Category: Misc.

Interesting PLoS One paper on local assembly from short reads by "tagging" DNA via restriction enzymes

Quick one here. Interesting paper from Paul Etter et al. from Eric Johnson’s lab at U. Oregon in PLoS ONE: PLoS ONE: Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads



Here is the abstract:

“Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using paired-end sequencing of restriction-site associatedDNA (RAD-PE) fragments. We use this RAD-PE contig approach to identify single nucleotide polymorphisms (SNPs) and determine haplotype structure in threespine stickleback and to sequence E. coli and stickleback genomic DNA with overlapping contigs of several hundred nucleotides. We also demonstrate that adding a circularization step allows the local assembly of contigs up to 5 kilobases (kb) in length. The ease of assembly and accuracy of the individual contigs produced from each RAD site sequence suggests RAD-PE sequencing is a useful way to convert genome-wide short reads into individually-assembled sequences hundreds or thousands of nucleotides long.”


Note as they note in the paper “Competing interests: E.A.J. has patents filed on the RAD marker, and partial interest in a company commercializing the system. This does not alter the authors’ adherence to all the PLoS ONE policies on sharing data and material” This seems like it would have potential in metagenomic applications.  I note, we are working on a similar approach – and kind of got scooped here in a way. Hope their patent does not limit what we can do.

——–
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.

——–

Nice review/commentary on challenges in phylogenomic analysis in PLoS Bio by Philippe et al. #fb

This one is definitely worth a read for phylogeneticists and phylogenomicists (is that a word?) out there: PLoS Biology: Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough. Philippe et al. discuss some important issues in using genomes to infer phylogenies of species in this commentary/review paper.  They discuss in particular some recent studies of animal evolution but they cover a lot of useful ground here and include a good review of terminology and some of the basic issues at play.  I am personally going to have to read it in more detail to help deal with some of the issues in our recent study of novel sequences in metagenomic data.

——–
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.

——–

Richard Branson getting into microbial diversity (a little bit)

Just a quick one here. For those interested in the deep-sea and microbial diversity you might want to check out this article: Richard Branson launches Virgin Oceanic: deep-sea exploring submarines – Boing Boing. It discusses how Branson will be working with Katrina Edwards, Doug Bartlett and others to study microbial diversity in the deep sea as a component of his project to make dives in his personal submarine.

——–
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.

——–

Request for #UCDavis affiliates to help Japan from Chancellor Katehi

Just got this email from the Chancellor of UC Davis Linda Katehi and thought I would share

To the UC Davis Community,

The crisis and devastation in Japan following the March 11 earthquake and tsunami continue, and as with any natural disaster of this magnitude, healing will be neither simple nor immediate. Our thoughts and hearts are with the Japanese people and with their many loved ones who are teaching and learning on our campus and in our community.

Inevitably, the disaster will fall from the headlines, but the UC Davis community will not look away. We will continue to reach out in comfort and with assistance to honor those who are hurting and in respect for our deep connection to Japan. Nearly 200 Japanese residents are currently studying at UC Davis, and this year, we have more than 50 Japanese faculty members visiting our campus. Our students were also at five universities in Japan at the time of the disaster, including in areas with heavy damage, and we are grateful that all are safe.

There is still much to do, and you can help, too. Please see this link for a variety of charities aiding the Japanese people:

http://www.charitynavigator.org/index.cfm?bay=content.view&cpid=1221

UC Davis has a compassionate spirit, and I thank you for proving that once again.

Linda P.B. Katehi
Chancellor

– Posted using BlogPress from my iPad

——–
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.

——–

My twitter wrap up of the Joint Genome Institute User Meeting #JGIUM

Off to another meeting so don’t have time to write up details of the JGI User Meeting that just ended.  But I am posting my tweets and some related tweets here.  Also, apparently videos of the talks will be available soon. Will try to clean up the style of the posts ASAP but on the road …

kucsbl CSBL at Korea Univ.
RT @phylogenomics Rob Knight discussing the rationale behind his UNIFRAC metric to comparing communities using phylogeny #JGIUM
5 hours ago Favorite Retweet Reply

CackleofRad CackleofRad
@
@Tideliar @jadebio You know who else I think is awesome? Try @phylogenomics and maybe #JGIUM Not medical per se but cool things in the werks
17 hours ago

phylogenomics Jonathan Eisen

Uy vey: got home from #JGIUM & my kids had chlamydia, anthrax, E. coli, malaria, athletes foot, Helicobacter & giardia yfrog.com/gzk75auj
20 hours ago

phylogenomics Jonathan Eisen
Next up at #JGIUM Dan Distel on Shipworm symbionts – note here is a picture of Dan (foreground) from 1992 cruise http://twitpic.com/4cvb3w
22 hours ago

phylogenomics Jonathan Eisen

Apologies all – have to skip end of #JGIUM – follow this hashtag for other’s posts
23 hours ago

phylogenomics Jonathan Eisen
Scholin hacked into unsecured wireless network while on vacation in Death Valley to communicate w/ his sensors in Newport Beach #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Scholin has some of these remote sensors moored off of Newport Beach pier to survey for toxic diatoms #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Holy ecogenomic sensor batman – this remote ESP thing is very cool mbari.org/ESP/esp_2G.htm – can do DNA analysis remotely #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next up Chris Scholin on remote detection of marine microbes in coastal waters and deep sea #JGIUM
24 Mar

phylogenomics Jonathan Eisen
In the Q and A period for Dan Distel some music has now come on over the speakers #oscars? #exitmusic #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel discussing proteomics of shipworm symbionts communities – uses method that focuses on proteins in symbionts not host #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Oh no – Distel mentioned the CaZome when discussing carbohydrate active enzymes in shipworm symbionts #badomicsword #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel: the gill symbionts are in addition to symbionts living in the gut that are known to degrade cellulose #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel: many (~10) types of closely related bacterial symbionts live inside the cells of shipworm in the gill #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Note – here is a link to my #PLoSONE paper with Distel on the genome of a shipworm symbiont plosone.org/article/info:d… #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel: shipworms are very diverse and can live off all sorts of wood & wood like stuff – major wood consuming organisms in ocean #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Dan Distel Works at the Ocean Genome Legacy foundation #JGIUM #coolgroup oglf.org/DistelCV.htm
24 Mar

phylogenomics Jonathan Eisen
Distel: shipworms (which are actually clams) cause billions of dollars of economic damage each year #JGIUM
24 Mar

doe_jgi Joint Genome Inst.
RT @phylogenomics Distel expressing thanks to JGI b/c despite claims by many that sequencing is free, nobody has told his acctg dept #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Distel expressing thanks to JGI b/c despite claims by many that sequencing is free, nobody has told his accounting department #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next at #JGIUM Dan Distel on shipworm symbionts – note here’s a pic of Dan (foreground) from ’02 http://www.scancafe.com/p-59386415-38fa9f
24 Mar

sharmanedit Anna Sharman
Wow. MT @phylogenomics [Ed] Buckler: any two corn [maize] plants are as different from each other as humans and chimpanzees #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next at #JGIUM Mary Ann Moran; Note paper I have w/ her is one Nature fails to make free despite promises nature.com/nature/journal… #opengate
24 Mar

phylogenomics Jonathan Eisen
Buckler described Genotyping by sequencing method from his in press #PLoSOne paper #JGIUM maizegenetics.net/images/stories…
24 Mar

phylogenomics Jonathan Eisen
Buckler suggests the genetic diversity in maize allows it to adapt to local environments better than other species #JGIUM #notbuyingit
24 Mar

phylogenomics Jonathan Eisen
Buckler: genomic domestication analysis w/ Ross-Ibarra lab from #ucdavis: little loss in diversity from landraces -> improved lines #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Buckler: Tripsacum genome has different retrotransposons than maize but otherwise may be useful as source of genetic variants #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Buckler also sequencing Tripsacum – sister genus of maize #JGIUM no chromosomal duplications, very similar gene content to maize
24 Mar

phylogenomics Jonathan Eisen
Buckler: doing maize HAPMAP2 to survey genetic diversity in corn #JGIUM
24 Mar

leonidkruglyak Leonid Kruglyak
So are yeast strains RT @phylogenomics: Buckler: any two corn plants as different as human and chimp #JGIUM #myspeciesisbetterthanyours
24 Mar

phylogenomics Jonathan Eisen
Buckler: any two corn plants are as different from each other as humans and chimpanzees #JGIUM #myspeciesisbetterthanyours
24 Mar

leonidkruglyak Leonid Kruglyak
Ed Buckler RT @phylogenomics: Next up Ed Buckley from Cornell discussing sequencing/using maize genome #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Next up Ed Buckley from Cornell discussing sequencing/using maize genome #JGIUM
24 Mar

sarahcpwilliams sarahcpwilliams
@phylogenomics enjoying yr tweets from #jgium. i’m a big fan of ley and knight. covered their work last year for hhmi: http://bit.ly/g2NEug
24 Mar

phylogenomics Jonathan Eisen
Ley : to study diversity of microbes associated with maize had to get primers that did not amplify chloroplast rDNA #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ley: doing a QTL experiment on maize/corn treating microbes as their quantitative trait #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ley now expanding human microbiome GWAS twin study to include surveying microbes all over body #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley: GWAS studies of human twins has IDd many loci that appear to affect microbial diversity – including some immune system loci #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley is now doing GWAS studies w/ human twins where the phenotype they are looking at is microbial diversity #JGIUM #verycool
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley discussing survey of microbes in one child over two years #JGIUM
24 Mar

phylogenomics Jonathan Eisen
Ruth Ley now up at the JGI User Meeting discussing maize, human microbiotas #JGIUM … Note – I love her work #brilliant
24 Mar

kevinswilson66 Kevin Scott Wilson
@
@phylogenomics : Many thanks for your notes on #JGIUM . I was captivated by them
23 Mar

Symbiologica Juliana Mastronunzio
Thanks for tweets on the JGI meeting #JGIUM from @phylogenomics and @iGenomics.
23 Mar

sdaxen Seth D. Axen
RT @phylogenomics: Schuster: “I would like to finish my talk by discussing sequencing the devil” #JGIUM
23 Mar

Pathh1 Pat Heslop-Harrison
Done that – I found the devil in the detail. RT @phylogenomics: Schuster “like to finish my talk by discussing sequencing the devil” #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: “I would like to finish my talk by discussing sequencing the devil” #JGIUM
23 Mar

iGenomics Dawei Lin
RT @phylogenomics: Schuster: Stays away from traditional sources of ancient DNA like bone and uses hair #JGIUM
23 Mar

doe_jgi Joint Genome Inst.
RT @phylogenomics Schuster: got .1g of hair from 200 year old mammoth sample from Russia and can get mitochondrial genome #JGIUM #fb
23 Mar

phylogenomics Jonathan Eisen
Schuster: got .1g of hair from 200 year old mammoth sample from Russia and can get mitochondrial genome #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster working on thylacine (tasmanian tiger) mitochondrial genomes #JGIUM thylacine.psu.edu
23 Mar

phylogenomics Jonathan Eisen
For more on mammoth genomics see mammoth.psu.edu #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: when you sample extinct organisms you have to remember that different samples may come from different times #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: “You would not believe how much mammoth hair I have washed off myself” #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: Stays away from traditional sources of ancient DNA like bone and uses hair #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster – redundancy in genome sequencing with ancient genomes helps build quality genome assemblies #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: one reason to focus on mitochondrial genomes is that there are lots of copies of the genome per cell #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster : “dont forget about mitochondrial genomes” still lots of species that do not have mt genome sequences #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Schuster: discussing mammoths, moas, thylacines, tasmanian devils and polar bears #JGIUM #museomics #conservation #endangered
23 Mar

phylogenomics Jonathan Eisen
For more on Schusters work on extinct species see cidd.psu.edu/people/scs19 #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Next up Stephan Schuster discussing the Genomics of Extinct and Endangered Species #JGIUM #museomics
23 Mar

Energy_Science Energy Science News
@doe_jgi: RT @phylogenomics Why #badomics words can also be very good: a case in study with museomics #JGIUM http://ff.im/-zyA86 #fb
23 Mar

doe_jgi Joint Genome Inst.
RT @phylogenomics Why #badomics words can also be very good: a case in study with museomics #JGIUM http://ff.im/-zyA86 #fb
23 Mar

phylogenomics Jonathan Eisen
Why #badomics words can also be very good: a case in study with museomics #JGIUM http://ff.im/-zyA86
23 Mar

phylogenomics Jonathan Eisen

Eddy Rubin at the #JGIUM is soliciting input from crowd on future needs of the community
23 Mar

Energy_Science Energy Science News
@doe_jgi: #JGIUM bingo anyone? DOE JGI Director Rubin mentions @phylogenomics GEBA project in his talk on future of DOE JGI #fb
23 Mar

phylogenomics Jonathan Eisen

The perils of giving out #badomics word awards – a prior recipient at #JGIUM just told me he’s still angry at me phylogenomics.blogspot.com/2009/01/worst-…
23 Mar

doe_jgi Joint Genome Inst.
#JGIUM bingo anyone? DOE JGI Director Rubin mentions @phylogenomics GEBA project in his talk on future of DOE JGI #fb
23 Mar

Energy_Science Energy Science News
@doe_jgi: #JGIUM Rob Knight: “There is one universal tree of life which is why projects such as @phylogenomics GEBA are so critical” #fb
23 Mar

phylogenomics Jonathan Eisen
All I can say is that when I was rejected by HHMI a few yrs ago I felt better when I heard Rob Knight got it b/c, well, he rocks #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight – in human microbiome studies you actually need VERY few sequences per sample to get overall trends #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight: “There is one universal tree of life” and giving props to my GEBA genomic encyclopedia project #JGIUM
23 Mar

doe_jgi Joint Genome Inst.
#JGIUM Rob Knight: “There is one universal tree of life which is why projects such as @phylogenomics GEBA are so critical” #fb
23 Mar

phylogenomics Jonathan Eisen
Rob Knight discussing the rationale behind his UNIFRAC metric to comparing communities using phylogeny #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight discussing how sequencing has gotten so cheap and high throughout that analysis tools are the limiting step in many cases #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Rob Knight now up at #JGIUM – he publishes more cool papers per month than just about anyone in microbial research
23 Mar

phylogenomics Jonathan Eisen
Silver: took sugar secreting cyanobacterium and got macrophage to take them up and they survive a little bit #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver: injected sugar secreted cyanobacterium into zebrafish zygotes and get functional fish with cyanos all throughout them #jgium
23 Mar

phylogenomics Jonathan Eisen
Silver: engineered a cyanobacterium secrete sugars so thought maybe they could use this to make photosynthetic animals #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver also interested in biohydrogen production #JGIUM but two problems: most hydrogenases are oxygen sensitive and electron competition
23 Mar

phylogenomics Jonathan Eisen
Silver is working on engineering 3hydroxypropionate carbon fixation pathway from Chloroflexus in E. Coli #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver claimed that Cyanobacteria are responsible for 50% of photosynthesis on earth but I think that must be too high #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Silver working on redesigning photosynthesis via cyanobacteria #JGIUM – says they need to learn a lot of biology still
23 Mar

phylogenomics Jonathan Eisen
Silver: though she tries to get $$ from basic scion agencies , they never fund her #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Pam Silver: uses “redesign of a system can test our understanding of it’s components” to try to get $$ from basic science agencies #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Pam Silver “Biology is the technology of this century” is the message she wants to gt across #JGIUM
23 Mar

phylogenomics Jonathan Eisen
Jerry Tuskan getting some hard but good questions after his talk at #JGIUM – Q and A much more interesting than talks usually
23 Mar

phylogenomics Jonathan Eisen
Next up at #JGIUM Pam Silver – not only brilliant – but also her lab is the source of a good Lady Gaga spoof youtube.com/watch?v=ZilqYp…
23 Mar

phylogenomics Jonathan Eisen

Tuskan using Genome and RNA sequencing and high throughout phenotyping for massive poplar association study #jgium
23 Mar

phylogenomics Jonathan Eisen

At #JGIUM listening to Jerry Tuscan discuss poplar genomics – the place is packed yfrog.com/h82u1nnj
23 Mar

iGenomics Dawei Lin
@
@phylogenomics Terry Hazen talked about it. It can be easily forgot how many people worked behind the scene. #jgium
22 Mar

phylogenomics Jonathan Eisen

Tell me about it: “@iGenomics: It is hard to include all people working on a project into the author list these days. #jgium”
22 Mar

Energy_Science Energy Science News
@doe_jgi: RT @phylogenomics: Personal trivia re: SLAC director Perisis Drell at #JGIUM – previous director Artie Bienenstock was a st…
22 Mar

phylogenomics Jonathan Eisen

Personal trivia re: SLAC director Perisis Drell at #JGIUM – previous director Artie Bienenstock was a student of my grandfather Ben Post
22 Mar

EpiExperts Epigenetics Experts
RT @phylogenomics @doe_jgi: SLAC National Accelerator Lab Director Persis Drell kicks off DOE JGI User Mtg 5pm-use #JGIUM to follow
22 Mar Favorite Retweet Reply

——–
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.

——–

I know – Ego Blogging is so 2010 – But I won. I won. I won. (The Ben Franklin Award …)

OK so the title is a bit much. But I am really happy that I won this years Benjamin Franklin Award, given out by the Bioinformatics Organization. For more on this see …
I found out a few days ago and am rearranging some things to go to Boston April 13 for the award ceremony at the Bio-IT World Conference and Expo.  
From the Bioinformatics Organization web site:

Benjamin Franklin (1706-1790) was one of the most remarkable men of his time. Scientist, inventor, statesman, he freely and openly shared his ideas and refused to patent his inventions. It is the opinion of the founders of the Bioinformatics Organization, Inc. that he embodied the best traits of a scientist, and we seek to honor those who share these virtues

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences.

I like the general sentiment very much.  And perhaps more important – the list of prior winners is an impressive crew.  Again, from the Bioinformatics Organization web site:

Note – my brother won the first one.

Anyway – am thinking about what to say in the awards ceremony.  Probably going to say something about how openness is more than about being at no charge.  Also I might discuss how it would be good to have a female winner one of these days.  Speaking of which – maybe people can give suggestions for women to nominate for next year …

UPDATE 9/25/12: See this Friendfeed discussion for some more comments about possible female candidates. I have copied the text below in case Friendfeed disappears: “maybe people can give suggestions for women to nominate for next year …”. OK, I’ll start: how about Rosie Redfield? If it weren’t for the Life Sciences focus I’d also suggest Heather Joseph. Speaking of Heathers, one H. Piwowar springs to mind whenever Open Foo is mentioned. – Bill Hooker heh, that would be cool someday 🙂 For now, how about Helen M. Berman, Judith A. Blake, Maryann E. Martone, Catherine Ball, or other pioneers in open databases? – Heather Piwowar Janet Thornton. – Heather Piwowar Agreed! – Egon Willighagen In an award speech at ISMB 2005, Janet Thornton expressed gratitude she was able to take years out-with-family and then pick up again. Inspirational. Not relevant for the Ben Franklin award, but wanted to mention it because it made such an impact. – Heather Piwowar

——–
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.

——–

Interesting take (though not completely convincing) take on NEJM farm microbe story

There is an interesting take in Forbes on a recent study NEJM on microbes and people growing up on farms.

Not totally convinced of the opinion of the writer, but with a look.

– Posted using BlogPress from my iPhone

——–
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.

——–

Calling for Nature Publishing Group to return all money charged for articles that were supposed to be free #OpenAccess

Well, in case you did not see, yesterday I got really pissed off at Nature Publishing Group.  Short summary – many articles of mine that were supposed to be freely available on their journal sites were not.  For more information see

People from Nature Publishing Group have responded quite quickly saying they will look into this and try to fix it and indeed they have fixed many if not all of the mistakes in accessibility I found yesterday.  Glad they responded so quickly.  However, their response raises quite a few questions.  Like “what happened?” – as in – why did access get closed off?  And why were they charging to for article use when they should not have been?
It would be good for Nature to publish / post a full description of what went wrong.  And perhaps they will.  Apparently, it was just a glitch in the system.  Whatever the cause however, almost certainly some people paid for access for articles that were supposed to be freely available.  I am calling on Nature here to audit their systems and return all money that was paid for such access.
——–
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.

——–

Today is a day to be annoyed with Nature (Publishing Group that is) #NatureFail

Yuck.  Am getting really pissed off right now.  It is 1:30 AM.  I am tired.  And I am now angry.  I was writing a post about a recent trip, and wanted to link to an article I was a coauthor on.  The article was the paper on sequencing and analysis of the genome of Arabidopsis thaliana.  So I googled “Arabidopsis Genome Initiative” and found the link to the paper at Nature.  And much to my surprise I found this waiting for me:

Why is that a surprise?  Because the genome paper is supposed to be freely available to all forever, under a policy Nature developed for papers reporting new genome sequence data.  I am tired or I would write more about the history of this.  But another time.

So then I looked for other genome papers I have published in Nature.  And so I looked for the Plasmodium genome paper.  And I got this:

Grand.  That one was supposed to be free forever too.

And so I looked at many others.  And for most, I got the same thing.  Not freely available.  If I were not at home, I would not have noticed this because I have access at work.  And I could get access at home by setting up the UC Davis library VPN system.  But fortunately I do not do that or I would not have discovered that Nature, not for the first time mind you, has turned articles that were supposed to be freely available forever into charge for access articles.  I know.  I know.  This is probably just some glitch in their system.  They really do seem committed to trying to make these available.  But clearly, the system either does not work well.  Or they are not committed to it.  Either way this is really annoying.  In some cases, the papers were sold to communities of scientists in part with the “These will be freely available to all forever” line as part of the sell.  I am deeply worried about my recent Genomic Encyclopedia paper which is also supposed to be freely available forever.  Right now it still is, which is good.  But how long will that last?  And I note, though Nature people have said they would try and fix it, Nature still incorrectly claims Copyright to that article on the PDF.  Personally, I like most of the people I know at Nature Publishing Group and like many of the things NPG does.  But this is getting really annoying.  And it just goes to show – the ONLY way to go it seems is full, complete Open Access which the journals cannot magically then take away.

——–
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.

——–

Norman R. Pace visit to #UCDavis; discussing microbiology of the built environment #microBEnet

Norman R. Pace, from UC Boulder, gave a talk at UC Davis last week about microbial diversity.  In his talk he discussed some of his recent Sloan Foundation funded work on “microbiology of the built environment” including studies of shower heads, indoor swimming pools, water supplies, and hospitals.

Pace is one of the pioneers of DNA based studies of microbes in the environment.  His initial work on studies of ribosomal RNA from uncultured organisms (started more than 20 years ago) helped launch the field.  For more information on his work see his lab page here

If you are interested in the microbes that are found in showerheads, his PNAS paper on this (which can be found here) on this from 2 years ago got a lot of press.  See for example this Science Friday
and this New York Times article by Nicholas Wade.

Pace was at UC Davis as part of the Storer Major Issues in Modern Biology Lecture Series.

I note, I have written about Pace before a few times including this:
Here’s hoping molecular classification/systematics of cultured & uncultured microbes wins #NobelPrize in medicine

I note we have a new project as part of this Sloan program to facilitate communication and networking and sharing information as part of this project.  My lab is creating something called “microBEnet” – the microbiology of the built environment network.  We are just getting our real site up and running.  For now you can find out some information at a temporary page http://microbenet.blogspot.com/

——–
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.

——–