Category: Misc.

DOE-JGI Call for LOIs for Large-Scale Genomics Proposals due April 10, 2014

The DOE Joint Genome Institute (DOE JGI) Community Science Program (CSP) is now accepting Letters of Intent for large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in sustainable biofuel production, global carbon cycling, and biogeochemistry. Priority for this call will be given to projects that address the following areas of special emphasis and exploit the diversity of DOE JGI capabilities. The CSP data is immediately made publicly available, without exception.

A summary of the 2015 CSP Call is below. The full Call can be found here:

I. Functional Genomics and Microbiomes of DOE JGI Flagship Plants: Emphasis will be on proposals related to DOE JGI’s “flagship” plant genomes, including poplar, sorghum, Brachypodium, Chlamydomonas, soybean, foxtail millet, Physcomitrella, switchgrass, and miscanthus. These species are of special interest as biofuel feedstocks or as comparators that provide insight into feedstock evolution and phenotype. Projects may fall into the following categories:

a) Gene Atlas and ENCODE-like projects;

b) Large-scale resequencing projects;

c) Plant microbiomes.

II. Probing functional diversity of microbes: To complement its Genomic Encyclopedia of Bacteria &Archaea (GEBA) and 1000 FungalGenomes initiatives, the DOE JGI has begun to explore microbial functional diversity. Proposals are encouraged that extend this effort using high-throughput sequencing, and the DOE JGI’s DNA synthesis capabilities and are expected to use one or a combination of the DOE JGI’s (meta-) genome, (meta-) transcriptome, single-cell and isolate sequencing and resequencing pipelines. ENCODE-like projects for functional genomics that could serve as model organisms for DOE-relevant problems are encouraged and could include new DOE JGI capabilities for genome-wide transcriptomics, including non-coding and small RNAs, and epigenomics, including methylation detection and ChIP-seq.

III. Microbial emission and capture of greenhouse gases in terrestrial systems: Proposals are encouraged that will provide insight into global carbon (including methane) and nitrogen cycles, and/or suggest novel strategies for carbon capture, nitrogen processing, or methane reduction through gene/genome engineering.

IV. Discovery and expression of natural product pathways relevant to energy-related and environmental processes: The DOE JGI has developed a platform that enables the discovery of novel natural products based on technology combining computational genomics, pathway refactoring, host engineering, and high-throughput analytics.

Deadlines

Letters of intent (LOI) will only be accepted electronically and should be submitted at http://proposals.jgi-psf.org/.

· LOI due: April 10, 2014

· Full proposals invited: April 24, 2014

· Full proposals due: June 5, 2014

· Projects begin: October 2014

Questions? Contact:

Axel Visel (avisel), DOE JGI Strategic Planning-Science Lead.

"Phylogeny driven approaches to genomics and metagenomics": slides w/ audio from my talk at #UCDavis 1/29

Gave a talk here at UC Davis last week. Alas, not my best talk – too rushed. But, anyway, here is a video of the slideshow w/ audio. Title “Phylogeny driven approaches to genomics and metagenomics”

 

——–
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.

——–

Quick post – Outbreaker and the "Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data"

Interesting new paper out: PLOS Computational Biology: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data.

Full Citation:  Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, et al. (2014) Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. PLoS Comput Biol 10(1): e1003457. doi:10.1371/journal.pcbi.1003457

Abstract:

Recent years have seen progress in the development of statistically rigorous frameworks to infer outbreak transmission trees (“who infected whom”) from epidemiological and genetic data. Making use of pathogen genome sequences in such analyses remains a challenge, however, with a variety of heuristic approaches having been explored to date. We introduce a statistical method exploiting both pathogen sequences and collection dates to unravel the dynamics of densely sampled outbreaks. Our approach identifies likely transmission events and infers dates of infections, unobserved cases and separate introductions of the disease. It also proves useful for inferring numbers of secondary infections and identifying heterogeneous infectivity and super-spreaders. After testing our approach using simulations, we illustrate the method with the analysis of the beginning of the 2003 Singaporean outbreak of Severe Acute Respiratory Syndrome (SARS), providing new insights into the early stage of this epidemic. Our approach is the first tool for disease outbreak reconstruction from genetic data widely available as free software, the R package outbreaker. It is applicable to various densely sampled epidemics, and improves previous approaches by detecting unobserved and imported cases, as well as allowing multiple introductions of the pathogen. Because of its generality, we believe this method will become a tool of choice for the analysis of densely sampled disease outbreaks, and will form a rigorous framework for subsequent methodological developments.

Check out the nice figure on a SARS outbreak:

Figure 5. Results of the analysis of the SARS data using outbreaker. This figure summarizes the reconstruction of the outbreak, showing putative transmissions (arrows) amongst individuals (rows). Arrows represent ancestries with a least 5% of support in the posterior distributions, while boxes correspond to the posterior distributions of the infection dates. Arrows are annotated by number of mutations and posterior support of the ancestries, and colored by numbers of mutations, with lighter shades of grey for larger genetic distances. The actual sequence collection dates are plotted as plain black dots. Bubbles are used to represent the generation time distribution, with larger disks used for greater infectivity. Shades of blue indicate the degree of certainty for inferring the origin of different cases, as measured by the entropy of ancestries (see methods and equation 12): blue represents conclusive identification of the ancestor of the case (low entropy), while grey shades are uncertain (high entropy).

And then the consensus transmission tree

Figure 6. Consensus transmission tree reconstruction of the SARS outbreak. This figure indicates the most supported transmission tree reconstructed by outbreaker. Cases are represented by spheres colored according to their collection dates. Edges are colored according to the corresponding numbers of mutations, with lighter shades of grey for larger numbers. Edge annotations indicate numbers of mutations and frequencies of the ancestries in the posterior samples.

Outbreaker is available here: http://cran.r-project.org/web/packages/outbreaker/index.html

I also like the 1st line of their Acknowledgements:

We are thankful to Sourceforge (http://sourceforge.net/) and CRAN (http://cran.r-project.org/) for providing great resources for developing and hosting outbreaker.

Definitely worth checking out.

——–
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 Quest for a Field Guide to the Microbes: talk at "Science in the River City"

I got invited a while back to give a talk at a “Science in the River City” workshop for 3rd – 12th grade science teachers.  I proposed (and they said yes) to the idea of talking about my “Quest for A Field Guide to the Microbes.”  I recorded the screen (slides) and audio from my talk using Camtasia and have now posted the slideshow and slides.  Here they are:

Talk slideshow with Audio on Youtube:

 

 Slides on Slideshare

——–
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.

——–

Workshop at #UCDavis 3/24 From Science to Storytelling: Effective Communication for Policy Change

From Science to Storytelling: Effective Communication for Policy Change

Conveying the results of your scientific research to legislators and government agencies can help influence policy – but only if you communicate effectively! If you are motivated in part by applying your research to environmental and social issues such as climate change, this workshop will give you some useful concepts and tools. Using discussion, role plays, expert advice from media consultants and individual exercises, we will explore the challenges of translating your scientific findings to policymakers and advocates, and will offer some tools for improving your communications skills. We will focus on simplifying your messages and honing your presentations.

Invited participants:

Academic researchers working on climate change and agriculture. Registered participants may also invite one graduate student.

Organizers:

California Climate and Agriculture Network (CalCAN) and Resource Media

Date, time, location:

March 24, 1:00 – 4:00

Big Hanna Room, Asmundson Hall, UC Davis

Cost: Free

To register: Email Renata Brillinger at CalCAN (renata@calclimateag.org) with your name, department, institution and phone number. If you would like to bring one graduate student, please include their information as well. Space is limited.

Science Communication workshop 3-24-14.pdf

Using Social Media to Promote Your Research (workshop)

I’ll be running a social media workshop next Friday in the Genome Center – anyone on campus is welcome to attend! Details as follows:

Using Social Media
to Promote Your Research

Friday, February 7, 2014
12:30-2:30pm
Room 4202, Genome Center

Many view social media as either a fun distraction, a waste of time – or both!  But social media tools can be a tremendous resource for academics seeking to share their research, find new collaborations, and ultimately advance their careers.

Attend this workshop to learn how to:

  • Use social media to share and promote your research
  • Identify appropriate audiences and avoid pitfalls
  • Choose the right platforms to help you achieve your goals

Please pre-register using this online form: http://bit.ly/1ajX6Pc (Pre-registration will help to guide the format of the workshop and the type of social media tools covered)

PDF Flyer available here

Wanted – examples of ways to get DOIs for blog posts & how they are used

For many years I have been wondering about the best way to get more formal credit for blog posts I have written.  It seems like the simplest way to do this would be to get a DOI for a blog post under some sort of publishing system and to use that DOI as the citable unit for the post.  I remember a while back Titus Brown wrote about this exact idea: Posting blog entries to figshare – Living in an Ivory Basement but I have not seen much else out there on ways to do this and what the implications are.  Anyone else out there know examples of how people have gotten DOIs for blog posts and if this has been useful?  Thanks

 

 

Pete Seeger, RIP, on women in engineering …

When I was growing up, we went to Pete Seeger and Arlo Guthrie concerts every year at Wolf Trap. I have loved Seeger since then and thus was very sad to hear he died a few days ago. My mom is visiting right now and she and I have been talking about “Women in Science” issues (and for example she brought me some nice presents which I posted about Monday).

//platform.twitter.com/widgets.js And in talking to my mom today she reminded me of this song Seeger used to sing every year when we saw the show. It is by his sister. And it is a good rallying cry for “Women in STEM” fields, I think. Here it is:

——–
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.

——–

Interested in #OpenAccess publishing?: definitely take a look at this working paper from CREATe

Well, this is certainly the most comprehensive treatise I have ever seen on Open Access publishing: Open Access Publishing: A Literature Review | CREATe.  It was written by “Giancarlo Frosio under the supervision of Estelle Derclaye (2014)” and

comes from the Centre for Copyright and New Business Models in the Creative Economy (CREATe).  It is VERY comprehensive and has discussion, review, and comments on just about every issue associated with Open Access publishing that one could think of. I do not know if there is any particular “angle” to the writings here.  What I looked at (not all of the document) seemed to be a relatively objective assessment of various OA issues.  Anyway, it is definitely worth a look for anyone interested in scholarly publishing or Open Access publishing or related issues.

Sarah Kendzior @sarahkendzior on “What’s the Point of Academic Publishing?”

In the run up to our meeting on “Publish or perish? The future of academic publishing and careers February 13 – 14, 2014 at UC Davis” I am going to be writing some blog posts about the topics of the meeting.  Just as I started to do a few web searches for one such post – I discovered a very timely article published a few days ago in Vitae: What’s the Point of Academic Publishing?.  The article is by Sarah Kendzior who is a writer who I have interacted with a few times here and there (she writes for Al Jazeera English and writes a lot about Academia).  It is an interesting read.