Wednesday, October 30, 2013

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.

Thursday, October 24, 2013

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.

Tuesday, October 22, 2013

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

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

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

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.


Friday, October 18, 2013

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.

Tuesday, October 15, 2013

Spammy journal invite of the day: Journal of Immunology & Clinical Research!


I like sharing these SPAMMY journal invites on my blog so that when people google the name of the journal they might end up here.  Here is the latest invite I have gotten:

Dear Dr. Jonathan Eisen,Greetings from Journal of Immunology & Clinical Research!It is our privilege to invite you, in view of your scientific reputation and trustworthiness in your field, we would like to invite you to submit your valuable Research/Review/ Short communication/Perspective on your research area for publication in our upcoming issue.We have gone your latest quality research with work “ ”Journal of Immunology & Clinical Research is ardent to promote erudite, pragmatic, and contemporaneous research in the fields of Immunology & Clinical Research through open Access platform. This open access journal facilitates rapid publication with unlimited dissemination of knowledge to readers.As you are an eminent researcher we request you to support us.If you are interested, kindly let us know your possible date of submission.Anticipating your kind positive response, please revert promptly.Sincerely,
Thanks & Regards

Saturday, October 12, 2013

All figures from all my papers

Made a collection of all the figures from all the papers on which I am an author (well all of the papers that are not genome report papers (e.g., papers in the SIGS journal - going to take some time to add those since I am an author on 150+ ..). Thought it would be fun to share this slideshow - in temporal order ...

Friday, October 11, 2013

Giving thanks ... Acknowledgements cannot be said / posted enough ...

Got reminded on Twitter today about the Acknowledgements in my PhD thesis.








I think Acknowledgements are a very undervalued part of science and I always have tried to spend serious effort remembering and thanking people who contributed to my work.  Science is not done in isolation and so many people play a role in each piece of work - and they deserve to be recognized and thanked if they helped in any way.

Thursday, October 10, 2013

Victoria Schlesinger in Al Jazeera America on Open Data Pros and Cons

Got interviewed last week by Victoria Schlesinger about open science and open data issues and she has now posted her article: Scientists threatened by demands to share data | Al Jazeera America.  The article includes a discussion primarily about the push for more open release of data (and also a bit about papers) and some of the challenges associated with this push.  There are some good quotes in the article both from Schlesinger's text and from some key players in the field of data access including:

  • Christopher Lortie:  “There will be fantastic discoveries, and that’s all that really matters,” says Lortie.
  • From Schlesigner (a quote I do not agree with all of but some may like the metaphor): Sharing the results of scientific research is a bit like unveiling a newly built house, and scientists generally want it widely viewed, so the growth in open access publishing is a boon for most. Sharing data, on the other hand, is comparable to handing over the architectural plans and building materials used to construct the house. Others can scrutinize the quality of work and reuse the basic components to build their own house. That raises fears about discovery of errors and theft of future research ideas.
  • Heather Piwowar: “I think the public thinks that we’re all learning from everyone else’s work. That’s not true, and furthermore, it’s not true in ways that are even worse than you might think,” says Piwowar=
  • Me: “People are busy,” says Jonathan Eisen, a genetics professor at the University of California, Davis. “Everyone is overwhelmed with life and email and, in academia, trying to get funding and write papers. Whether something is open or not open is not highest on the priority list. There’s still need for making people aware of open science issues and making it easy for them to participate if they want to.”
  • Titus Brown: “My general attitude about open science is that I’d much rather be relevant. In science, that’s harder than anything else,” says Titus Brown, an assistant professor at Michigan State University who runs a genomics, evolution and development lab and practices open science. “If I make my work available, I have a higher chance of being relevant.” 
  • It has transformed the way we do science across biological scales, from the molecular all the way up to studying whole ecosystems,” says Carl Boettiger, a postdoctoral student at UC Santa Cruz. “The value is in enabling science to progress faster.”
The article is worth a look ...

Rob Desalle Talk at UC Davis - Storification of Twitter Notes

Wednesday, October 09, 2013

Sunday, October 06, 2013

It may have been a flawed #OpenAccess "Sting" but WE ROCKED IT so submit to our journal ...

I suppose I knew this was coming ... but did not expect it so soon ... see the email I received below.  Focus in particular on the part highlighted in yellow .... 

Dear Colleague, 
British Biotechnology Journal (BBJ) is an OPEN peer-reviewed, OPEN access, INTERNATIONAL journal, inspired from the great OPEN Access Movement. We offer both Online publication as well as Reprints (Hard copy) options. Article Processing Charge is only 50 US$ as per present offer. This journal is at present publishing Volume 4 (i.e. Fourth year of operation). 
2. Transparent and High standard Peer review:
In order to maintain highest level of transparency and high standard of review, this journal presently follows highly respected and toughest Advanced OPEN peer-review system(Example Link1, Link2, Link3, Link4, Link5, Link6, Link7, Link8, Link9, Link10,Link11, etc). We hope that you will appreciate this Advanced OPEN peer-review system, which is expected to give doubtless scholarly benefit and impact to the authors in long run. Additionally we strongly encourage and promote “Post-publication Peer review” by ourcomment section. 
As per a recent report (Link) of Science journal (present Impact factor 31), one of our journal passed a stringent test of quality of Peer review by rejecting a fake article (Link1,Link2, Link3). We applaud the dedication and hard-work of our peer reviewers and editors to maintain the high standard of our journals. It was reported that only few journals (20), out of total 304 journals tested, rejected the fake article after substantial peer review. We are happy that our journal was among these few successful journals along with industry leaders like PLoS One, Hindawi, etc. We believe that the result of this experiment also proved the efficacy of our Advanced OPEN peer review and ‘post publication’ peer review system. Though the report is debated, as it did not include subscription journals, we normally support any effort to improve the quality and transparency of peer review. 
3. Proposed Time Schedule:
Submission to first editorial decision with review comments: 3 weeks
Submission to publication: 6 weeks
State-of-the-art ‘running issue’ concept gives authors the benefit of 'Zero Waiting Time' for the officially accepted manuscripts to be published.
4. Abstracting/indexing:
Many respected abstracting/indexing services covered our journals.

Saturday, October 05, 2013

Love these QTL experiment where microbe relative abundance is the quantitative trait being studied

Just got pointed to this very interesting paper by one of the authors: Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering : Nature Communications : Nature Publishing Group.  I really really love this new approach of doing QTL experiments where the quantitative trait being measured is the relative abundance of various microbes.  The first paper of this kind I know of that did such a QTL analysis was Benson et al. 2010 in PNAS in mouse.  There have been a few others using this approach (e.g., Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits) and I am sure we will see many many more.  Basically this approach allows one to identify genes / polymorphisms / regions of the genome in a host that influence the relative abundance of specific microbes.  And such information will be critical in understanding the interactions of microbial communities with hosts.

Friday, October 04, 2013

Who are the microbes in your neighborhood? Quite a few are from Melainabacteria - a new phylum sister to Cyanobacteria

I just love this paper ... The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria | eLife from the labs of Ruth Ley and Jill Banfield (1st author is the co-first authors are Sara C. Di Rienzi and Itai Sharon).  It represents a landmark study in something that has intrigued many microbial diversity / human microbiome researchers for many years.  Early in the history of sequencing rRNA genes from human microbiome samples, researchers discovered something a bit weird - quite a few sequences were coming from what appeared to be close relatives of Cyanobacteria.  This was weird because all known Cyanobacteria were thought to be photosynthetic and - well - there is not too much light in the human gut.

Now - one possible explanation for this was that these sequences were coming from photosynthetic bacteria but these bacteria were not residents of the human gut but came via consumable items (i.e., food and drink).  Perhaps they were actually from chloroplasts of something in the diet (after all - chloroplasts are derived versions of cyanobacteria). This idea was discussed at many meetings I attended.  But there was no evidence for this.  Another possibility was that there was in fact some light in the human gut - leaking through from the outside or being produced from the inside. And perhaps this was enough to do a little photosynthesis.  Sound crazy?  Well, not so crazy after reports of photosynthesis in the deep sea.  A third possibility was that these sequences were coming from residents of the human gut that were related to (or even within) cyanobacteria but were not photosynthetic.  More detail on possible explanations are in this new paper and in some of the material cited therein.

Anyway - Ruth Ley has been discussing these unusual sequences for years and now in this paper her group and the group of Jill Banfield at Berkeley (along with some others) has used metagenomics and detailed assembly and phylogenetic analysis to reveal many new insights into these sequences.  I could write much more about this.  But, I think the paper really speaks for itself.  And it is open access so anyone and everyone can check it out.  And you should.  It is wonderful.
Fig 2 from Di Rienzi et al.

UPDATED 10/9/2013 to correct that there were co-first authors