Month: February 2010

Genome Sequencer FLX Bay Area Regional User Group Meeting

Just got this email – may be of interest to some:

Genome Sequencer FLX Bay Area Regional User Group Meeting

Roche 454 Life Sciences invites you to the Bay Area Regional Genome Sequencer FLX User Group meeting which will be held at Roche Diagnostics in Pleasanton, CA on March 8th and 9th.

We will kickoff the meeting the afternoon of March 8 with interactive sessions with our BioInformatics Specialist Teri Mueller and Regional Applications Consultant Shamali Roy. Bring any questions or ideas you may want to address. Teri will present on the most recent upgrades to our Data Analysis software and Shamali will be available for experimental design advice. This will be a user driven question and answer event scheduled from 1:00-4:00 pm.

Tuesday will feature local scientists presenting their 454 Genome Sequencer FLX work for a variety of applications. Presentations will begin at 10:00 am and conclude at 4:00 pm.

Speakers for the event include

Robert Shaffer, MD – Associate Professor of Medicine and Pathology, Stanford University

Feng Chen, PhD – Group Lead, Technology and Applications, US DOE Joint Genome Institute

Matt Ashby, PhD – President and Chief Scientific Officer, Taxon Biosciences

Henry Erlich, PhD – Vice President Discovery Research, Roche Molecular Systems

This meeting is designed to allow GS FLX users to share experiences and knowledge about the platform, creating a community of users where tips and tools can be shared. Other than a brief introduction by Roche 454, this will be a Science for Scientists event. Please feel free to share this invitation with colleagues.

Come and network with other researchers using Roche 454 technology as well as learn tips ranging from sample management to base calling to whole genome analysis, and much more. This event is free of charge and is open to everyone with an interest in using this exciting technology for accelerating your research and discovery. Lunch will be provided on March 9.
Space is limited and registration is required. To register for the event please RSVP to either courtney.brady@roche.com or goli.shariat@roche.com Please indicate if you will be attending March 8th or 9th or both days.

The address for the event is Roche Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588. There is a BART station nearby and shuttles to Roche can be arranged.

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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.

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Visit to #UCDavis Bohart Museum of Entomology

For those of you who know me, and for those of you who do not, you may not know that I am generally a fanatic about bugs.  And in this case, I do not mean microbes (which I also love).  I mean insects and their relatives.  So it was with great pleasure that yesterday I finally got to go to the UC Davis Bohart Museum of Entomology.  I have been meaning to go for a while but it just never happened.  And then, a graduate student in my lab, Lizzy Wilbanks, asked for suggestions for activities that might be interesting to do with Jared Leadbetter who was the speaker the Microbiology Graduate Students were hosting here at Davis.  Now, I know Leadbetter a tiny bit and know that he really likes bugs too (both kinds …).  So I suggested – why not see if you can get a tour of the museum. And like magic, Lizzy arranged it.  Any yesterday, Marc Facciotti and I took Leadbetter over the the museum after he had lunch with students.  And it was very cool.

I will try to write up more about the museum at a later point but here are some pictures.

http://picasaweb.google.com/s/c/bin/slideshow.swf

For details on Leadbetter’s talk see my Friendfeed posts below:

http://friendfeed.com/treeoflife/2e737b2f/getting-tour-of-ucdavis-bohart-museum?embed=1

——–
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.

——–

Letter from #UCDavis Chancellor Katehi on "Rallies in support of higher education"

Just got a letter from UC Davis Chencellor Katehi addressed to the UC Davis community (so presumably this went out to 1000s) regarding some upcoming rallies in support of higher education and I thought it might be of interest to share it here because it may be of interest to some who did not receive it:

Dear UC Davis Community Members:

Next week’s rallies in support of public higher education provide us with another opportunity to work together on behalf of the University of California and in support of the California Master Plan for Higher Education — a visionary plan forged in 1960 that viewed higher education as a collective good and as the primary engine of social mobility.

That plan is threatened today with the state’s steady and steep disinvestment in UC, in California State University and in the California Community Colleges. I know you feel the impact of that disinvestment in very real, very personal ways.

The Governor’s January budget proposal offers us some hope, but it’s critical that we persuade lawmakers to make public higher education a funding priority. Together, we can help our state to re-prioritize.

Three advocacy opportunities are fast approaching. While on-campus responsibilities must always come first, I’m hopeful that, with attentive planning, you’ll be able to help deliver the message to Sacramento that our public colleges and universities need greater state investment.

On Monday, March 1, the UC Student Association will hold a march, rally and press conference at the State Capitol between 11:30 a.m. and 2 p.m. UCSA leaders have asked UC President Mark Yudof and several regents and chancellors to join them in meetings with key legislative leaders throughout the day. I am pleased to do so, and am looking forward to accompanying our students to Sacramento. If you’re able, I hope you will join us and add your voice to others advocating for keeping our public university truly public. If you need transportation, our Government and Community Relations Office is working with student leaders to coordinate UC-provided buses.

On Thursday, March 4, a national day of action in defense of public higher education is being planned by a coalition of K-14 and UC and CSU students, employees and other education stakeholders. Rallies are planned at the State Capitol and throughout the state.

And on Tuesday, April 27, another advocacy day at the State Capitol is being planned by a coalition of UC, CSU and California Community Colleges advocates throughout the state. It’s hoped that a broad alliance of public higher education supporters will participate, including students, parents, alumni, faculty, staff, business leaders and community organizers.

I hope we can continue to work together on the university’s behalf, raising issues and raising our voices effectively and respectfully. Together, we can make our best case for preserving affordable, accessible and world-class public higher education. That was the state’s vision in 1960, and that must remain its commitment today. Please join me in carrying that message to the State Capitol and ensuring that the principles of the California Master Plan endure.

Sincerely,

Linda P.B. Katehi
Chancellor

——–
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.

——–

New #UCDavis Open Science Group & OpenWetWare page

Just got an email about this group from Carl Boettiger and thought I would help spread the word. If interested in open science and affiliated with Davis please sign up:

I just met some students recently who were talking about creating an Open Science group at UC Davis. Thought you might be interested in joining their mailing list: openscience@ucdavis.edu

email listproc@ucdavis.edu with
subscribe openscience firstname lastname
in the body.

Some more info here: http://openwetware.org/wiki/UC_Davis_Open_Science

——–
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.

——–

Evolution word of the week: bislagiatt (& check out WSJ evolution article too)

Normally I spend some time here criticizing bad words used in various areas of science in which I work. Today I am praising a word. The word is bislagiatt and I had never seen it until reading a Wall Street Journal article today. The article (Blame Evolution for Disease – WSJ.com) has some good and bad moments. It presents some arguments for why some human diseases today are in essence side effects of historical natural selection that no longer applies well. Many of the arguments seem OK but smell of adaptationism in reverse – just so stories that may not have a lot of evidence on their side. But the article overall is good and has some nice figures with it. But the best part of the article is the introduction of a new word

“And some body parts that provided a benefit at some time in human history pose challenges today—a phenomenon Texas Tech University geneticist Lewis I. Held Jr. calls “bislagiatt,” an acronym for “but it seemed like a good idea at the time.””

Now that is a perfectly good evolution term. And though I have never seen it used anywhere else, the use in this article I think will lead to it being used more commonly in the field. And thus today I am giving out a new award “Best new evolution word” to “bislagiatt” and to Dr. Lewis Held for at least using it here if not coining it.

——–
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.

——–

Funny Mobio ad "No microbe will be left unsequenced" #DNA #genomics

Funny ad from Mobio on their web site and YouTube “No Microbe Will be Left Unsequenced.” Perhaps they are familiar with my obsession to create a Field Guide to the Microbes (e.g., see here and here) and my obsession with creating a Genomic Encyclopedia of them? Who knows? But I do know my lab uses lots of MoBio kits – they are quite nice.

——–
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.

——–

Call me a curmudgeon but I do not do "reciprocal links" on my blog

Arrg.  I am so sick of getting emails from people hawking some blog site saying “We like your blog … if you link to us we will link to you.”  Here is an examply I just got

Saw the “The Tree of Life” blog and thought it was great. I wanted to introduce our blog to you. The XXX Blog (http://www.XXXX.com/blog/) has been created as a place where blah blah blah. Would you be interested in reciprocal linking? We will link to you on the XXX Blog http://www.xxxx.com/blog/ and our other blog the xxxxx http://xxx.wordpress.com/. If you are interested feel free to contact us xxx@xxxx.com .

Here is another one:

Greetings:      

My latest site is dedicated to xxxxx. If you would like to exchange links I would be more than happy to trade my link in exchange for a reciprocal link on your site. If you agree, please place my link: 

TEXT: xxxx                       

URL: http://www.xxxx.com

Desc. (optional): The top xxxx xxx xxx for your xxx xxx. .  

Send link placement and your link information to wrap up the exchange

Thanks  

I am sorry but I put up links that I find interesting.  And I do not post links in exchange for others posting links to me.  Am I somehow missing out on something?  I know people are trying to game google hits but I want nothing to do with it.

——–
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.

——–

Bad omics word of the day: religionome

And so they go – on and on.  I am addicted to bad omics words.  They are a bit fascinating ion that the spread of the ome suffix is astonishing.  And here is one that is both funny and a bit sad: religionome.  Not that new.  But out there.  And winner of today’s “Bad omics word of the day.” Not sure exactly where it started but here is one of the first uses I could find:

We have a lot of new data we are working on, and one of the thoughts I’ve come up with recently is can we create something similar to the human genome – perhaps we can call it the religionome – with which we can begin to look at all of the different beliefs and practices and traditions and try to evaluate and understand them not just from a spiritual perspective or a subjective perspective, but from physiological and biological and social and cultural perspectives as well

This is from a transcript of a conference involving Andrew Newberg from U. Penn.

Some other things on this include:

——–
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.

——–

Oldy but baddy: bad omics word of the day – "speechome"

I know I swore to quit but I could not help myself here. I was going through old draft blog posts that I never finished and found this link to an article about the “Human Speechome Project” BBC NEWS | Science & Environment | Big brother untangles baby babble

Basically, the idea is they are recording everything a particular child hears and says and categorizing it all to create “the Human Speechome project“

“Just as the Human Genome Project illuminates the innate genetic code that shapes us, the Speechome Project is an important first step toward creating a map of how the environment shapes human development and learning,” said Frank Moss, the director of MIT’s Media Lab at the time.

In some ways – the project is eerily fascinating. But in many ways it is more on the creepy side of things. Regardless of whether one likes the project or not, the word “speechome” has just got to go. So, quite a few months late – I am still giving this my “Bad Omics Word of the Day” award.

——–
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.

——–

Received my first soliciation regarding "Broader Impact" reqs for grants

Got an interesting email the other day:

What do the following research programs have in common?

1. Lost Ladybug Cornell (Cornell University, NY)
2. Museum of the Earth (Ithaca, NY)
3. Crossing Boundaries (Hobart and William Smith Colleges, NY)
4. High School Polar Outreach Project (Charleston, SC)
5. Go Inquire Project (George Mason University, VA)
6. Project Wetkids (University of Southern Mississippi)

Answer: They decided to hire Next Interactives to develop a highly engaging research website to help fulfill their Broader Impact and Outreach requirements.

Sound interesting? Simply reply to this email for a free website consultation.

Regards,
XXXX

Outreach Project Manager
Next Interactives LLC
Our portfolio: http://www.nextinteractives.com

This seems to be focused specifically on the “Broader Impact” requirement in National Science Foundation grants.  I have never received a solicitation like this before.  Anyone else out there get anything like this?  What do people think?  I think it is possibly a good thing that some companies are thinking there is a niche for them in Broader Impact and outreach assistance.

——–
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.

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