Here are some comments from FriendFeed
Tuesday, June 30, 2009
Here are some comments from FriendFeed
Sunday, June 28, 2009
This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. As of version 1.2.0 we have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, and unifrac. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools. If you would like to contribute code to the project feel free to download the source code and make your own improvements. Alternatively, if you have an idea or a need, but lack the programming expertise, let us know and we'll add it to the queue of features we would like to add. Our current goal is to release a new iteration of the project monthly.Anyway, thanks to my student Amber Hartman for pointing this out --- I will be perusing it but thought others should too. Hopefully, we can include some of the software from my lab such as AMPHORA, STAP, etc. into their code at some point.
Subject: Application for Ph.D. studies
Hope for your best. I am working as lecturer, Department of XXXX, XXXX University, XXXX, Pakistan. I have completed my M.Phil (Biotechnology) from XXXX University XXXXX, Pakistan (Thesis title something about microbe interactions with plants). I have recently secured a fully funded scholarship for Ph.D studies (funding agency: Higher Education Commission, Islamabad, Pakistan). This scholarship includes living expenses, university fees and travel expenses etc. I wish to conduct my Ph.D studies at your esteemed university (in any area of biological sciences) . I will highly appreciate if you kindly send me an acceptance letter for Ph,.D studies under your esteemed supervision, so that I can proceed with my paper work with Higher Education commission, Islamabad. Please also find attached herewith my brief CV.
Department of XXXX
XXXX University, XXXX
Here are some comments from FriendFeed
Saturday, June 27, 2009
Another reason to publish as Open Access - libraries hurting big time financially and they will be cancelling many subscriptions
Who should have acess to publications supported by federal money? Well, everyone. See Federal Research Public Access Act
Every federal agency with an annual extramural research budget of $100 million or more will implement a public access policy that is consistent with and advances the federal purpose of the respective agency. Each agency must:
- Require each researcher – funded totally or partially by the agency – to submit an electronic copy of the final manuscript that has been accepted for publication in a peer-reviewed journal.
- Ensure that the manuscript is preserved in a stable digital repository maintained by that agency or in another suitable repository that permits free public access, interoperability, and long-term preservation. Agencies have the flexibility to choose the best suitable location for their repository.
- Require that free, online access to each taxpayer-funded manuscript be available as soon as possible, and no later than six months after the article has been published in a peer-reviewed journal.
To whom this policy applies:
- Any researcher employed by a federal agency with an annual research budget exceeding $100 million who publishes an article based on the work done for the funding agency in a peer-reviewed journal.
- Any researcher funded by a federal agency with an annual research budget exceeding $100 million who publishes an article based on the funded research in a peer-reviewed journal.
What is not covered by this legislation:
- The public access policy does not apply to laboratory notes, preliminary data analyses, author notes, phone logs, or other information used to produce the final manuscript.
- The policy does not apply to classified research. Research that results in works that generate revenue or royalties for the author (such as books), or patentable discoveries are exempt only to the extent necessary to protect copyright or a patent.
Also see below from the Congressional Record (and Hat Tip to Heather Joseph from SPARC for pointing all of this out).
From June 25 Congressional Record: By Mr. LIEBERMAN (for himself and Mr. Cornyn):
S. 1373. A bill to provide for Federal agencies to develop public access policies relating to research conducted by employees of that agency; or from funds administered by that agency to the Committee on Homeland Security and Governmental Affairs
Mr. CORNYN. Mr. President, I rise to introduce the Federal Research Public Access Act. I am very pleased to be joined again by my good friend and colleague, Senator Joe Lieberman, who has remained dedicated to seeing this important legislation passed. This bipartisan bill is the same legislation we introduced in the 109th Congress. The purpose of this legislation is to ensure American taxpayers' dollars are spent wisely, which is even more important now in this time of fiscal tension.
To put things in perspective, the Federal Government spends upwards of $55 billion on investments for basic and applied research every year. There are approximately 11 departments/agencies that are the recipients of these investments, including: the National Institutes of Health, National Science Foundation, NASA, the Department of Energy, the Department of Defense, and the Department of Agriculture. These departments/agencies then distribute the taxpayers' money to fund research which is typically conducted by outside researchers working for universities, health care systems, and other groups.
While this research is undoubtedly necessary and is beneficial to America, it remains the case that not all Americans are capable of experiencing these benefits firsthand. Usually the results of the researchers are published in academic journals. Despite the fact that the research was paid for by Americans' tax dollars, most citizens are unable to attain timely access to the wealth of information that the research provides.
Some Federal agencies, most notably the NIH, have recognized this lack of availability and have proceeded to take positive steps in the right direction by requiring that those articles based on government- funded research be easily accessible to the public in a timely manner. I am proud to report that the NIH's public access policy has been a success over the past few years. By the NIH implementing a groundbreaking public access policy, there has been strong progress in making the NIH's federally funded research available to the public, and has helped to energize this debate.
Although this has surely been an encouraging and important step forward, Senator Lieberman and I believe there is more that can and must be done, as this is just a small part of the research funded by the Federal Government.
With that in mind, Senator Lieberman and I find it necessary to reintroduce the Federal Research Public Access Act that will build on and refine the work done by the NIH and require that the Federal Government's leading underwriters of research adopt meaningful public access policies. Our legislation provides a simple and practical solution to giving the public access to the research it funds.
Our bill will ask all Federal departments and agencies that invest $100 million or more annually in research to develop a public access policy. Our goal is to have the results of all government-funded research to be disseminated and made available to the largest possible audience. By speeding access to this research, we can help promote the advancement of science, accelerate the pace of new discoveries and innovations, and improve the lives and welfare of people at home and abroad.
Each policy that these departments and agencies develop will require that articles resulting from federal funding must be presented in some publicly accessible archive within six months of publication. In doing so, the American taxpayers will have guaranteed access to the latest research, ensuring that they do not have to pay for the same research twice--first to conduct it and then again to view the results.
This simple legislation will provide our government with an opportunity to better leverage our investment in research and in turn ensure a greater return on that investment. All Americans stand to benefit from this bill, including patients diagnosed with a disease who will have the ability to use the Internet to read the latest articles in their entirety concerning their prognosis, students who will be able to find full abundant research as they further their education, or researchers who will have their findings more broadly evaluated which will lead to further discovery and innovation.
While a comprehensive competitiveness agenda is still a work-in- progress, this legislation is good step forward. Providing public access to cutting-edge scientific information is one way we can encourage public interest in these fields and help accelerate the pace of discovery and innovation. In promoting this legislation, I hope to guarantee that students, researchers, and every American can access the published results of the research they funded.
Thursday, June 25, 2009
For example, the Center for Bioinformatics and Computational Biology - at U. Maryland is hiring faculty and post docs. UC Davis is continuing searches for faculty positions that are in progress (and we have some good candidates for people for the Genome Center). In evolution, a good place to look for job positings is Evoldir on the web or on Twitter.
And very shortly I will be posting ads for some bioinformatics related positions in my group - but have not finished writing the ads. Anyway - though the financial condition of many US Universities is less than ideal, those fields with a lot of government grant support seems to be doing OK.
Tuesday, June 23, 2009
We in the biomedical research community at the University of California, Santa Cruz are writing to express serious concerns about the salary budget cuts proposed as of 6/17/09. This letter represents the concerns of technicians, graduate students, postdoctoral scholars and fellows, research specialists, and project scientists in the departments of Molecular, Cell and Developmental Biology, Microbiology and Environmental Toxicology, Chemistry, Biomolecular Engineering, and Computer Engineering. We generally fall into the category of “staff”, and thus we understand that any staff salary cuts instituted in the future will affect all of us. However, it is important to understand that nearly all of us are paid by funds that do not come from the state of California, but rather from federal grants awarded by the National Institute of Health, the National Science Foundation, and grants awarded by many other public and private agencies. In many cases, the grant has been awarded to a Principal Investigator, and then is used by the Principal Investigator to pay us for our research work. In other cases, the grants are awarded directly to us to cover the salary necessary for our scientific training. So, as the majority of our salaries are not provided by the California state budget, a mandatory salary cut for our staff will not ease the University budget crisis, while it will indeed make our day-to-day living more difficult. Other effects of a mandatory reduction of our salaries are that: 1) This will actually reduce the amount of money the University receives in indirect costs from grants. 2) This will decrease the amount of income tax we pay to the state of California, further exacerbating the existing budget crisis. 3) The depletion of the funds coming into the University of California due to these salary cuts will make it increasingly difficult for the University to support its employees. 4) Lastly, the salary cut propos al may, in the longer-term, undermine confidence in the University of California system and lead talented people to move to states that are able and willing to support higher education and scientific research.See also
In summary, we strongly urge that no salary cut be instituted for University of California-affiliated personnel like ourselves whose salary is independent from the California state budget. Below you will find our signatures along with those of our supporting staff and Principal Investigators. Sincerely, The biomedical researchers of the University of California, Santa Cruz
- Chronicle for Higher Education article
- Green Economics Blog
- Paul Thompson from UCLA wrote a letter to UC President Yudoff here
Here is a communication from UC about the furloughs:
June 18, 2009
UC Furlough/Salary Reduction Plan Options – Questions & Answers
A summary of options for systemwide furloughs/salary reductions was sent to the UC
community on June 17, 2009. Following broad consultation, President Yudof intends to present
a specific option for approval to The Regents at their July 2009 meeting. To date, no decisions
have been made as to which option will be implemented. Below are answers to questions about
the proposals. Additional information will be added throughout this process as answers to other
questions become available and as the University approaches a decision on this issue.
Are these furloughs/salary reductions intended to be permanent?
No – the intent is for these actions to be temporary or short-term in nature, to help the University
through the current budget crisis. As indicated, the proposed duration for all three options is
August 1, 2009 through July 31, 2010 unless extended by the Regents.
Will furloughs/salary cuts apply to all employees, including faculty and represented
Yes. In order to ensure equity across the University, whichever option is chosen would apply to
all faculty and staff, except student employees. The Academic Senate has been closely involved
in consultation on these options. Implementation of the final plan is subject to collective
bargaining for represented employees. The President may recommend a hybrid Plan that
achieves the eight percent reduction in slightly different ways for the various employee groups.
If my salary is not supported by state funds, will I still have to take a furlough or salary cut?
Yes – participation is not based on the source of salary funds. Each of the options would apply to
UC employees whose salaries are funded by contracts and grants, clinical income and other
auxiliary activity, and general funds.
Will the proposed reductions apply to employees at the Lawrence Berkeley National
The intent is for whatever option is selected to apply to all UC employees, including LBNL
employees. Since LBNL is funded by the Department of Energy (DOE), UC will comply with
all contractual obligations with the DOE.
W ill this be additive for the senior leaders who have already taken a five percent pay cut?
The senior UC officials who voluntarily agreed to have their salary reduced by five percent will
have their salaries reduced by a total of at least eight percent under these options.
How will the furlough/salary reduction impact vacation and sick leave accruals, UCRP service
credit and benefit calculations, and other benefits?
Under each option, the intent is to protect benefits and leave accruals to the extent possible. This
may not be possible in all situations. This issue continues to be evaluated and no final decisions
have been made yet. Approval from the Regents is required to protect UCRP benefits from being
impacted by a furlough/salary reduction plan.
I volunteered to participate in START to help the University manage the budget situation. Will
I have to take further reductions if a systemwide furlough or salary reduction is implemented?
How these options impact/relate to the START program is currently being analyzed. More
information on this issue is expected soon.
What’s the difference between the three options?
All three options are intended to achieve the same budgetary savings and have the same impact
on employee pay -- each option is closely equivalent to an eight percent pay reduction. Option I
is a straight pay reduction with no changes to work hours. Under Options II and III, employees
will be scheduled to work fewer days and a number of holidays will no longer be paid holidays.
In Options II and III, will I be able to schedule the unpaid day at a time that’s convenient for
me and my department, or will the days be pre-scheduled?
This is still being looked at. The unpaid days would include a combination of University
holidays and additional days, but the precise mix of holidays vs. additional days has not been
determined. The additional days may be pre-scheduled by the University in order to manage
critical operations, for example to ensure patient care at a medical center.
For unpaid days, can I "make up" for the lost salary by using my vacation leave, sick leave, or
compensatory time off?
No. The objective of these options is for the University to achieve budgetary savings. Accrued
vacation, paid time off (PTO), comp time and/or sick leave all are forms of paid time off and
thus may not be substituted for unpaid days.
Will furloughs or salary reductions affect the health of the UC retirement plan?
The potential impact of the options on the funding status of the UC retirement plan is being
analyzed by the Plan Actuary, and this will be taken into consideration as decisions are made.
also see Friendfeed comments
Tuesday, June 16, 2009
CIFAR on integrated microbial diversity
It is my Kind of meeting in every way
1. On the coast
2. Few talks with lots of discussion and free time
3. Really diverse with runs and bacteria and archaea and viruses covered
4 not all about genomics (some meetings I go to are)
5. Did I say it is on the coast?
6 ford Doolittle is supposed to be here . He is one of my science heroes
7. The meeting is VERY small but still seems great
8 My family came (little Kids and wife)
And already felt welcome
9 I do not know many of the people
10 Elio Schaechter of Small Things Considered is giving a special talk
This is such a contrast to the big ASM meeting .. Which was fun in
ways and useful but overwhelming
Looking forward to the week
Note added after the fact -
Here are my tweets about the meeting (mostly mine) some by Rosie Alegadorosiealegado Listening to Jonathan Eisen at #CIFAR talk about a genomic encyclopedia for bacteria & archaea. 2 days ago from Tweetie phylogenomics Huge % of talks at #CIFAR make use of Venter Sargasso or GOS metagenomic data 2 days ago from TwitterFon phylogenomics I am next at #CIFAR talking about a phylogeny driven genomic encyclopedia of bacteria and archaea 2 days ago from TwitterFon phylogenomics The one and only WF Doolittle is talking at #CIFAR about Thermotogales and lateral transfer 2 days ago from TwitterFon phylogenomics Rebecca Rundell is talking at #CIFAR about the amazing diversity of "meiofauna" (not big nor tiny) in marine samples 2 days ago from TwitterFon phylogenomics Nicole King at #CIFAR is talking about using choanoflagellate genomics/experiments to study the origins of multicellularity in animals 2 days ago from TwitterFon phylogenomics Barry Leadbetter at #CIFAR is using modelling/microscopy to study how choanoflagellates (single celled animal relatives) move/assemble 2 days ago from TwitterFon nthmost #ff @phylogenomics is live-tweeting some very interesting stuff from #CIFAR (Canadian Institute for Advanced Research): http://bit.ly/Eei6X 2 days ago from TweetDeck phylogenomics Michael Worobey at #CIFAR is telling how phylogenetics of archival samples helps resolve questions about the history of HIV movement 2 days ago from TwitterFon phylogenomics Michael Worobey at #CiFAR just told the story of how the brilliant WD Hamilton died after their trip to Africa to get chimp SIV samples 2 days ago from TwitterFon phylogenomics Michael Worobey who does fantastic "open science" flu work is talking at #CIFAR about HIV and swine flu origins 2 days ago from TwitterFon MicrobeWorld @phylogenomics Is there a site for this #CIFAR event? 2 days ago from web phylogenomics Relman at #CIFAR outlines benefits from microbes in gut: vitamins, digestion, infection protection, developmnt, immune training, etc 2 days ago from TwitterFon phylogenomics David Relman at #CIFAR is talking about humans as an ecological collective with microbes as an extension/component of self 2 days ago from TwitterFon CigarRadio @NetworkCacher Thanks, glad you enjoyed tghe show. #cigars #cifar #dogwatch 3 days ago from TweetDeck domonicmongello RT @phylogenomics Rob Beiko at #CIFAR is talking re: geospatial visualization of microbial diversity - genomics .. http://bit.ly/AYVEJ 3 days ago from twitterfeed aeroculus RT @phylogenomics Rob Beiko at #CIFAR is talking re: geospatial visualization of microbial diversity - genomics ecology geography - GenGIS 3 days ago from web phylogenomics Rob Beiko at #CIFAR is talking re: geospatial visualization of microbial diversity - merging of genomics, ecology and geography - GenGIS 3 days ago from TwitterFon phylogenomics Rebeeca Case is taking at #CIFAR about how marine algae also suffer from bleaching like coral 3 days ago from TwitterFon rosiealegado Listening to Kevin Carpenter #CIFAR. Learned a new word: ectosymbiont. 3 days ago from Tweetie phylogenomics Kevin Carpenter at #CIFAR is talking about and showing aamazing picture of microbes that live in termite and cockroach guts 3 days ago from TwitterFon phylogenomics Jan Janouskovec talking at #CIFAR about alveolate plastids "assessing the evidence" & how # of membranes are useful to know 4 days ago from TwitterFon phylogenomics Adrian Reyes-Prieto at #CIFAR is talking about plastid and chromatophore evolution 4 days ago from TwitterFon pathoadaptation @phylogenomics #CIFAR exactly the kind of meeting I need to get back to going to...must work harder to get out of my government 'hole'. 4 days ago from Tweetie phylogenomics Andrew Roger at #CIFAR is talking about the origin and evolution of mitochondria and related organelles 4 days ago from TwitterFon phylogenomics Joel Dacks at #CIFAR is talking about evolution of eukaryotic membrane traffiicking & how it is about "more than just eating" 4 days ago from TwitterFon JATetro @phylogenomics Will there be a proceedings or at least a review of the meeting? #CIFAR 4 days ago from Seesmic Desktop phylogenomics Tom Cavalier-Smith at #CIFAR is one of the few people who can really mix molecar phylogenetics and function/morphology for microbial euks 4 days ago from TwitterFon phylogenomics Listening to THE Tom Cavalier-Smith talking about eukaryotic evolution at #CIFAR - I don't always agree with him but he still rocks 4 days ago from TwitterFon phylogenomics Yan Boucher at #CIFAR is talking about "the life aquatic - vibrio an their mobile gene pool" - looking at lateral transfer & recombination 4 days ago from TwitterFon matthewherper RT @phylogenomics Alex Worden at #CIFAR communities of microbes are not a black box "physiology is not a bulk or an average property" 4 days ago from web matthewherper RT @phylogenomicsAlex Worden at #CIFAR communities of microbes are not a black box "physiology is not a bulk or an average property" 4 days ago from web phylogenomics Alex Worden at #CIFAR says we cannot treat communities of microbes as a black box "physiology is not a bulk or an average property" 4 days ago from TwitterFon phylogenomics Listening to Andrew Allen talk about phylogenomics, transposins, and gene transfer in diatoms at #CIFAR 4 days ago from TwitterFon phylogenomics Hearing Robert Morris from UW talking about proteomic studies of functions of bacterioplankton in Atlantic ocean at #CIFAR 4 days ago from TwitterFon phylogenomics Hearing Jennifer Foster discuss diatom bacterial symbioses and nitrogen fixation in oceans at #CIFAR microbial diversity meeting
Friday, June 12, 2009
The position will provide competitive salaries and benefits. The postdoc will be based in the School of Biology at Georgia Tech, with a preferred start date of September 2009, though the start date is flexible. The initial appointment will be for one year, with renewal up to three years subject to satisfactory progress and mutual agreement.
REQUIREMENTS: (1) PhD in computational biology, physics, mathematics, microbiology, ecology or related area; (2) Demonstrated research excellence; (3) Strong quantitative skills; (4) Strong oral and written communication skills. Ideal candidates from the biological sciences should have experience with scientific programming. Ideal candidates from the physical/mathematical sciences should have prior exposure to research in the biological sciences. However, outstanding applicants looking to broaden their field of interest will also be considered.
TO APPLY: Applications should be emailed to jsweitz(at)gatech.edu and consist of (1) a cover letter describing your interest in the position, (2) the names and contact information for three references, (3) a curriculum vita (including publications). Applications will be reviewed upon receipt, and continue until the position is filled.
ABOUT THE GROUP: The Weitz group is supported by grants from the Burroughs Wellcome Fund, the James F. McDonnell Foundation, DARPA, and the National Science Foundation. For more information, consult the Weitz group website or contact Joshua Weitz: jsweitz(at)gatech.edu.
Tuesday, June 09, 2009
Imagine my surprise when I opened the New York Times a few days ago and saw a giant picture of Michael Ashburner the Drosophila genomics guru, open science advocate, and Won for All author. Now, Ashburner is one of my favorite people in all of science (see my posting from a while ago recruiting him top start a blog to which he even responded). I mean, sure, people I know are in the Times everyonce in a while but this was astonishing. Here he was in some sort of fashions of the Times type of section, shirt unbuttoned, lounging in some field.
Alas, closer examination and some google searching found the truth. This is alas not Ashburner, but actually Francis Ford Coppola and his daughter Sofia. But I mean - look at the pics of Ashburner below. It really could have been him. Oh well, maybe next time ...
Friday, June 05, 2009
The article by Leslie Kaufman discussed how there are attempts in some dairy farms in the US to change the diet of cows to reduce their methane output. The methane is a strong greenhouse gas and in total cows make a surprisingly large global contribution to greenhouse gases. The article states:
Cows have digestive bacteria in their stomachs that cause them to belch methane, the second-most-significant heat-trapping emission associated with global warming after carbon dioxide.Alas, this is not correct. Yes, bacteria in the cow rumen contribute to the production of methane. But they do not make the methane. The methane is made by archaea (for those not in the know, archaea are a distinct group of organisms relative to bacteria - they resemble bacteria in many ways but are a separate branch on the tree of life). For those of us who study archaea this is a major slight. A diss. A taunt. A sad day. And all those other things. Not sure how we archaea fans will have our revenge but I swear we will. Too bad Carl Zimmer does not think that this is important enough to go on one of his newspaper fact chekcing investigations.
Thursday, June 04, 2009
Amazingly this is indeed the same David Byrne of them Talking Heads. It turns out he has a book coming out in the fall called "Bicycle Diaries." Anyway he reviews this book on the effect of bicyclists on American Cities and right there in the review are some props for my town, Davis, CA. The article is worth checking out and I will both be buying this book and awaiting Byrne's. Maybe we can have a reading here in Davis when the Bicycling Hall of Fame opens its doors.