Eisen Lab Blog

Obsession with #Badomics words gets covered in the Wall Street Journal

My obsession with #Badomics words got covered by Robert Lee Hotz on the front page of the Wall Street Journal: Heres an Omical Tale: Scientists Discover Spreading Suffix – WSJ.com.

For more on this see my Tree of Life blog here.

Bill and Melinda Gates want to give you $250,000 #Vaccines

All you have to do is apply and, well, win … just got this email from the Gates Foundation – definitely worth nominating someone if you think they are doing good work.  Once again, the Gates Foundation is helping change the world … Jenny McCarthy need not apply.  Here is the email:

Dear Colleagues:

Do you know someone who is improving vaccine delivery in the developing world? Now is the time to nominate that person or group of people for the second annual Gates Vaccine Innovation Award. Time is running out — the deadline for nominations is August 31, 2012.

The Gates Vaccine Innovation Award is open to individuals from any discipline who work on the delivery of vaccines. Candidates from academic institutions, governments, health care facilities, research institutions, non-profit organizations and for-profit companies may be nominated.

We are looking for ideas, big or small, that have resulted in tangible improvements in immunization coverage in developing countries.

We invite you to nominate individuals or groups of individuals who have achieved significant improvements in the prevention, control, or elimination of vaccine preventable diseases through immunization.

The winning nomination will be recognized with a $250,000 award.

Read about the 2012 Gates Vaccine Innovation Award winner Dr. Asm Amjad Hossain here.

Thank you for your continued support of this important 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.

——–

MMMMM: Microbes, Metagenomics, Minnesota, Mississippi, & Morrison

A really cool project is discussed in an issue of the University of Minnesota News: Microbes in the Mississippi : UMNews : University of Minnesota.  I found out about it through an automated web search I have running in the background via Google.  The news story discusses a project in which scientists from U. Minnesota are sampling the microbes in the Mississippi River using metagenomics.  Their data is (apparently) deposited into the IMG database and shared with the world (though I note – no link is provided).  This is exactly the kind of new project that cheap sequencing enables …  I hope to see many many more like this …

——–
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.

——–

Lab meeting Thursday August 16th

We will be meeting on THURDSAY this week from 1:30 to 3:30 in room 6202 of the Genome Center.
Srijak bhatnagar will be presenting his work.

Amazing video from Louie Schwartzberg / Moving Art "The Beauty of Pollination" #scifoo

I met Louie Schwartzberg at the SciFoo meeting last week. He makes absolutely amazing Nature videos … here is one.

——–
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.

——–

The recursive tree of life – how a Twitter -> Blogger loop was created and broken

Earlier today I wrote a post that went something like this

Still searching for a good way to post a roundup of my twitter conversations to my blog. There don’t seem to be any good systems for doing this on Blogger. So I have, at least this week, created a Storification of my tweets and some of the associated conversations … not ideal probably but still …

I am not sure how it finished because, well, I deleted the post by accident a bit later in the day as you will see.

I do recall I posted an embedded version of this storification.

And this led to some useful responses such as

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js SO this seemed potentially interesting .. and I decided to look into IFTTT. It took a bit to figure out anything about it but at first glance it seemed not right. So I posted a response

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js So I created an IFTTT account and hacked around for a bit. I connected IFTTT to some of my social networks and then I set up two automated feeds. One that would post from Twitter to Blogger and one that would archive my Tweets to Dropbox.

 And then I ran a test. I wrote a tweet to see where it would end up and whether / how it would end up on blogger. The tweet read something like “I am testing IFTTT for autoposting my tweets to my blog” and then I went to blogger and looked to see if anything showed up there (I note – I ended up deleting this tweet later in the day – more on this in a bit). But alas it did not. At least at first. So I looked at IFTTT in more detail and something there said it usually scanned twitter every 15 minutes so it might take some time for the tweets to show up on my blog.

Meanwhile I made another test tweet that read:

Testing http://t.co/1nWox0lt again . please ignore August 12, 2012 at 09:00AM http://twitter.com/phylogenomics/status/234680659233357824 Alas I deleted this one too (again – more on this deletion frenzy in a bit).

I note – I ended up deleting this one too – but by this point I had launched the “tweet to dropbox” system at IFTTT so this tweet was archived.

And then here was the big big big mistake.  I left the house – first to go shopping and then to a wedding (of a brilliant PhD student at UC Davis).  And I shut off my phone.  After the ceremony I turned on my phone again to take some pictures.  And (of course) I checked Twitter.  And thats when I noticed something had gone horribly wrong.

This is what I saw first:

//platform.twitter.com/widgets.js “Hmm” I thought. What could that be about? First, I thought it was about all the microbe posts from yesterday. But then I saw some other posts.

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

Uh oh.  Or more like “Oh shit.”  What the $&$# was going on?  And suddenly I realized, I must still have a “blogger to twitter” autopost feature set up through blogger.  So IFTTT was posting to blogger anything I tweeted and then Blogger was posting anything there to Twitter.  A loop.  Oh no.  A loop.  Not supposed to happen to me.

So I dreadfully looked at my Twitter feed to see how many tweets had been posted in this loop.  And it was quite a few.  Oh no.  What to do?  And I panicked a bit.  I just started deleting tweets so that people would not be driven crazy by the loop (at this point I did not know how many were in the loop).  And I ended up deleting not too many but more than a few (something like ten).   I can’t embed them of course, because I deleted them.  But I do have them in my new Dropbox twitter archive.

The Tree of Life: The Tree of Life: Testing an http://t.co/1nWox0lt IFTTT system for posting tweets to… http://t.co/xtuELMBb
August 12, 2012 at 09:06AM
http://twitter.com/phylogenomics/status/234682399693352962
– – – – –
The Tree of Life: Testing http://t.co/1nWox0lt again . please ignoreTesting tweet to blogger system from IFTTT http://t.co/THhFkG7S
August 12, 2012 at 09:06AM
http://twitter.com/phylogenomics/status/234682401337524224
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: Testing an http://t.co/1nWox0lt IFTTT system for posting… http://t.co/LKd976jR
August 12, 2012 at 09:22AM
http://twitter.com/phylogenomics/status/234686366678654976
– – – – –
The Tree of Life: The Tree of Life: Testing http://t.co/1nWox0lt again . please ignoreTesting tweet to blogger… http://t.co/bOVmkEB0
August 12, 2012 at 09:22AM
http://twitter.com/phylogenomics/status/234686368612245505
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: Testing http://t.co/1nWox0lt again . please ignoreTesting… http://t.co/EGWmjifq
August 12, 2012 at 09:37AM
http://twitter.com/phylogenomics/status/234690113525915648
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing an http://t.co/1nWox0lt IFTTT system… http://t.co/h8iOJFey
August 12, 2012 at 09:37AM
http://twitter.com/phylogenomics/status/234690132605804545
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing http://t.co/1nWox0lt again . please… http://t.co/RYKpNwdE
August 12, 2012 at 09:51AM
http://twitter.com/phylogenomics/status/234693721545920512
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing http://t.co/iXtneMx2… http://t.co/Ueg9mK2F
August 12, 2012 at 10:07AM
http://twitter.com/phylogenomics/status/234697523661512705
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing… http://t.co/lwELrRso
August 12, 2012 at 10:21AM
http://twitter.com/phylogenomics/status/234701228347633664
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/Vz9GDrUI
August 12, 2012 at 10:36AM
http://twitter.com/phylogenomics/status/234704905246494721
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/PcTqp1mg
August 12, 2012 at 10:51AM
http://twitter.com/phylogenomics/status/234708632443441152
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/YecKMslQ
August 12, 2012 at 11:05AM
http://twitter.com/phylogenomics/status/234712346797428736
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/T2rE2shW
August 12, 2012 at 11:21AM
http://twitter.com/phylogenomics/status/234716246023745536
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/lYFK57gx
August 12, 2012 at 11:35AM
http://twitter.com/phylogenomics/status/234719738536796160
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/7X0Bypuj
August 12, 2012 at 11:50AM
http://twitter.com/phylogenomics/status/234723474831204352
– – – – – 

Oooh – that was bad.  But how to control it?  I first tried to unlink the IFTTT app from Twitter from inside Twitter.  That is, I tried to remove the permissions the IFTTT app had to post/read my twitter feed.  But Twitter seems to not provide access to applications control from a mobile device.  Crap.
So then I tried to log on to Google Blogger and unlink it from IFTTT.  Also no success.  Seems that many systems default to mobile options and do not provide access to full features no matter what.  
So then I called up my brother and thankfully he was there and after telling him my Twitter password (risky I know .. given my families tendency for pranks) – he deactivated the IFTTT access to Twitter.  Phew.  That hopefully would break the loop.  But to be safe I decided to check Blogger.  And Oh man- there were a lot of posts there too.  That was going to drive people crazy I am sure just as all the tweets did.  So I kind of panicked again and deleted all the IFTTT posts.  And I even accidentally deleted the post that launched all of this (see above).  Uggh.  I don’t like it when people delete posts but I needed to get control of this loop.  I figured, even if the IFTT Twitter -> Blogger system kept going – because it apparently only checked Twitter every 15 minutes I could keep the loop under control by monitoring Twitter and Blogger and deleting any posts before they got reposted somewhere else. 
So – while sitting at the wedding reception I did exactly this.  And it seemed under control.  So I posted to Twitter to apologize and tell people things seemed better.

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js So – seemed under control – sort of. And then I made the mistake of looking at Facebook. Oh no. Autofeeds there up the wazoo too. I am going to delete those later. What a nightmare. And it could have ben much worse if I did not catch it at the wedding. Because now I have to head to Berkeley for a birthday party for my brother’s kids. Hopefully – the loop is broken. And I have only one think left to say. The tree of life. The tree of life. The tree of life. The tree of life ….

UPDATE: My brother did indeed make use of my Twitter password, the bastard

——–
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.

——–

Interested in MiSeq Illumina sequencing of low diversity libs – read this

Everyone -if you are interested in using the Illumina MiSeq to sequencing low diversity libraries – read this … Sequencing low diversity libraries on Illumina MiSeq from THE Nick Loman.

——–
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.

——–

History of the Lake Arrowhead Microbial Genomes meetings

Recommended meeting for those interested in microbial diversity and/or microbial genomics: Microbial Genomics – ARROWHEAD 2012

Among the reasons to go:

And if you want to know more about past meetings see below:

——–
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.

——–

Lake Arrowhead past meeting notes

Posting notes and notebooks from past Lake Arrowhead genomes meetings

Notes and materials from MARS Sample Handling Workshops 2000-2001 #Curiosity

I had the pleasure of serving as a panel member for some NASA sponsored “Mars Sample Handling Workshops” in 2000-2001 and thereabouts.  I have all these materials still from those meetings and in light of the Mars Curiosity Rover landing and other recent activities I thought it would be good to share them.  Most/all are public domain materials but not all are easy to find so I thought I would post them here.  Note – I have done no clean up of scans – will do so at some point. Enjoy.