Tag: Moore Foundation

Gordon and Betty Moore Foundation hiring fellow for Marine Microbiology program #bioinformatics

Interesting Job Opportunity: Program Fellow, Marine Microbiology Initiative – Gordon and Betty Moore Foundation

See key details of the ad below:

The Bioinformatics Fellow position will be a 1-2 year term. 
The Program Fellow will: 
  • Contribute to developing strategy and implementation plans for the bioinformatics portfolio within the Marine Microbiology Initiative.  The fellow will prepare needs assessment for cyberinfrastruture to support research and discovery by marine microbial ecologists.  The fellow will also coordinate bioinformatics-related activities within MMI. (60% time effort)  
  • Help convene, facilitate and participate in meetings about cyberinfrastructure related to the MMI community to gather and disseminate knowledge, and produce meeting reports or white papers. (30% effort)  
  • Collaborate with MMI Program Officers on grants management related to bioinformatics and data management. (10% effort)  

Key Responsibilities  
The Program Fellow will: 
  • Help develop a strategy and the implementation plans for cyberinfrastructures related to MMI activities. 
  • Communicate with the research community, other funders, commercial vendors, and others to prepare a needs analysis for cyberinfrastructure that includes a description of ongoing or past activities and existing infrastructure. 
  • Convene meetings and workshops in cooperation with grantees and other funders as necessary. 
  • Maintain solid knowledge of the field and key emerging trends.  
  • Contribute effectively on a variety of Program- and Foundation-wide issues beyond the Initiative as required. 
Experience and Education  
The candidate will have: 
  • A Doctorate degree in environmental microbiology, bioinformatics, biology or other relevant field.   
  • Demonstrated knowledge and/or experience with computing environments and sequencing technologies.   
  • Demonstrated experience with using bioinformatics tools.   
Competencies and Attributes  
The ideal candidate also will have:  
  • Good communications skills including demonstrated writing skills.  
  • Demonstrated knowledge of the bioinformatics community and/or existing cyberinfrastructure that supports environmental science.    
  • A desire to promote and work on a complex partnership and multi-stakeholder project to achieve tangible outcomes.  
  • Ability to synthesize diverse points of view to develop solutions. 
  • Demonstrated strong teamwork and interpersonal skills, with ability to develop productive relationships with colleagues, grantees, and stakeholders. Collegial and energetic working style.   
  • Demonstrated comfort with and experience in public speaking and meeting organization/facilitation.    
  • Demonstrated ability and openness to quickly adapt and adjust strategy and approach to changing conditions. 
  • Personal motivation to support the Foundation mission and goals.   
  • Ability and interest in traveling to grantee meetings, site visits, and national/international conferences.   
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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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Amazing opportunity: California Science and Technology Policy Fellowship

This is a great opportunity for anyone who wants to mix science and technology with policy: California Science and Technology Policy Fellowship.  This Fellowship is basically a modified version of the well known AAAS Fellowships.  But it is better because, well, it is in California.  The first PhD student to finish from my lab did this a few years ago and is now working at the White House.  More information about the program is available here: PROGRAM DESCRIPTION.

To be eligible one must possess a PhD or equivalent degree or an MS in an engineering discipline plus at least three years post degree work experience.

Instructions for applying are available here.  Some FAQs about eligibility and the program are here. 

Previous Fellows are listed here:

Applications are due Feb 28, 2013.
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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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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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New openaccess paper from my lab on "Zorro" software for automated masking of sequence alignments

A new Open Access paper from my lab was just published in PLoS One: Accounting For Alignment Uncertainty in Phylogenomics. Wu M, Chatterji S, Eisen JA (2012) Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288. doi:10.1371/journal.pone.0030288

The paper describes the software “Zorro” which is used for automated “masking” of sequence alignments.  Basically, if you have a multiple sequence alignment you would like to use to infer a phylogenetic tree, in some cases it is desirable to block out regions of the alignment that are not reliable.  This blocking is called “masking.”

Masking is thought by many to be important because sequence alignments are in essence a hypothesis about the common ancestry of specific residues in different genes/proteins/regions of the genome.  This “positional homology” is not always easy to assign and for regions where positional homology is ambiguous it may be better to ignore such regions when inferring phylogenetic trees from alignments.

Historically, masking has been done by hand/eye looking for columns in a multiple sequence alignment that seem to have issues and then either eliminating those columns or giving them a lower weight and using a weighting scheme in the phylogenetic analysis.

What Zorro does is it removes much of the subjectivity of this process and generates automated masking patterns for sequence alignments.  It does this by assigning confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.

The software is available at Sourceforge: ZORRO – probabilistic masking for phylogenetics.  It was written primarily by Martin Wu (who is now a Professor at the University of Virginia) and Sourav Chatterji with a little help here and there from Aaron Darling I think.  The development of Zorro was part of my “iSEEM” project that was supported by the Gordon and Betty Moore Foundation.

In the interest of sharing, since the paper is fully open access, I am posting it here below the fold. UPDATE 2/9 – decided to remove this since it got in the way of getting to the comments …

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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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