Eisen Lab Blog

Good kids activity around Davis: Aerospace Museum of California

Good time today with my kids at the Aerospace Museum of California. Just East of Sacramento – with a nice facility, great outdoor playground, and lots of plances and satellites and rockets and other things. My kids loved it. Here are some pics:

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

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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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Quick one here: nice pic of "Earth From Mars" from NASA

Just a wee bit humbling here. H/T to Andy Fell.

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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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New hotel at #UCDavis is quite nice

Here is a little video I made when I went to pick up Rebecca Skloot for her talk at UC Davis last week. She was staying at the new UC Davis hotel University of California Davis Hotel | Hyatt Place which is on campus right near the Mondavi Center. The hotel seemed very very nice.

Just thought I would post the vid — seems like it is a good addition to the area hotels with the one exception that it is not in downtown.

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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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Protect that biodiversity – wear protection

Here are some pics of some biodiversity protecting devices seen around here ..

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

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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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47170 papers referring to #HeLa in PubMed Central (re talk today by @rebeccaskloot )

Wow – did a search of PubMed Central for the keyword HeLa because Rebecca Skloot is here today to talk about her book “The immortal Life of Henrietta Lacks” which is about the woman behind the HeLa cells.
And there are a wopping 47170 papers in PMC that come up. I am sure some of these will be not about HeLa cells but most seem to be.
Here is a link to the results: hela – PMC Results
That’s pretty incredible – 47000 or so papers, freely available, all with some reference to this one human cell line.
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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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Yuck – rRNA databases restrictions on sharing/reuse create major complications

Well, this is annoying. I started to look at the sharing policies for data from various ribosomal RNA databases. And boy was I surprised. One database, the RDP, run out of Michigan State University has a page with information about their policies. The page says the following:

By downloading data (“Data”) from the Ribosomal Database Project (“RDP”), you agree as follows:

Data are copyrighted by the Michigan State University Board of Trustees. 

You may use the Data for your own non-commercial research purposes, and may make derivatives from the Data for your own non-commercial research purposes. All other rights are reserved by Michigan State University. 

You may not sell the Data or any derivatives you prepare from the Data, nor may you provide the Data or derivatives you prepare to any third party for commercial purposes. 

MSU makes no warranty, express or implied, to you or to any other person or entity, including without limitation the implied warranties of merchantability or fitness for a particular purpose of the data. MSU will not be liable for special, incidental, consequential, indirect or other similar damages, even if MSU or its employees have been advised of the possibility of such damages. 

You will only distribute the Data or derivatives with copyright notices. 

If you publish from the Data, you will acknowledge the contribution of Michigan State University and the Ribosomal Database Project 

This cannot be right? Most of the data came from Genbank so certainly they cannot Copyright it. Now it may be that they are referring to sequence alignments and other derivatives of the raw data but this implies that all the data in the RDP is Copyrighted.

Mind you, I do not like the policy even if it is just for the derivatives of the data (e.g., alignments) since this will certainly make some things very difficult in terms of publishing.  For example, if I use an alignment from RDP, how do I provide the alignment when I publish a paper? If I provide it, do I only provide it to non commercial entities? Does that mean, in essence, commercial entities would not be allowed to see alignment figures?

I get that people do not want people to download and then redisplay all of their content, thereby in essence possibly killing the original database.  But Copyrighting all the data in the database?  Even data that is not theirs?  Is this just a scare tactic of some sort?  A mistake? I cannot tell.  There must be better ways to prevent someone from redisplaying the entire database structure and content without such severe tactics. 

So – is this an issue just with RDP? Turns out – no. The SILVA database in Europe has some restrictions too:


The SILVA databases and services/tools offered at http://www.arb-silva.de are FREE FOR ACADEMIC USE. All downloads can be used, modified and redistributed within the academic environment without any limitations.

Users from NON-ACADEMIC/COMMERCIAL ENVIRONMENTS can also directly access all downloads including the results of the SILVA Webaligner (SINA) but only for limited/temporary use (only for test purposes).

If you are interested in unlimited usage of the SILVA databases/services or parts of them within a non-academic/commercial environment, please send an e-mail to ….

Though thankfully they do not seem to be trying to Copyright or reserve rights for other people’s data. They simply refer to downloads from their database and what one can do with such downloads. They never say they own in any way the data itself.

Fortunately greengenes seems to have no restrictions on the use of data or anything downloaded from there.  Though I am still looking into this.

I think it is time for rRNA researchers to think carefully about using data/alignments/etc from databases like Silva and RDP.  If one uses an alignment from one of these databases it is possible one would be violating the DB policies if one released the alignment as part of a paper.  Yet, if one uses the alignment in the paper, one should release it.  So seems better to seek out and used fully open datasets and alignments and other results.

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Below are some discussions relating to some tweets I posted about this issue yesterday:

http://friendfeed.com/treeoflife/864b7ec9/rrna-database-rdp-says-it-copyrights-data-how?embed=1

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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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After 20 yrs of email my first "reply all" SNAFU; reply all apology etiquette?

Oh well. I had a good run. I have been really careful over the years with avoiding the “reply all by accident” mistake that has created so much comedy and pain to others. I am not sure how I have avoided it so well – in part I am careful – but in part clearly just lucky. And I have witnessed some pretty pretty funny reply all mistakes as I am sure have most people out there. The funniest was one by well known evolutionary biologist who made a bit of a faux pas in replying to a message sent to the evoldir mailing list in the early 1990s. After witnessing what happened in particular with that one, I did become more careful with replying.

So then yesterday, while at Stanford for an Evolutionary Genomics Symposium, I was tweeting and friendfeeding the talks (will post notes in a little while) and I was doing this all on my iPhone. I like the iPhone, but typing notes on it, and looking up Urls of papers, and copying and pasting things to Friendfeed or twitter, is not that easy. But I was trying to keep up. And I logged in to my gmail to look up the schedule, and saw an email message from Jim Bristow the Deputy Director of the Joint Genome Institute that I had meant to respond to earlier.
In his email Jim requested, quite reasonably, that people that have projects that are done in collaboration with (or entirely by) the Joint Genome Institute, add a little statement to their Acknowledgements in their publications, regarding the funding for the JGI.
We had had a paper come out Friday supported by DOE and done in part at the JGI, and I looked at the paper on the PLoS One site and we had the right acknowledgement in our paper, thanks to a suggestion from David Gilbert who handles Public Affairs at the JGI.
So I wrote a little email response to Bristow’s email. My email was brief:

I think we did it right here
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010209

Just a link to the paper and a suck up statement telling Jim that I think we did the Acknowledgement the way he wanted it.

All sounds pretty boring right? That was until I clicked send, which sent the email, somehow, to all the people on the DOE mailing list – basically all people that have ever worked with JGI. And if you reread my message, it sounds like I am bragging “did it right” about how great our paper was.
I have already gotten three responses, all thinking I meant that our paper was “right”.
So here is my question for everyone. What do I do now? Do I send another message to all saying “Oops – I did not mean to send that to everyone and that I was not bragging about our paper? Or do I lie low and let it blow over?
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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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Experiments in scientific sharing contd: Biotorrents

Yesterday a paper from my lab (by Morgan Langille, with me as co-author) was published in PLoS On: BioTorrents: A File Sharing Service for Scientific Data

In it we describe a new website dedicated to the sharing of biology related files via BitTorrent, the popular distributed file sharing system. The abstract sums things up prety well:

The transfer of scientific data has emerged as a significant challenge, as datasets continue to grow in size and demand for open access sharing increases. Current methods for file transfer do not scale well for large files and can cause long transfer times. In this study we present BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology. BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. BioTorrents is available at http://www.biotorrents.net.

Personally, I am not sure if Biotorrents is going to end up being used extensively. I hope so. I think it is a great idea of Morgan’s. But more importantly, I believe it represents something we need more and more of in the “Open Science” movement. We need experimentation with all sorts of methods for improving sharing. The sharing of large electronic files, such as datasets of some kind (e.g., sequences, pictures, mass spec results, etc) are rapidly becoming a major complication in scientific research. If one publishes a paper on whatever, or even before one publishes a paper, sharing the data associated with the work is not always simple. Biotorrents could help in this in that sharing files via BitTorrent is very simple and easy. And if some data sets are of great interest, and if a lot of people start using Biotorrents, then the download and distribution of the data sets of interest will get faster as more and more people serve as hosts to contribute to the distributed file sharing.
If you want to learn more about Biotorrent, the best place to go is to Morgan’s blog “Beta Science“. In particular you should read “An interview with the creator of Biotorrents” where he interviews himself.
Also, Janet Fang of Nature News has just written a brief post on Biotorrents: “Biotorrent aims to open data sharing floodgates” where they quote me and Morgan. I particularly like the ending:

“Someone could download all the Nature papers and post them there, but we’re not encouraging that,” Eisen jokes. All PLoS papers are already on BioTorrents.

More on the web is coming out regarding Biotorrents and I will try to post some links here, including to some slightly older stuff
Some links:
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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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Davis, CA schools and their class size issues

Cross posting here from my “normal” non science life as a parent and resident of Davis, CA. This video was made by Hal And Carin Sloane, who are both neighbors and friends of mine. It is part of a fundraising effort for the Davis Schools Foundation and a general awareness raising campaign about the effects of budget cuts on K-12 education.

http://vimeo.com/moogaloop.swf?clip_id=10872193&server=vimeo.com&show_title=1&show_byline=1&show_portrait=1&color=&fullscreen=1

Davis Schools Foundation “Class Size” from Hal Sloane on Vimeo.

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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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Things to do to wish "Happy Birthday" to my brother, Michael Eisen

Just to make sure people know I am posting here happy birthday wishes to my brother, Michael Eisen. If you want to get him something, I suggest doing one/all of the following things

If people have any other suggestions about what to do in honor of Dr. Michael Eisen, please post …
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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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