  

        • Eörs Szathmáry

        Science 27 May 2011: 1201399Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Stefan Oehler

        Science 27 May 2011: 1201381Published online 27 May 2011

      • Editor’s Note

        • Bruce Alberts

        Science 27 May 2011: 1208877Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • David W. Borhani

        Science 27 May 2011: 1201255Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Steven A. Benner

        Science 27 May 2011: 1201304Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Patricia L. Foster

        Science 27 May 2011: 1201551Published online 27 May 2011

      • A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus

        • Felisa Wolfe-Simon, 
        • Jodi Switzer Blum, 
        • Thomas R. Kulp, 
        • Gwyneth W. Gordon, 
        • Shelley E. Hoeft,
        • Jennifer Pett-Ridge, 
        • John F. Stolz, 
        • Samuel M. Webb, 
        • Peter K. Weber, 
        • Paul C. W. Davies,
        • Ariel D. Anbar, 
        • and Ronald S. Oremland

        Science 2 December 2010: 1197258Published online 2 December 2010

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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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