Well, however you feel about the Wildhorse Ranch vote in Davis, this whole election just seems absurd. A whole election just to vote on this one thing? And do they really need a multi-page color sample ballot? So if I could, I would vote to require these “special” elections about rezoning to only happen if there already was another important election going on. Even if the pro-Ranch crown pays for the election, it just seems like a waste …
Category: Misc.
Walkscore – software for walkability of communities goes open source
Just got this email (see below) from WalkScore that I thought might be of interest to Davisites. Walk Score is one of several types of “software for civic life” from Frontseat. This systems allows one to evaluate the walkability of a community or address. And now they are looking to release the software for WalkScore at Walkscore.Org as an open source development. And they are trying to get more people involved in this – including asking for what new developments they should make. I have suggested previously that they should incorporate bikability. And if you agree, you should vote for it here.
Dear Jonathan,
You deserve a break. Take a sec to:
- Cast your vote on how to improve the Walk Score algorithm.
- Friend us on Facebook so we can claim the Walk Score URL.
Also, we’re thrilled to announce our Rockefeller Foundation grant (see below).
— The Front Seat Team
Vote on Walk Score improvements
We just launched WalkScore.org — a new website where you can vote on Walk Score improvements. We’re also releasing open source code for Walk Score on this site.
Friends with benefits
Can you help us get to 100 fans on Facebook so we can claim a URL for our Facebook page?
Let’s create a Facebook group of people who support walkable neighborhoods.
Rockefeller Foundation grant
We’re using our new grant from the Rockefeller Foundation to improve Walk Score and make it open source. Sign up on WalkScore.org to get notified when the code is available.
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#OPenAccess Week event at #UCDavis today 10/20: C. Mitchell from California Digital Library
“Take Control of Your Publications with eScholarship”
An Open Access Week Presentation
Catherine Mitchell
Director, CDL Publishing Group
University of California
Tuesday, October 20, 2009
1:00 p.m. – 2:30 p.m.
Shields Library, Second Floor Instruction Room
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Help save viral ecology (or, when a corporate takeover can kill a field of science)
Just got this an interesting email below from a friend and colleague, Eric Wommack at U. Delaware. In the email, Eric discusses how the recent purchase of Whatman by GE Helathcare has apparently wreaked havoc on the field of viral ecology. You see, a key tool in many studies of viruses in the field turns out to be filters with really small pore sizes to collect the viruses. And, alas, apparently, GE Healthcare has decided to end sales of the filters that a lot of viral ecology researchers use and cannot replace.
So a seemingly small decision by GE Healthcare could severely harm viral ecology work. Eric (and others) are encouraging researchers to write to GE Healthcare to ask them to reconsider the discontinuation of these filters. I encourage you to do so. A person to wrote to at GE is listed in the email below
I’m writing in hopes that you can help the viral ecology research field build a grass roots campaign to convince GE Healthcare to reverse its decision to discontinue manufacture of all 0.02 µm Anodisc filters. GE Healthcare recently acquired Whatman the sole manufacturer of these filters. Presently, 0.02 µm Anodiscs are the only means of collecting direct counts of free virus particles by epifluorescence microscopy. All other types of filter membranes with suitably small pore sizes (sub 30 nm) simply do no work. Viral direct counts are a baseline inventory measurement throughout the field and the loss of these filters will effectively shut down all cutting-edge viral ecology research productivity.
The official word from GE Healthcare is that the company will fill existing orders and then discontinue the entire product line as of December. According to an openly honest Whatman tech support worker, who was entirely sympathetic with our plight, this decision is entirely financial. The irony is that the company has an effective monopoly in this niche so those labs who absolutely rely on these filters would find a way to pay whatever is necessary to make the product financially viable. The tech support guy said that Whatman actually manufactures Anodisks, so unless another company steps forward to adopt the technology viral ecology research will grind to a crawl over the next couple of years. I know this scenario sounds dramatic, but I’ve seen a nearly complete work stoppage on three projects since the Anodisc supply dried up in July.
Please mail the letters to:
Navin.Pathirana@ge.com
Navin Pathirana, Ph.D., CChem
Regional Product Manager
Whatman, Inc.
GE Healthcare Bio-Sciences Corp.*
800 Centennial Avenue***
Building 1*
Piscataway**, NJ 08855 USA***
Here are some PLOS Open Access papers using these filters
Here are some links to papers found in Google Scholar that have used these things:
- Enumeration of marine viruses in culture and natural samples by flow cytometry
- Application of digital image analysis and flow cytometry to enumerate marine viruses …
- Virus-like particles associated with Lyngbya majuscula (Cyanophyta; Oscillatoriacea) bloom …
- Rapid virus production and removal as measured with fluorescently labeled viruses as …
- A comparison of methods for counting viruses in aquatic systems
- Abundance and diversity of viruses in six Delaware soils
- Viral effects on bacterial community composition in marine plankton microcosms
- Viral lysis and bacterivory during a phytoplankton bloom in a coastal water microcosm
- Accurate estimation of viral abundance by epifluorescence microscopy
- Sampling natural viral communities from soil for culture-independent analyses
- Viral distribution and activity in Antarctic waters
- Regeneration of dissolved organic matter by viral lysis in marine microbial communities
- Reconsidering transmission electron microscopy based estimates of viral infection of …
- Global redistribution of bacterioplankton and virioplankton communities
- Phage community dynamics in hot springs
- Isolation of a virus infecting the novel shellfish-killing dinoflagellate Heterocapsa …
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Open Access Week October 19-23, 2009
To broaden awareness and understanding of Open Access — Open Access Week – October 19-23, 2009
Hope everyone is going to do something ….
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Adopt a GEBA genome program for education – from the DOE/JGI
The DOE Joint Genome Institute’s Education Program is providing opportunities for colleges and universities across the country to “adopt” bacterial genomes, such as those sequenced as part of the “Genomic Encyclopedia of Bacteria and Archaea” (GEBA project), for analysis. This “Adopt a GEBA Genome” Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. The organisms ideally provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, and use gene ortholog neighborhoods for comparative genomics and annotate biochemical pathways, while learning the underlying biological concepts in a variety of science courses.
For more information, and to apply for the November 2, 2009 deadline, see:
http://www.jgi.doe.gov/education/genomeannotation.html
For more on the GEBA project, which I am coordinating, see a video of a talk I gave about it at the JGI User meeting. Slides from that talk are on slideshare here.
Data fro the GEBA project is available at a dedicated IMG site here.
http://www.scivee.tv/flash/embedCast.swf
A much much much older talk, from when we just started the project is here:
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3rd Annual Western Evolutionary Biology Meeting 12/5/09 at Berkeley
The 3rd Annual Western Evolutionary Biology Meeting will be at UC Berkeley. This is a meeting of the UC Network for Experimental Research on Evolution (NERE), attendees from the UC campuses will be present, other evolutionary biologists, researchers, teachers and writers are encouraged to participate as well.
When: Sat. 5 December FREE registration – deadline, 29 October 2009 Submit Abstracts – deadline 16 October 2009 – or present a poster
Where: On the UCB Campus in VLSB, see website for details NOMINATE: Western Evolutionary Biologist of the Year by 9 Oct. 2009
See website for details. Open to Researchers, Teachers, Writers.
REGISTER at http://www.lifesci.ucsb.edu/nere-web/
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Some tweets of mine with links about #PLoS papers by #Nobel winners
NYTimes advice on probiotics: "go to Pubmed" but ignores #openaccess issues
There was an article on probiotics in the New York Times today. By Tara Parker-Pope it addresses some important issues rarely covered in the press about probiotics (see Well – Probiotics – Looking Underneath the Yogurt Label – NYTimes.com).
On the one hand, the article does a decent job of pointing out that there is great strain to strain variation among microbes labelled as probiotics. In this regard there is a great quote by Gregor Reid:
Lactobacillus is just the bacterium,” said Gregor Reid, director of the Canadian Research and Development Center for Probiotics. “To say a product contains Lactobacillus is like saying you’re bringing George Clooney to a party. It may be the actor, or it may be an 85-year-old guy from Atlanta who just happens to be named George Clooney. With probiotics, there are strain-to-strain differences.”
Personally I think the article did a poor job of discussing one of the real complexities of probiotics (and actually any drug) in that seems to suggest that particular strains are going to be useful for certain ailments or not. In reality, the human gut is a horribly complex place, and the effectiveness of particular strains is no doubt going to depend on health status, history, other microbes being present, gender, age, genetics, and much much more. Thus it would have been good to include some more discussion of just how complex the interaction between probiotics and “health” is likely to be.
Interestingly, the article suggests:
Consumers interested in probiotics should look for products that list the specific strain on the label and offer readers easy access to scientific studies supporting the claims. A good place to find studies on various probiotic strains is the Web site www.PubMed.gov.
On the one hand, I am very happy that the Times is suggesting consumers look up information in Pubmed, a great resource. On the other hand, much of the published work on probiotics is still hidden from consumers being the veil of corporate and society publishing practices. Perhaps the Times author had access to all these articles. But the consumer right now does not. Too bad the Times missed a chance to discuss this important component of getting consumers involved in making their own health decisions.
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East Quad Farmers Market
Another nice thing for the fall and spring on Campus at UC Davis – Wednesday from 10-2 or so there is a Farmer’s Market in the quad. It is not huge, but if you want some fresh/local produce – this is a good place to get something. See here for more detail: East Quad Farmers Market
Jonathan Eisen's Lab 