Eisen Lab Blog

NIH Announces Revised Genome Data Release Policies

Just got notified of this by the UC Davis Med. School grants administration: NOT-OD-14-124: NIH Genomic Data Sharing Policy.  Lots of interesting things in here including a summary of the comments that they received on the draft policy.

I have copied some of the more interesting and relevant bits below:

  • Sharing research data supports the NIH mission and is essential to facilitate the translation of research results into knowledge, products, and procedures that improve human health.  NIH has longstanding policies to make a broad range of research data, in addition to genomic data, publicly available in a timely manner from the research activities that it funds. 
  • The public comments have been posted on the NIH GDS website. http://gds.nih.gov/pdf/GDS_Policy_Public_Comments.PDF
  • The statement of scope remains intentionally general enough to accommodate the evolving nature of genomic technologies and the broad range of research that generates genomic data.
  • Several comments were submitted by representatives or members of tribal organizations about data access.  Tribal groups expressed concerns about the ability of DACs to represent tribal preferences in the review of requests for tribal data.
  • The GDS Policy expects that basic sequence and certain related data made available through NIH-designated data repositories and all conclusions derived from them will be freely available.  It discourages patenting of “upstream” discoveries, which are considered pre-competitive, while it encourages the patenting of “downstream” applications appropriate for intellectual property.  
  • NIH expects investigators and their institutions to provide basic plans for following this Policy in the “Genomic Data Sharing Plan” located in the Resource Sharing Plan section of funding applications and proposals.  Any resources that may be needed to support a proposed genomic data sharing plan (e.g., preparation of data for submission) should be included in the project’s budget. 
  • Large-scale non-human genomic data, including data from microbes, microbiomes, and model organisms, as well as relevant associated data (e.g., phenotype and exposure data), are to be shared in a timely manner. 
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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.

——–

Kudos to Dr. Roizen’s Personalized, Preventive, & Integrative Medicine "Focus on Women’s Health" Conference #NoMoreYAMMMs

Quick post here as I have a bit of a cold.  I post a lot of critiques here about meetings that have bad gender ratios for the speakers.  But I do focus on the negative and am trying to also call attention to the good cases.  Well here is one: the 12th Annual Dr. Roizen’s Personalized, Preventive, and Integrative Medicine Conference with a focus on Women’s Health.  And unlike the recent Ovarian Club meeting (see No Ovaries? Well this Ovarian Club Conference is For You (YAMMMs for everyone)) which had few female speakers despite the topic, Dr. Roizen and the other organizers (including one of my favorite colleagues Rosane Oliveira) did a great job.  The gender ratio of organizers, moderators and speakers all looks good (see images below).  Kudos to all involved.

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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.

——–

Could be interesting: @jennomics “Biogeography of microbial communities associated with seagrasses”

Postdoc Seminar Series presents:

Jenna Morgan Lang

Eisen lab, Genome Center

Biogeography of microbial communities associated with seagrasses

1022 Life Sciences

12:10 pm on Tuesday 2nd September

Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards (RFA)

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28 August, 2014 • Announcement from the Simons Foundation
The Simons Foundation is now accepting applications for its Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards. The deadline for receiptof letters of intent (LOI) is October 15, 2014, 5:00 p.m. Eastern Time.

The purpose of these awards is to launch the careers of outstanding investigators who use quantitative approaches to advance our understanding of marine microbial ecology and evolution. Investigators will focus directly on marine microbes or on fundamental problems that are highly relevant to understanding marine microbial ecosystems. Applicants may currently be working in a related field, but must submit an innovative proposal for research that will advance the understanding of marine microbial ecology or evolution.

Among other eligibility requirements, applicants must have significant training in a quantitative field and have held an independent position (tenure-track or equivalent) for at least three years and no more than eight years.

•••

The Simons Foundation’s mission is to advance the frontiers of research in mathematics and the basic sciences.

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UC Davis Genome Center job: #Bioinformatics Core Manager #Genomics

You know you want this job:

The UC Davis Genome Center integrates experimental and computational approaches to address

key problems at the forefront of genomics. The Center is housed in a new research building with state-of-the-art computational and laboratory facilities. The Center comprises 23 research faculty and five technology service cores that serve the whole campus. The faculty and

service cores contribute to an internationally recognized program in genomics research at Davis, building on and enhancing the unique strengths and unmatched breadth of the life sciences on the UC Davis campus.

The Bioinformatics Service Core provides a broad range of services in computational biology and bioinformatics on a recharge basis to diverse research groups on campus. The Core is responsible for providing consulting, software and access to computational resources to address needs in all areas of bioinformatics, including data acquisition and curation, database construction and integration, sequence analysis, molecular structure and network analyses, expression profile analysis and statistics.

The Genome Center invites applications for the position of
Bioinformatics Core Manager. The incumbent will be responsible for the day-to-day running of the Bioinformatics Service Core. This includes but is not limited to management of staff and computational
infrastructure and budgetary aspects of the core. The manager will be responsible for ongoing assessment of computational needs, including staff, hardware, software and databases required to perform the multiple types of bioinformatics analyses for cutting- edge genomics research. The manager also will be responsible for recruiting and training staff, assessing the campus-wide needs for bioinformatics services and prioritizing their provision, representation of the Genome Center at scientific conferences and the writing and submission of grant proposals to maintain the core with state-of-the-art resources.

This position requires a Ph.D. or equivalent in a relevant area, such as Computer Science, Statistics, Applied Mathematics or Computational or Mathematical Biology. Applicants should have experience in the management of a production bioinformatics facility and broad technical knowledge sufficient to supervise technical staff, troubleshoot problems, acquire and maintain hardware, refine bioinformatics approaches, and advise faculty and their research groups. The position will be open until filled. Consideration of applications will begin October 1, 2014. Applicants should apply on line at
https://recruit.ucdavis.edu/apply/JPF00320

Further information about genomics and bioinformatics at UC Davis is available at http://www.genomecenter.ucdavis.edu .

The University of California is an affirmative action/equal opportunity employer
Bio Core Manager Advert 8-2014.pdf

Overselling the Microbiome Award: The Microbiome Diet Book

Well, umm, I do not know what to say: The Microbiome Diet: The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss: Raphael Kellman MD: 9780738217659: Amazon.com: Books.  I got pointed to this book by Dorothy Timmermans and she wondered if this was a case of “overselling the microbiome” or not.  I guess I don’t know because I have not read the book.  Nor will I most likely.  But I think almost certainly it is a case of “Overselling the Microbiome” based just on reading the blurb on Amazon from the Publisher which I paste below.  It contains a litany of over the top statements:

Cutting-edge science has shown that the microbiome is the secret to healthy weight loss and to feeling healthy, energized, optimistic, and at the top of your game. The microbiome is a whole inner world that lives within your intestines—trillions of tiny microbes that help you extract the nutrients from your food, balance your mood, and sharpen your clarity and focus.

These beneficial bacteria make up a separate ecology within the body and have an enormous influence on your metabolism, your hormones, your cravings—even your genes. The microbiome’s health is intimately involved with yours: when it flourishes, you flourish. When it craves sugar, so do you. When it operates at peak efficiency, so does your metabolism. And when your microbiome is out of balance, you might find yourself gaining weight or unable to lose weight, no matter how much you exercise or how carefully you eat. To achieve your ideal weight, you need the help of your microbiome.

Now, drawing from nearly two decades of experience as a specialist in functional medicine and intestinal health, Raphael Kellman, MD, has developed the first diet based upon on these scientific breakthroughs. The Microbiome Diet offers an effective three-phase plan to heal your gut, reset your metabolism, and achieve dramatic, sustainable weight loss. The Microbiome Diet will help you…

Reset your metabolism

Free yourself from food cravings and uncontrollable appetite

Incorporate prebiotics, probiotics, and healing foods into every meal

Lose weight—and keep it off—with a nonrestrictive life plan

With delicious recipes, convenient meal plans, and helpful information on Microbiome Superfoods and Supersupplements—including prebiotics and probiotics—The Microbiome Diet gives you the tools to achieve your healthy weight, boost your mood, regain your mental focus, and be in your best shape for life.

Sound too good to be true?  Well, that is because 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.

——–

The Agricultural Bioscience International Conference #ABIC2014 run by @ABICFoundation: where you can hear lots of talks by men #YAMMM

Well, here is this week’s YAMMM (yet another mostly male meeting) alert: The Agricultural Bioscience International Conference in Saskatchewan.

Male Speakers: 40
Female speakers 4

  1. Marc Albertsen
  2. Robert Carberry
  3. David Fischhoff
  4. Maurice Moloney
  5. Frédéric Seppey
  6. Juliana Alexandre
  7. Tom Carrato
  8. Michael Frodyma
  9. Carlo Montemagno
  10. Tim Sharbel
  11. Simon Barber
  12. David Chalack
  13. Richard Gray
  14. Giuseppe Natale
  15. Roman Szumski
  16. Roger Beachy
  17. Raju Datla
  18. Wayne Hunter
  19. Matthew O’Mara
  20. Albert Vandenberg
  21. Suzanne Bertrand
  22. Swapan Datta
  23. David Irvin
  24. Peter Phillips
  25. Victor Villalobos
  26. Julie Borlaug
  27. Maurice Delage
  28. Lawrence Kent
  29. Ingo Potrykus
  30. Simon Warner
  31. Jim Brandle
  32. David Dent
  33. Ganesh Kishore
  34. Andrew Potter
  35. Howard Wheater
  36. John Buchanan
  37. Claude Fauquet
  38. Robert Lamb
  39. Thomas Redick
  40. Hong-Wei Xue
  41. Derek Byerlee
  42. Nina Fedoroff
  43. Greg Meredith
  44. Andrew Reed

Who gets the credit/blame for this wonderful arrangment? 
  1. Chair, Wilf Keller, Ag-WestBio Inc.
  2. Jerome Konecsni, Innovation Saskatchewan
  3. Muriel Adams, ABIC Foundation
  4. Art Froehlich, Ad Farm
  5. Pierre Fobert, National Research Council
  6. Graham Scoles, University of Saskatchewan
  7. Peter Phillips, Johnson-Shoyama Graduate School of Public Policy
  8. Paul McCaughey, Agriculture and Agri-Food Canada
  9. Dr.Abdul Jalil, Saskatchewan Ministry of Agriculture (originally colored green)
  10. Janice Tranberg, Saskatchewan Ministry of Agriculture
This goes with another YAMMM from Canada recently: Today’s YAMMM (Yet Another Mostly Male Meeting) Brought to You by CIFAR & NAS.  I have not done any analysis of meetings organized by country but I am thinking it might be worth looking into.  I would really suggest if anyone is considering going to this meeting for you to skip it.  There should be consequences for such a skewed ratio.  And while you are at it consider writing to the organizers and sponsors.  I will …
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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.

——–

Post doc at #UCDavis USDA on metagenomics to study possible causes of a “mysterious”, rapidly emerging walnut canker disease

Postdoc RA-14-018-HR Browne DCA.pdf

Want to prevent someone from taking copyright on something- have it be made by a monkey

Well, this is both strange and surreal and fascinating: Who Owns A Monkey’s Selfie? No One Can, U.S. Says : The Two-Way : NPR.  Turns out the UC Copyright office says a photo taken by a monkey cannot by copyrighted because apparently copyright is reserved for humans (and I guess human corporations).  NPR implies that an Ars Technica article by David Kravets is what caught their attention as well as that of others.

I wonder – if one could teach a monkey to type maybe one could get them to type up some papers and then nobody could have copyright on them?  What if one wrote a paper where a monkey was a co-author but did not do all the work?  Would that mean one could not transfer copyright to anyone else?  Seems like I should / could include monkeys on all my work.

——–
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.

——–

Job Ad: Macquarie University faculty positions in Synthetic Biology and Bioinformatics & More

Got this by email:

Dear Colleagues

Macquarie University is currently advertising several faculty positions in synthetic biology, bioinformatics and microbiology, if you know anyone who would be interested please encourage them to apply. The advertised positions consist of:
– 3 lvl B/C continuing faculty positions (2 in Synthetic Biology and 1 in Bioinformatics)-
http://jobs.mq.edu.au/cw/en/job/494553/lecturersenior-lecturer-level-bc-in-synthetic-biology-research-fellow-level-b-in-synthetic-biology-lecturersenior-lecturer-level-bc-in-bioinformatics – 1 lvl B continuing faculty position in Microbiology-
http://jobs.mq.edu.au/cw/en/job/494581/lecturer-in-microbiology

Lvl B/C faculty positions would approximately be the equivalent of Assistant Professor level in the US system, i.e., junior faculty positions

Additionally, we have two Research Fellow positions available as part of the Yeast 2.0 synthetic biology project
(http://mq.edu.au/thisweek/2014/06/02/yeast-2-0-synthetic-biology-project-launched/#.U_K54mNeJzU). We’re particularly interested in candidates with a background in yeast genetics for these 2 positions.
Please contact me if anyone has any questions.
Yours sincerely,

Ian