Category: Misc.
A tale of salt and gender: participation of women in halophile research
Interesting paper on women in science of direct relevance to my work: Frontiers | Salty sisters: The women of halophiles | Extreme Microbiology. I have been working on halophilic archaea for many years (since introduced to them in graduate school) and published papers on this topic (e.g., see The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon and Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux and more coming). However, I have never been to a meeting dedicated to the topic and confess I have not thought specifically about the gender of scientists in this field and at meetings in the field and such. Thus I was pleasantly surprised to see this analysis from Bonnie Baxter, Nina Gunde-Cimerman and Ahoren Oren. Their abstract is below:
A history of halophile research reveals the commitment of scientists to uncovering the secrets of the limits of life, in particular life in high salt concentration and under extreme osmotic pressure. During the last 40 years, halophile scientists have indeed made important contributions to extremophile research, and prior international halophiles congresses have documented both the historical and the current work. During this period of salty discoveries, female scientists, in general, have grown in number worldwide. But those who worked in the field when there were small numbers of women sometimes saw their important contributions overshadowed by their male counterparts. Recent studies suggest that modern female scientists experience gender bias in matters such as conference invitations and even representation among full professors. In the field of halophilic microbiology, what is the impact of gender bias? How has the participation of women changed over time? What do women uniquely contribute to this field? What are factors that impact current female scientists to a greater degree? This essay emphasizes the “her story” (not “history”) of halophile discovery.
As part of their paper they analyze participation of women at conference on halophiles:
This is a useful analysis and compendium and it would be great to see this done for as many fields as possible.
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Mesquite "A modular system for evolutionary analysis" v3.0 released from Team Maddison
Just found out about this on Facebook via Rod Page: Mesquite V3.0 has been released. Mesquite is from Team Maddison (Wayne and David). I have been using their software since 1987 when I took Stephen Jay Gould’s course at Harvard and they were TAs for the course demoing an early version of MacClade. Lots of nice features and it is available in Mac, Unix/Linux, and Windows versions. They describe “What Mesquite Does” on their Wikispaces site in the following way:
Mesquite is software for evolutionary biology, designed to help biologists manage and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses and management features available depend on the modules installed. Here is a brief overview of some of Mesquite’s features. See also a more complete outline of features, and the Mesquite Project Youtube channel, with instructional videos helping you learn Mesquite.
Despite Mesquite’s broad analytical capabilities, the developers of Mesquite find that we use Mesquite most often to provide a workflow of data editing, management, and processing. We will therefore begin there.
Definitely worth a look.
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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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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
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Simons Early Career Investigator in Marine Microbial Ecology and Evolution Awards (RFA)
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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
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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
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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
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A Celebration of Kevin Rice: Plant Ecology, Evolution, and Conservation Symposium: 5 September 2014
Received this by email:
Dear Colleagues
On 5 September 2014 a 1-day research symposium will take place on the UC Davis campus.
This symposium celebrates the career and research themes of Dr. Kevin Rice (retiring in 2014 from UC Davis) by highlighting innovative scientific approaches to answer fundamental questions and solve practical problems in conservation biology, restoration ecology, and invasion biology. Speakers represent diverse study systems to explore the evolutionary ecology of natural plant populations, and will present results that will inform future efforts to study adaptation and conserve native communities.
Please join us.
DATE: 5 September 2014
LOCATION: UC Davis
REGISTRATION: http://ucanr.edu/survey/survey.cfm?surveynumber=3D13084
This symposium is free of charge.
SPEAKERS
Sally Aitken
Spencer Barrett
Nancy Emery
Elizabeth Leger
Richard Mack
John McKay
Kevin Rice
Annie Schmitt
Jason Sexton
Sharon Strauss
Sonia Sultan
MORE INFO: https://sites.google.com/site/bigscience2014/home
