Category: Misc.

Announcement: Workshop on Multiple Sequence Alignment and Phylogeny Estimation

Posting this for Tandy Warnow

Workshop on Advances in Multiple Sequence Alignment and Phylogeny Estimation

May 20 and 21, 2012, Smithsonian Institution, Washington, DC

The workshop is funded by the National Science Foundation through grant DEB 0733029 to the University of Texas. Registration is required, and attendance is limited to 40 participants. The workshop will include presentations of new methods for multiple sequence alignment and phylogeny estimation, also training in the use of these methods, and personal assistance in analyzing datasets using the SATé software (see this page). Applications for the workshop (and for travel support) are due by February 15, 2012, and will be responded to by March 1. We expect to be able to provide support to all attendees. Please click here for the application form. For more information, please send an email to Tandy Warnow (see below).

Letter from Tandy explaining workshop:
Dear Colleagues,
We are writing to let you know about a workshop and symposium that we will hold on May 20-22, 2012, at the Smithsonian Institution in Washington, DC. The workshop will provide training in advanced methods for multiple sequence alignment and phylogeny estimation, and will take place on May 20 and 21; the symposium will follow immediately and will feature research presentations on the same topic. This workshop is funded by:
The workshop will include presentations of new methods for maximum likelihood phylogeny estimation of large sequence alignments (including GARLI and FastTree), for comparing different alignments of the same dataset, for phylogenetic analyses of datasets that include partial sequences (e.g., short reads generated in a metagenomic analysis), for supertree estimation, and for simulating sequence evolution. However, a main focus is to train participants in both basic and advanced use of the SATé software (Liu et al. 2009, Science, Vol. 324, no. 5934, pp. 1561-1564) for simultaneous estimation of alignments and trees (SATé software available for download at http://phylo.bio.ku.edu/software/sate/sate.html ).
Workshop participants are expected to bring laptops with them to the workshop, so that they can perform alignment and phylogenetic tree estimations. We will provide test datasets for you to learn how to use SATé, but strongly encourage you to bring your own datasets to analyze.
Attendance at the workshop is limited to 40 participants, and registration is required. If you are interested in attending the workshop, whether or not you are requesting travel support, please fill out the Word document available at http://www.cs.utexas.edu/users/tandy/workshop-application.doc, and return it to Laurie Alvarez (lauriea@austin.utexas.edu) by February 15, 2012. We will respond to requests for registration by March 1, 2012.
For more information on the workshop, please contact me (Tandy Warnow), at tandy@cs.utexas.edu. For more information on the Symposium, please contact Mike Braun (braunm@si.edu). We look forward to seeing you at the Smithsonian workshop and symposium!
Regards,
Tandy Warnow and Mike Braun
On behalf of the AToL project team:
  • Michael Braun, The Smithsonian Institution 
  • Mark Holder, The University of Kansas
  • Jim Leebens-Mack, The University of Georgia 
  • Randy Linder, The University of Texas 
  • Etsuko Moriyama, The University of Nebraska 
  • Tandy Warnow, The University of Texas
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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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Draft post cleanup #9: Open Access spam from Bentham

Yet another post in my “draft blog post cleanup” series.  Here is #9; from June 2008.  It can in a way be viewed as an extension of my post from a few days ago about Bentham.  Here is what I wrote in 2008:

OK, I know I am supposed to be supportive of Open Access journals, just because a journal is OA does not mean it is OK. Take “The Open Evolution Journal.” being published by Bentham.

On paper, this could be a useful contribution to the list of OA journals. They have some good people on their Editorial Board and I am glad to see such a big list of people in Evolution seemingly supporting OA publishing.

And Bentham is certainly doing the OA talk and pushing OA as a major option for their publications. In fact, they might be pushing OA a bit too much. For example, in their letter to me they say

All published open access articles will receive massive international exposure and as is usually the case for open access publications, articles will also receive high citations.

Hmm. A bit over the top no? I love OA mind you. But OA in and of itself does not guarantee citations and exposure.

But this is a minor quibble. My real issue with them is the SPAM. I keep getting frigging emails from Bentham for all sorts of journals. And some of the emails I get are for accounts that I cannot easily send email from to use their lame unsubscribe option. I assume others out there get these emails from Bentham too, as I have gotten them from like 20 of their journals so far. And many are in areas that I have no expertise in (I just got one for a Geology journal).

Just goes to show – OA sometimes means “Objectively Annoying.”

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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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YHGTBFKM: Ecological Society of America letter regarding #OpenAccess is disturbing

Wow — I am really disturbed by the letter the Ecological Society of America (ESA) has written to the White House OSTP in regard to Open Access publishing. (For some background see Dear Representatives Issa and Maloney – Are you kidding me? Stop this bill now #ClosedAccess and Calling on Publishers to Resign from The Association of American Publishers Re Anti-Open Access Stance).

In the letter they make many statements that bother me deeply including:

However, it is important to note that there is a significant difference between research results and peer-reviewed publications.

Really – how are they different exactly?

Publishers such as ESA have a long record of reporting, analyzing and interpreting federally funded research.

OMG – seriously?  Apparently ESA is doing the analyzing and reporting and interpreting.  Not the scientists writing the papers.  But the publisher.  Seriously.  This is completely ridiculous.

It is not appropriate for the federal government to expropriate the additional value publishers add to research results.

They can’t be serious.  This is not expropriation in any way.  This is the trying to guarantee that research taxpayers have paid for – that is done by scientists that taxpayers pay the salaries of – is not then published in a way that forces the taxpayers to pay for it again.

Furthermore, subscription revenue helps to support other Society services, including scientific conferences, education programs, and the distribution of science information resources to policymakers and the public.

So now what they are saying is that the government should hand them money via subscription fees so that they can then carry out some services they think are important.  How about this – how about the ESA applies for peer reviewed grants to fund their activities so that these can be reviewed by others.  As it is ESA can do whatever it wants with that money – being fed to it without any peer review – via indirect costs and grant money.

Papers published in ESA journals may therefore be just as relevant in several years as they are today, which means that any potential embargo period will do little to mitigate the financial losses that would result from full open access.

So – the justification here for not making ecological articles available is that they are MORE important over time?  So the taxpayers pays for research that is valuable and because it is valuable over time we should make it less freely available?  Seriously?

And here is the best one:

One way to make taxpayer funded research more visible and accessible to interested members of the public would be to require federally-funded grantees to provide a second version of the research summaries they already prepare, specifically for the lay reader. To aid in online searches, these summaries could also include the source of federal funding institutions and grant numbers. Publishers could also include grant information in paper abstracts which are usually available without a subscription.

That is right, they are suggesting that scientists write a second paper to go with their science papers that would be for the lay reader.  And that these summaries could include grant IDs to help in online searches.  WTF?  So now rather than making the actual scientific papers available they are proposing that scientists write a second paper because lay people would not be able to understand the first paper?  And what about scientists who want to read the papers but are at small institutions?  And never mind that “open access” is not just about money – it is also about “freedom” in the usage of published material.

The ESA has really gone off the deep end on this.  I note – I am in full support of companies and publishers making money.  I am also generally against government regulations.  But this issue is about taxpayers rights, government waste, and the progress of science.  It is simply inexcusable for the government to not use taxpayer money judiciously.


If the government pays for the research, pays for the research supplies, pays the salaries of researchers and peer reviewers, then it is unacceptable that publishers would then limit access to papers and force taxpayers to pay for them again.

The ESA basically is saying “taxpayers should be required to subsidize us“.

Or – another way to look at this – ESA is saying: “Taxpayers – we want your money -but you are too stupid to understand what we are doing with it.“

Ridiculous.

Hat tip to Karen Cranston for pointing this out.

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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.

——–

Draft post cleanup #8: Don’t let a hospital kill you – CNN.com

Yet another post in my “draft blog post cleanup” series.  Here is #8 from 5-1-2008
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Saw an interesting article today on CNN.Com: Don’t let a hospital kill you – CNN.com.  It has some useful suggestions for how to protect yourself from infection in a hospital.  In many cases we have an excessive fear of germs which can be a bad thing.  But in hospitals, staying clean is almost certainly a good idea …

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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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Go PLOS Biology – getting lots of press coverage for recent pubs

Just got this email from PLoS Biology and thought I would share – it has links to press coverage of recent PLoS Bio papers  :


We are writing to update you on some papers recently published in PLoS Biology.This is a summary of our recent media coverage for PLoS Biology board members, friends, and for editors. Thank you again for your support of the journal.


On January 3, PLoS Biology published an article by Prof. Alex Rogers et al., which detailed a survey of Antarctic waters along the East Scotia Ridge in the Southern Ocean, revealing a new vent biogeographic province among previously uncharacterized deep-sea hydrothermal vent communities. This received significant coverage in the media, a selection of which is below:

BBC
The New York Times
The Guardian
Washington Post


PBS News Hour (video)
BBC World Service (audio)
Press Association
Discovery News
Reuters (video)
The Telegraph
Wired
Scientific American
National Geographic
Nature
ABC (Australia)
Sydney Morning Herald
MSNBC
CBC (Canada)
Fox News
New Scientist
The Mirror
The Daily Mail
Indian Express

In the same issue, PLoS Biology published an article by Dr David Ornitz and colleagues, which described how FGF20 signaling in mice is required specifically for the differentiation of cochlear outer hair cells – the cells most often damaged during age-related hearing loss. This also received attention in the media, including the following:

NHS Choices
Press Association
The Mirror
The Daily Mail
Scotsman
Irish Examiner

——–
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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Dear Representatives Issa and Maloney – Are you kidding me? Stop this bill now #ClosedAccess

Should the results of research funded by taxpayer money be freely available? Apparently two in Congress think no – Darrell Issa and Carolyn Maloney have cosponsored a bill that would reverse the NIH open access policies.

Why would they do this? Well, if you follow the money, you can see that they are well supported by Elsevier – one of the publishers vehemently against open access to scientific research results.

For more on this see

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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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Draft post cleanup #6 from 2005: Hydrogen producing microbe mea culpa

Yet another post in my “draft blog post cleanup” series.  Here is #6. From 2005. (Yes, the bottom of my draft list).  In fact, this would have been my second blog post if I had posted it …

I had written

OK, so a few months ago we published a paper on a hydrogen producing microbe and issued a press release. I think the paper we published was pretty cool – lots of interesting science.

Then we (me and our public affairs person) wrote a press release about the project. We were fortunate enough to have the press release picked up by all sorts of bloggers and web commentary groups. Examples include Softpedia (article here) and probably most importantly Slashdot.

So – what was wrong?  Well, I was starting to get more and more jaded with bad press releases about science papers.  And I felt ours had at least one really lame part – my quote

So if you’re interested in making clean fuels, this microbe makes an excellent starting point.

Well, WTF?  I have never done anything with biofuels and I really knew nothing about them then.  That quote should never have been in the press release and I am not sure I even said it.

Other parts of the PR are OK I think but I wish that quote had never been in there.  I note – I do like the end though

What we want to have is a field guide for these microbes, like those available for birds and mammals,” Eisen says. “Right now, we can’t even answer simple questions. Do similar hot springs , a world apart, share similar microbes? How do microbes move between hot springs? Our new work will help us find out.

I agree with that.   I have indeed been obsessed with a Field Guide to the Microbes for a long time …

——–
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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Draft post cleanup #3: The Open Knowledge Foundation

Yet another post in my “draft blog post cleanup” series.  Here is #3 from just a few weeks ago:

Interesting article in PLoS Biology:  PLoS Biology: The Open Knowledge Foundation: Open Data Means Better Science.  It discusses many issues in open science especially as they relate to open data.

Some links from this paper are worth checking out

This article reminds me that I keep meaning to push for the development of a “Datawatch” system much like the “RetractionWatch” systems of Ivan Oransky. I have discussed this with Ivan but we have not yet gotten around to doing it … 
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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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Note @David_Dobbs @mbeisen had nice family PM yesterday watching wrapup of 2004 ALCS @David_Dobbs @mbeisen

Image
——–
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.

——–

Draft blog post cleanup #2: Metagenomics meets animals

OK – I am cleaning out my draft blog post list.  I start many posts and don’t finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is #2:

Saw an interesting story on Genome Web: ‘Denizens’ of the Deep | The Daily Scan | GenomeWeb.  I have not been able to get the original article yet, but it seems that what they have done can basically be considered metagenomics for animals.  They collected sloughed off cells and other material from a lake and surveyed it for animal DNA.  This seems like a very cool derivative of metagenomic approaches and has enormous potential.  But alas, I never got down to getting access to the paper: Monitoring endangered freshwater biodiversity using environmental DNA so this will have to stay as a mini post.  Damn non open access journals …

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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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