Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Twitter chatter / links of interest: October 2013

Well, I post to Twitter a lot of links to stories of possible interest to readers of this blog.  If you want to keep up with all of this chatter and discussion from me and others, you should probably hang out on Twitter a bit.  But I know that is not for all.  So I am going to try to start posting some of the more relevant links here.

//storify.com/phylogenomics/links-of-interest-october-2013/embed//storify.com/phylogenomics/links-of-interest-october-2013.js[View the story “Links of interest October 2013” on Storify]
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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: I never meta data I didn’t like – especially re: standards for the built environment #IndoorMicro

New paper out from the microbiology of the built environment community: MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. The joint first authors are Elizabeth Glass and Yekaterina Dribinsky. And the senior author is Lynn Schriml.

The paper is simple but I think very important – it describes the development of what is a “suggested list of parameters to record and report for each sequenced sample and to compare data across studies”. Or, in other words, it is a recommended list of metadata to collect and record about samples from the built environment that are being sequenced. If you are interested in microbial diversity and/or the indoor/built environment, this is worth a look.

Oh, and, full disclosure, I am an author too.

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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 Graduate Student Child Care Grant for all Graduate Students

Forwarding this:.

Dear Colleagues,

We are pleased that beginning this Fall, the childcare reimbursement available to Academic Student Employees (ASEs: TA, Reader, AI, Tutor) will be available to all graduate students. However, there are changes to the process. To minimize confusion and simplify the process for student parents, administration of programs providing financial assistance for childcare expenses have been consolidated to one access point under the campus WorkLife program.

The new program, Graduate Student Child Care Grant (GSCCG), is available to all graduate and professional students, (excluding those students in self-supporting degree programs). Every graduate student parent with a child up to 12 years of age will be eligible to receive up to $600 per quarter, to offset child care expenses; funding of child care for additional children may be available under other need-based programs also administered by WorkLife.

The GSCCG replaces the ASE Childcare Reimbursement Program and starting Fall quarter, students now apply for the funding directly through WorkLife. However, if an ASE has child care expenses incurred during Summer quarter 2013, they should be reimbursed through their hiring unit, as it was done previously.

Attached here is a flyer about the program and how students should apply. Please forward to students in your program. All questions should be directed to WorkLife. http://www.hr.ucdavis.edu/worklife-wellness/uc-davis-child-care-subsidy

GSCCG Flyer.pdf

RIP Monica Riley of MBL, one of the true greats of E. coli biology, genetics & genomics

Just got this from Guy Plunkett III

 The E. coli annotation community lost a founding member when Monica Riley died from heart failure on October 11, 2013 in Richmond, CA. She was 87 years old. Monica will be missed by very many of us. There has not been any announcement that I can find, but I have some information from Gretta Serres at the Marine Biological Laboratory in Woods Hole, who is preparing an obituary for Microbe (the ASM newsletter). In lieu of flowers donations can be made to the Alumnae Association of Smith College. Nothing specific has been set up yet, but donations can be made in memory of Monica Riley, class of 1947, at <https://www.smith.edu/future/giving/giftform.php>.

Very sad.  Monica was an incredible woman.  I interacted with her on and off for the last twenty or so years and she played prominent roles much of my earlier work.  Among her many achievements she was central to the annotation of the E. coli genome and in keeping track of all the studies that had been done on various E. coli genes.  See for example http://nar.oxfordjournals.org/content/34/1/1.short.  Perhaps most important, she was just a wonderful wonderful person.  I will miss her.

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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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Interview of me and my brother (@mbeisen) regarding history of #PLOSBiology …

Interview of me and my brother regarding the history of PLOS Biology …

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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.

——–

Ideas wanted for workshop on the "Future of Academic Publishing and Careers"

UPDATE – the Workshop will be February 13-14 at UC Davis.  More information coming soon.

So – I am involved in this really cool new project at UC Davis on the “Innovation in Scholarly Communication” which is a collaboration between myself, Mario Biagioli from the UC Davis Law School and Mackenzie Smith, the Head Librarian at CU Davis  Anyway – much much more on the whole project later.  Right now I am writing to, well, be open.  And to ask for input.  You see, as part of our project we are going to be hosting a workshop at UC Davis in February 2014 on the Future of Scholarly Publishing where we hope to discuss two major issues – how scholarly publishing is changing (Day 1) and then how researchers are evaluated (given jobs, tenure, promotions, etc) in the context of the changing landscape of publishing.  More will be coming shortly on the details of the workshop (i.e., days, registration, etc).

Yesterday I posted a request on Twitter for ideas about Day 1 of the meeting.  I created a Storify post with the responses, which were diverse and very interesting and very helpful.  The Storify is embedded at the bottom. .

Among the major categories of ideas suggested:

  • Differences …
    • Between fields of science
    • Between science vs. humanities
    • Between types of professions (e.g., tenure track vs. AltAc)
  • New forms of papers
    • The living paper
    • Executable papers
    • Git pull
    • Web read views of content
    • Beyond JATS
    • Hypertextual book
    • Enhanced visuals, interactives, animations, 
    • Micropublication / accumulation of micro pubs
    • Nanopublications
    • Breaking the journal vs. monograph dichotomy
    • Interactive visualizations
    • Blurring of lines between blogs and papers
  • Beyond manuscripts
    • Data publishing
      • data curation and archiving
      • data papers
    • Code: 
      • publishing
      • openness
      • reproducibility
      • review
    • Full integration with research / scholarly workflow and notebooks
  • Mechanism of publishing
    • Uniform standards and styles (e.g., citation)
    • Semantic citations
    • Better authoring tools
    • Versioning
    • Better tools to connect small publishers
  • Peer review changes
    • Open, non anonymous peer review
    • Post publication review
    • Technical merit review
    • Adoption of the reviewers oath
    • Preprint deposition
    • Journal independent review
  • Changing face of the journal and where material is published
    • Role of societies in publishing
    • Journals s collections of preprints
    • Spread of open access spam
    • Preprints and repositories
  • Distribution
    • Getting scholarly research to the reader
    • Getting research to the public
    • Mobile computing
  • Privacy issues esp. in clinical data
  • Assessment and credit
    • Alt metrics
    • Giving and getting credit
    • Finding and sharing best practices for assessment
  • Using published material
    • Text mining
    • Figure/Image mining
  • Social media
    • New forms of papers
    • Assessment and alt metrics
  • Reproducibility
    • Publishing all methods, data, code, 
    • Making everything open

//storify.com/phylogenomics/request-for-ideas-topics-on-the-future-of-scholarl/embed//storify.com/phylogenomics/request-for-ideas-topics-on-the-future-of-scholarl.js[View the story “Request for ideas / topics on the future of scholarly publishing” on Storify]

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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.

——–

UCDavis ADVANCE Reading of the Day: How not to run a women in science campaign

Interesting article in The Guardian the other day that is worth taking a look at: How not to run a women in science campaign | Science | theguardian.com.  It is by Alice Bell and discusses, among many things, the European Commission video from last year on “Science: It’s a Girl Thing” (shown below) that sparked a lot of controversy.  The article also discusses many issues of relevance of improving the representation of women and minorities in the sciences including: the leaky pipe, the whiteness of science, and social mobility.  It is definitely worth a read for anyone interested in issues relating to women in science and minorities in science.

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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.

——–

Some great post doc opportunities at UC Davis

See these posts for more detail:

Another great post doc opportunity at #UCDavis
Great opportunity: Postdoc Fellowship at #UCDavis in Population Biology

And if you want to apply and want more information contact the people in the ads or me or comment here.  And furthermore if you are thinking of applying and want to work with me … well … definitely let me know.

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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.

——–

Another great post doc opportunity at #UCDavis

New Biology Postdoctoral Fellowships

College of Biological Sciences

UC Davis

The College of Biological Science at UC Davis announces the New Biology Postdoctoral Fellowship program that will bring outstanding young researchers to campus to conduct highly integrative research addressing major societal challenges. Fellows will have a home in a sponsoring CBS laboratory and will conduct research that leverages the tools and approaches represented by at least one additional laboratory at UC Davis.

A 2011 report by the National Research Council champions the power of deep integration of traditionally distinct research approaches and methods. The essence of the New Biology, as defined by this report, is integration – re-integration of the many sub-disciplines of biology, and the integration into biology of physicists, chemists, computer scientists, engineers, and mathematicians to create a research community with the capacity to tackle a broad range of scientific and societal problems.

Application: Interested early career individuals should establish communications with at least one host laboratory in the UC Davis College of Biological Sciences
(http://biosci.ucdavis.edu/the_college/index.html) and a second bridge laboratory from throughout the UC Davis community that can be from CBS or any other campus department. Applicants should submit a cover letter that includes names and addresses of three letter writers, with their CV, statement of research accomplishments (1-2 pages) and a project summary of not more than 4 pages describing the research goals, the proposed integration of approaches, and explains how the work will lead to progress on a major societal challenge in nutrition, energy, health or the environment. Applications must be made electronically at: https://recruit.ucdavis.edu/apply/JPF00168.

Duration: Fellows are awarded a two year appointment.

Duties of the Fellow: In addition to conducting new research, the fellow would engage the community at UCD on three levels throughout the term of the fellowship:

The fellow would give a research seminar near the inception of their tenure as an introduction of themselves and their research to the life sciences community at UCD.
During the course of their tenure the fellow would offer a workshop or discussion series aimed at graduate students and others involving the transferal of new methods, tools, techniques or concepts to the UCD community. This might take the form of a focused workshop to demonstrate the utility of new analytical techniques or a more distributed discussion group that stretched over the course of fellow’s tenure. This activity will be defined in collaboration with the primary host PI and normally will take place during the second year of the postdoc.
The fellow would engage the non-academic community in some form of public outreach activity. This could be a lecture aimed at the general public, an outreach event at local schools, picnic day, etc.

Together with the development of a fellow’s research program these three activities will help prepare the fellow for the multiple demands of academic life: research, teaching, and outreach.

Salary and Research Support: Awardees will be paid a salary of $50,000 per year ($34K from CBS, $8K from the hosting department, and $4K from each of the two sponsoring faculty members plus 15.6039% for benefits and GAEL). While some research infrastructure will be supported by the host labs, to allow the scholar to pursue his or her research independent of grant funding from the host labs, a $10,000 per year research and travel budget will be provided by the college.

Selection Criteria:

Ph.D. in biological sciences or related field at the time of appointment (but not necessarily at the time of nomination, as we would want to consider very recent PhDs.)
Publication and prior research record that shows strong evidence of independent thinking and “superstar” potential
Proposed research agenda / project that capitalizes on different research strengths of the two sponsoring faculty at UC Davis.

EFFECTIVE: October 14, 2013

APPLICATION DEADLINE: January 6, 2014
NEW BIOLOGY POSTDOCTORAL FELLOWSHIP Ad Final.docx

Registration is Open for December Bioinformatics Bootcamps at #UCDavis

Forwarding this …

“Registration is now open for Bioinformatics Bootcamps in December!

We’re excited to announce our next offering of Bioinformatics Bootcamps, which will be held on the UC Davis campus December 10-13.

These focused one-day courses are perfect for the student, postdoc, faculty, or industry professional looking to get up to speed quickly on the latest technologies and techniques in bioinformatics. Students will work on their own laptops and have continued access to software and example data used in the exercises through our public Amazon Web Services virtual machine (details here). The first three bootcamps will use the Galaxy platform, and the final bootcamp will use both Galaxy and the command-line. The Alignment and Assembly bootcamps (Dec. 11th & 12th) require you to know Galaxy, so if you are unfamiliar with Galaxy, you should also take the Introduction bootcamp on Dec. 10th.

Tuesday, December 10:

Introduction to Next-Generation Sequence Analysis with Galaxy

Wednesday, December 11:

Next-Generation Sequence Alignment and Variant Discovery

Thursday, December 12:

Genome Assembly using Next-Generation Sequence Data

Friday, December 13:

Introduction to the Amazon Cloud for Galaxy and the Command-Line

Daily instruction will run from 9am until 5pm. Lunch, light breakfast, and snacks will be provided. Enrollment for each bootcamp will be capped at 24 students. Please enroll early to be assured of a seat, as these bootcamps usually fill up quickly!

More information, including full descriptions of each bootcamp can be found at https://training.bioinformatics.ucdavis.edu/bootcamps/

Pricing and Payment

The cost for each bootcamp is $200 (academic/government) or $250 (non-academic/industry). We now accept credit cards. UC Davis attendees can also charge their registration directly to a DaFis account.

Questions

If you have any questions, please don’t hesitate to contact us:

· Training email: training.ucdbio@gmail.com

· Core email: ucdbio@gmail.com

· Core main telephone line: 530-752-2698

We hope to see you in December!

– The UC Davis Bioinformatics Core Team

http://training.bioinformatics.ucdavis.edu

http://bioinformatics.ucdavis.edu/