Eisen Lab Blog

Lab meeting Dec 11th 2012

We will be having lab meeting in room 5202 of the genome center from 11 to 1pm.
Holly Bik is presenting (our scheduled guest speaker cancelled).

Gonna be a busy week!

And I don’t mean with Finals! (just kidding, finals included!)

 

But in terms of our project, they are putting water into the second coral pond on Tuesday. Then they are going to inoculate both ponds on Wednesday with the tropical reef tank sediment. At this stage it is extremely crucial that we sample frequently because microbial communities will be rapidly changing. We’ll be doing AM and PM samples all week during our study breaks. On Monday we will sample the tropical reef tank before they transfer the sediment into the coral ponds. We will also sample the incoming water for Coral Pond #2.

 

When Friday comes around, we will run into another problem. Us undergrads are going home for three weeks, which leaves David and Matt a lot of sampling and water chemistry. Fortunately, sampling only takes a few minutes and can be stored in the freezer until we all get back. Water chemistry takes a bit of time, but with the new water filters on their way the process should be quicker than it has been.

 

And when we get back we’ll only have a couple hundred DNA extractions to do… no big deal. But for now, we’ll focus on this week. Sampling + Studying! Anyone want to quiz me while I measure nitrite levels in the water?

Attention all metagenomicists: put your pinky in the corner of your mouth & say "1 million dollars"

Already posted this to Twitter and Facebook but had to post here too.  This is wild.  DTRA has announced a $1 million prize for metagenomic analysis: DTRA Algorithm Challenge | Landing Page.  From their page

The Prize:
As nth generation DNA sequencing technology moves out of the research lab and closer to the diagnostician’s desktop, the process bottleneck will quickly become information processing. The Defense Threat Reduction Agency (DTRA) and the Department of Defense are interested in averting this logjam by fostering the development of new diagnostic algorithms capable of processing sequence data rapidly in a realistic, moderate-to-low resource setting. With this goal in mind, DTRA is sponsoring an algorithm development challenge. 

The Challenge:
Given raw sequence read data from a complex diagnostic sample, what algorithm can most rapidly and accurately characterize the sample, with the least computational overhead?

My instinct is to keep this to myself because, well, I want to win.  But my sharing side of things won out and I am posting here.  Maybe we (i..e, the community) can develop an open, collaborative project to do this?  Just a thought …

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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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Get the genomes of up to 12 type strains of bacteria and/or archaea sequenced, for free

Barny Whitman asked me to post this announcement and, well, I am.  I made one edit below (see strikethrough) in honor of Norm Pace.

Genomic Sequencing of Prokaryotic Bacterial and Archaeal Type Strains

The Community Sequencing Program (CSP) Quarterly Microbial call of the DOE Joint Genomes Institute provides a great opportunity to obtain draft genomic sequences of the type strains of bacterial and archaeal species. The type strains may also include proposed species prior to publication. Type strains must be relevant to DOE mission areas, such as bioenergy, biogeochemistry, bioremediation, carbon cycling, and phylogenetic diversity. However, strains of human pathogens and human associated species are not eligible. Proposals for genome sequencing of type strains can be submitted through the CSP Quarterly Microbial call, whose deadline is December 17, 2012, with approval usually being completed within one month. Up to 12 strains can be included in each proposal. Proposals for larger numbers of strains need to be submitted to the CSP annual call in the spring. If you cannot make the December call, Quarterly calls are also scheduled for March 25, June 17, and September 23, 2013.

Proposals may be completed on-line at: http://proposals.jgi-psf.org/proposals. You will need to register and sign in to this server. Once on the server, follow the links to the “CSP Quarterly Microbial/Metagenome”. All strains will have to have been deposited in a culture collection, including proposed type strains prior to publication. If a culture collection ID is not available, you can attach a copy of the Certification of Availability. Once approved, you will need to provide 5-10 µg of high molecular weight DNA.

For questions, contact Barny Whitman, University of Georgia (whitman@uga.edu).

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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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Further signs that microbiome work is getting hot: more $$ from NIH

Just got an email about this NIH program: RFA-RM-12-021: Evaluation of Multi-omic Data in Understanding the Human Microbiomes Role in Health and Disease (U54)

Some key points

  • Up to 3$ million per year
  • 1 or 2 awards
  • U54 Specialized Center
The human microbiome is, well, hot, and there continues to be money available to work on it …
——–
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.

——–

Guest post: uBiome puts microbiome science in the hands of the people

It is a fascinating time to be doing microbiology. One of the latest occurrences is the spread of work on the human microbiome and even more recently the launching of several crowdfunding / citizen science efforts in this area. (Full disclosure – I am a collaborator on one of these efforts – the American Gut Project).  Another one of these efforts is a startup called uBiome. After seeing the announcement of their launch I asked Zac Apte, one of the founders, if he would be interested in writing a guest post for my blog on what they are doing. And, well, he agreed. And it is below (the post title “uBiome puts microbiome science in the hands of the people is from him too – I added the pic).

uBiome puts microbiome science in the hands of the people

Most people think “germs” is a dirty word. That’s what we’re taught since preschool. But the truth is that microbes aren’t just good or bad — it’s a lot more complicated than that. We are surrounded by microbes (on and inside of us) that form a complex ecosystem that supports and nourishes our health.

uBiome (www.indiegogo.com/ubiome) is a citizen science startup focused on allowing people direct access to this cutting ed research. By amassing a large set of microbiome samples along with health and lifestyle data, we will perform a microbiome-wide association study, examining specific traits as well as diseases such as diabetes, heart disease, hypertension, and depression in the context of the human microbiome.

We hope participants will join our community and track themselves in the long term — as you change your diet or exercise regime, begin taking a new medication, such as an antibiotic, or simply as you age. Now is a great time for a first data point.

Finally, we’re not just polling people for their poop. We’re also polling them for their creativity in scientific research. When our first dataset goes live, we’re going to ask our citizen scientists to form their own cohorts and we’ll empower them (statistically speaking) to test their own hypotheses. That’s our vision.

Our team has expertise in metagenomics as well as roots in population genetics, computer science, and network mathematics. We also have a team of scientific advisors which includes inventor and MacArthur Genius award winner Dr. Joseph DeRisi, biotechnology pioneer and inventor of the recombinant Hepatitis B vaccine Pablo Valenzuela, as well as doctors, bioinformaticians, and researchers.

We really appreciate Jonathan Eisen reaching out to give us this opportunity to say hello on the Tree of Life blog — and we look forward to engaging with you!

By Zac, Will and Jessica – the uBiome team

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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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Genomics Standards Consortium meeting – GSC15, Bethesda, April 22-24, 2013

The 15th Workshop of the Genomic Standards Consortium (GSC15)

April
22-24, 2013, Bethesda, Maryland, USA.

Registration and EasyChair abstract submission website now open.

Theme: Standards-enabled Research in Genomics
URL: http://gensc.org/gc_wiki/index.php/GSC_15

The 15th Genomic Standards Consortium (GSC15) meeting will be held at
NIH (Bethesda, Maryland) from April 22-24th. This meeting will
highlight the utilization of genome metadata standards for the
enhancement of our biological understanding of microbes, the interaction
between microbial genomes, human health and disease. GSC15 will provide
a forum for standards developers, genome and metagenome researchers and
biological database developers to discuss their research, initiate
collaborations, join GSC working groups and engage in panel
discussions. The conference will include two days of plenary talks
featuring GSC projects and community standards efforts along with a
keynote speaker, discussion of standards among a government panel and
groups discussion panel. Day 3 of GSC15 will include concurrent GSC
working groups open to GSC15 participants.

Key Dates:
October 15, 2012: Registration opens, EasyChair abstract submission opens
December 20, 2012: Deadline for submission of abstracts
January 7, 2013: Decisions released on abstract
February 15, 2013: Registration closes

Abstract Submission:
Abstract for Outreach I and II session talks and GSC15 posters may be
submitted through EasyChair
(https://www.easychair.org/conferences/?conf=gsc15).

Outreach I and II and poster topics: Standards in Genomic and
Metagenomic projects. Development, integration and research findings
related to human, model organism or environmental projects, resources,
tools or databases.

Location: Natcher Conference Center, Building 45, NIH Campus, Bethesda,
Maryland, USA

For more detailed information, please visit the GSC 15 website at
gensc.org/gc_wiki/index.php/GSC_15

Daphne Koller (Coursera, MOOCs): Dec 6 3:30 pm Kemper 1003

Forwarding this:

Daphne Koller to Visit Davis

We are pleased to announce that Daphne Koller, co-founder of Coursera, a major provider of Massive Open Online Courses (MOOCs), will be visiting the UC Davis campus on Thursday, December 6 to deliver a lecture on this exciting new development in online learning. Please join us to learn more about the MOOC movement.

The Online Revolution: Education for Everyone
Thursday, December 6
3:30 – 4:30 pm
Kemper Hall 1003

Abstract: We are at the cusp of a major transformation in higher education. In the past year, we have seen the advent of MOOCs – massively open online classes (MOOCs) – top-quality courses from the best universities offered for free. These courses exploit technology to provide a real course experience to students, including video content, interactive exercises with meaningful feedback, using both auto-grading and peer-grading, and rich peer-to-peer interaction around the course materials. At Coursera, as of November 2012, we offer 207 courses from our 33 university partners, and over 1.9 million students from 196 countries. The courses start from bridge/gateway courses all the way through graduate courses, and span a range of topics including computer science, business, medicine, science, humanities, social sciences, and more. In this talk, I’ll report on this far-reaching experiment in education, and why we believe this model can provide both an improved classroom experience for our on-campus students, via a flipped classroom model, as well as a meaningful learning experience for the millions of students around the world who would otherwise never have access to education of this quality.

Daphne Koller
Professor of Computer Science, Stanford University; Co-Founder and co-CEO, Coursera

Daphne Koller is a Professor of Computer Science at Stanford University and the co-founder of Coursera, a social entrepreneurship company that works with top universities to make the best education freely accessible to everyone. In her research life, Koller works in the area of machine learning. She has received the Presidential Early Career Award for Scientists and Engineers, the MacArthur Foundation Fellowship, the ACM/ Infosys award, and membership in the National Academy of Engineering. She is an award-winning teacher who pioneered many of the ideas that underlie the Coursera user experience. She received her BSc and MSc from the Hebrew University of Jerusalem, and her PhD from Stanford in 1994.

Continuing with the sampling and water chemistry of the new coral pond

They’re going to add old sand, rocks, and animals from old reef tank next week, which will be crucial in our succession study. Fortunately (not!) next week is finals week for us undergrads. So basically our study breaks will consist of Sampling and water chemistry! 😛

 

Then over break David and Matt will get to have all the fun while the rest of us go home. But when we come back there will be so many DNA extractions to do I won’t even know where to start.

 

Today I did some DNA extractions from Day 1 and 2’s sediment samples of the new Coral Pond.

People not Projects: the Moore Foundation continues to revolutionize marine microbiology w/ its Investigator program

People not Projects.

It is such a simple concept.  But it is so powerful.  I first became aware of this idea as it relates to funding scientific research in regard to the Howard Hughes Medical Institute’s Investigator program.  Their approach (along with a decent chunk of money) has helped revolutionize biomedical science.  And thus I was personally thrilled to see the introduction of this concept in the area of Marine Microbiology a few years back with the Gordon and Betty Moore Foundation’s “Marine Microbiology Initiative Investigator” program.  Launched in 2004 it helped revolutionize marine microbiology studies in the same way HHMI’s investigator program revolutionized biomedical studies.

The first GBMF MMI Investigator program ran from 2004 -2012. And the people supported were pretty darn special:

Now I am I suppose a little biased in this because at the same time GBMF launched this program they also put a bunch of money into the general area of Marine Microbiology and I have been the recipient of some of that money.  For example, I got a small amount of money as part of the GBMF Funded work at the J. Craig Venter Institute on the Sargasso Sea and Global Ocean Sampling metagenomic sequencing projects and also had a subcontract from UCSD/JCVI to do some work as part of the “CAMERA” metagenomic database project.  I ended up being a coauthor on a diverse collection of papers associated with these projects including Sargasso metagenome and this review, and GOS1, GOS2 and my stalking the 4th domain paper.

I am also a bit biased in that I have worked with many of the people on the initial MMI Investigator list some before, some after the awards including papers with Jen Martiny, Ed Delong, Alex Worden and Ginger Armbrust, and Mary Ann Moran.

But perhaps most relevant in terms of possible bias towards the Gordon and Betty Moore Foundation is that in 2007 my lab received funds through the MMI program for a collaborative project with Jessica Green and Katie Pollard for our “iSEEM” project on “Integrating Statistical, Ecological and Evolutionary analyses of Metagenomic Data” (see http://iseem.org) which was one of the most successful collaborations in which I have ever been involved.  This project produced something like a dozen papers and many major new developments in analyses of metagenomic data including 16S copy correction, sifting families, microbeDB, PD of metagenomes, WATERs, BioTorrents, AMPHORA. and STAP.  This project just ended but Katie Pollard and I just got additional funds from GBMF to continue related work.

So sure – I am biased.  But the program is simply great.  In the eight years since the initial grants the Gordon and Betty Moore Foundation has helped revolutionize marine microbiology.  And a lot of this came from the Investigator program and it’s emphasis on people not projects.  I note – the Moore Foundation has clearly decided that this “people not projects” concept is a good one.  A few years ago they partnered with HHMI to launch a Plant Sciences Investigator Program  which I wrote about here.

It was thus with great excitement that I saw the call for applications for the second round of the MMI Investigator program.  I certainly pondered applying.  But for many reasons I decided not to.  And today the winners of this competition have been announced and, well, it is an very impressive crew:

Some of the same crowd as the previous round.  Some new people.  Some people not there from the previous round.  All of them are rock stars in their areas especially if one takes into account how senior they are (the more junior people are stars in development).  And all have done groundbreaking work in various areas relating to marine microbiology.  The organisms covered here run the gamut including viruses, bacteria, archaea, and microbial eukaryotes.  The areas of focus covered range from biogeochemistry to ecosystem modeling with everything in between.  It really is an impressive group. Delong pioneered metagenomics and helped launch studies of uncultured microbes in the oceans.  Karl has led the Hawaii Ocean Time series and done other brilliant work.  Sullivan and Rohwer and pushing the frontiers of viral studies in the oceans.  Allen, Armbrust, and Worden are among the leaders in genomic studies of microbial eukaryotes in the marine environment.   Dubilier, Bidle, Fuhrman and Follows Stocker (double listed Follows in original post …) – though they focus on very different aspects of marine microbes – are helping lead the charge in understanding interactions across the domains of life in the marine environment.  Orphan, Saito, Deutsch, Follows and Pearson are on the cutting edge of biogeochemical studies and trying to link experimental studies of microbes to biogeochemistry of oceans.

The great thing about the “people not projects” concept is that the people funded here get to follow their own path.  They are not going to be constrained by the complications and sometime idiocy of the grant review process.  They in essence get to do whatever they want.  Freedom to follow their noses.  Or their guts.  Or whatever.  It is a refreshing concept and as mentioned above has been revolutionary in various areas of science.  There has been a slow but steady spread of the “people not projects” concept to various federal agencies too but it seems to be more of a private foundation type of strategy.  Federal Agencies are so risk averse in funding that this type of concept does not work well there.  I wish there was more.  But I am at least thankful for what HHMI and GBMF and Wellcome and Sloan and other private groups are doing in this regard.  Now – sure – all of these private foundations do not do everything perfectly.  They have blunders here and there like everyone else.  But without a doubt I think we need more of the People not Projects concept.
Oh – and another good thing.  GBMF is quite a big supporter of Open Science in it’s various guises.  So one can expect much of the data, software, and papers from their funding to be widely and openly available.   
It is a grand time to be doing microbiology largely due to revolutions in technology and also to changes in the way we view microbes on the planet.  It is an even grander time to be doing marine microbiology due to the dedication of the Gordon and Betty Moore Foundation to this important topic.  
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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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