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Jonathan Eisen
RT @kittymicrobiome: WOWEE! @artologica painted some kitty microbiome species and they look SUPER!!!
Nils Reinton
GMOs: Gene Transfer Is Neither Unnatural Nor Dangerous -
GMOs: Gene Transfer Is Neither Unnatural Nor Dangerous
"Transferring a gene from a fish into a plant does not make the plant swim any more than stealing the radio from someone’s Maserati and putting it into my Honda Civic would turn it into a high-performance sports car. Indeed, scientists routinely use genes from mice, fungi, plants and even bacteria to substitute for their human counterparts, and vice-versa – which they often do perfectly." - Nils Reinton from Bookmarklet
Ana Nelson
So impatient for universal open access of journal articles and the platforms/networks of awesome that will be built on top of them.
Bret Taylor
We had a couple database issues, but FriendFeed should be back up and running now. Sorry for the trouble.
Thank you. - Anne Bouey
Thank you, Bret! - Melanie Reed
Thanks Bret.. Is it possible the image embeds broke during the glitch? I know it worked earlier today!! - Chris Myles
Deepak Singh
A different view on search results -
A new view that provides an interesting, alternative way of visualizing results from a search against the hmmer server. - Deepak Singh
Abhishek Tiwari
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega -
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal OmegaMultiple sequence alignments are fundamental to many sequence analysis methods. The new program Clustal Omega can align virtually any number of protein sequences quickly and has powerful features for adding sequences to existing precomputed alignments. - Abhishek Tiwari
Michael Nielsen
My new book on open science and related topics has just come out. It's currently available in hardcover from, and should by Oct 21 become available for Kindle, and from other booksellers (when it's not already). - Michael Nielsen
Server looks down. - Daniel Mietchen
Daniel: yes. I've had very few problems with my host (Dreamhost), but today the machine my blog is hosted on had filesystem problems. It should be up again very soon. - Michael Nielsen
And it's still not back up :-( - Michael Nielsen
Now back up :-) - Michael Nielsen
Allyson Lister
Fabulous lineL: HT @CameronNeylon RT @kissane: "Metadata is a love note to the future." #nypl_labs
Fabulous lineL: HT @CameronNeylon RT @kissane: "Metadata is a love note to the future." #nypl_labs
Pierre Lindenbaum
New blog post: A FUSE-based filesystem reproducing the NCBI Taxonomy hierarchy.
Hahaha... cool! I want my ontologies mounted like this! - Egon Willighagen
yep, GeneOntology was my first idea but as some nodes can have more than one parent, it would have been more difficult to implement. - Pierre Lindenbaum
But I wonder if we can use this API to create some "virtual project folders" : XML->filesystem with symbolic links to the flat files. - Pierre Lindenbaum
Wouldn't that just show files in multiple folders? You could do something fancy with 'symbolic links' if that child has a preferred parent... - Egon Willighagen
yes you're right. - Pierre Lindenbaum
Steve Koch
Erika Check Hayden's Nature News article about Rosie Redfield's Open Science replication of arsenic work
David Bradley
Backup all your GMail and Google+ data -
Google has a tremendous number of free services they offer which many of your probably take advantage of. But have you ever considered what you might lose if all of a sudden you lost access to your account? Just like all import data on your hard drive, your critical data in “the cloud” should also have backup consideration. Google lets you "liberate" all your data so that you can download and store with feet firmly on the ground rather than head in the clouds... - David Bradley
Cameron Neylon
Towards Executable Journals -
There is also Sweave of course... - Egon Willighagen
There are some small simple steps that chemistry publishers can use immediately to add "automatic executable functions" to catch errors in papers. For example simply running a melting point search using this free open tool would have caught a huge melting point error in a 2008 paper on this compound... more... - Jean-Claude Bradley
Have you started using Chem4Word yet? - Egon Willighagen
Egon - actually our institution no longer supports Microsoft Office for students as of the fall term :) - Jean-Claude Bradley
Oh, cool! - Egon Willighagen
How Nature's lawyers drown investigative science journalism | Brian Deer -
Nature apparently thinks they are "the house journal of science". Can you say "hubris", boys and girls? (And this is just an aside, quite separate from the odious contract issues.) - Bill Hooker
Wow, that contract language is amazingly similar to one I received on being asked to publish in a famous magazine - errr, no I, the little guy is not going to indemnify you, the magazine, for anything, kthxbai! Sadly, on receiving my heavily redlined copy back, I was told that most people eagerly sign up without making any changes whatsover. Unbelievable. - Sally Church
Rajarshi Guha
has anybody visualzed networks with ~ 30K nodes and 1.5M edges? What tools have you used? Were they interactive? Or batch mode? Pointers would be appreciated
I think the most important bit is here how to summarize the networks, rather than visualizing all edges... - Egon Willighagen
Try networkx for summary/exploration. Otherwise Cytoscape might work if you've got a system with tons of memory; I've used it to look at compound similarity across a chemical library. - Donnie Berkholz from BuddyFeed
Not sure that visualization will necessarily but that useful at that scale. Could you do dimensionality reduction by PCA or something? - Mr. Gunn
not sure that dimension reduction or PCA makes sense for this type of data - the connectivity is what I'm after (which I can obviously characterize via various metrics). Might have to go in to get subsets etc. But also, the visualization is more to get a (hopefully) pretty picture than anything else - Rajarshi Guha
I never had to look at any network of that size. I am not sure you can get much from looking it. I would try to reduce the complexity in some way. If you have genes/proteins you could bring it down to complexes/pathways/GO terms. - Pedro Beltrao
I would happily recommend igraph, callable from python, and also very nice integration as an R package. The interactive plotter works only for small graphs; you'll want to experiment with the layouts if your goal is to get a pretty picture (e.g. the Fruchterman-Reingold layout). Looking at network properties (degree distribution, assortativity, clustering coefficient, etc, is also very straightforward.) - Michael Krein
Thanks, I second your recommendtion - I'm using igraph to get the numeric metrics and it's sweet! - Rajarshi Guha
+1 iGraph. Have you tried Gephi Gephi is interactive, I have used it to visualize a similar bignetwork using Gephi. Also you could check the alternate way to visualize the networks as linear networks using Hive - Khader Shameer
Try this one for more information about using Graphviz for very large network graphs . Also Python NetworkX ( is quite robust, some one has already done a Hadoop plug for the NetworkX, I cant find URL though. - Abhishek Tiwari
The 30,000 nodes shouldn't be a problem. Showing the 1.5M edges creates a visual mess at the overview level. I found it best to leave them out of the projection all together, since proximity often shows the same macroscopic relationships Perhaps use semantic zoom and/or edge bundling to show them only when zooming in. For algorithms LGL and OpenOrd would be good. OpenOrd is implemented... more... - Don Pellegrino
@don, thnaks for the pointer. I think the general view that looking at the netire network is likely not useful - subsets are easier to view and work with. igraph is performing like a champ! - Rajarshi Guha
Mr. Gunn
Be honest. Curing cancer is not your primary goal | My Research Rants -
"Go and ask your fellow postdoctoral researchers in the biology, chemistry, medicine,… fields what it is their main goal. I’m always getting the same answer: I’m developing a cure for cancer (replace cancer by your “favourite” disease”). In fact, this is a big lie." - Mr. Gunn from Bookmarklet
Oh this is a nice sharp exposition of this idea. Definitely like...and need to write something similar and scathing soon as well... - Cameron Neylon
Jonathan Eisen
In 2007 Nature wrote editorial about free genome paper access; but they are not actually doing this fully #opengate -
Andy Maloney
Yep, open science works! My open dissertation outlines how to make a gliding motility assay using kinesin and microtubules. It took me nearly a year to perfect the procedure. It took a fellow graduate student at UCSC only two weeks to reproduce my procedures from my open dissertation and get the assay to work. Which, is not trivial and not easy.
Awesome! - Bill Hooker
Cool, found the dissertation page if anyone else wants to see - Mike Chelen
This is so cool! - Cesar Rodriguez-Rosario
Bill Hooker
Goodbye academia, I get a life. – blog.devicerandom -
"Until not so long, I thought that it was worth it. It was something that I had never questioned so far. I wanted to be a scientist since when I was five. I had done everything to become a scientist. I was a scientist in one of the top universities of the world, in one of the top five research groups on the subject. I had won a personal fellowship to fund myself. Most of my self-esteem, of my very concept of self-realization, relied on myself being a scientist. The very idea of quitting academia was a synonim of personal failure." That right there is the engine of the pyramid scheme. - Bill Hooker from Bookmarklet
I've heard more senior scientists dismiss this attitude as a 'typical cynical postdoc, not skilled/smart/hard working enough to make it to tenure'. These same senior scientists were junior scientists in a very different time, usually before the huge expansion of the number of available PhD candidates, where the ratio of supply to demand of graduates wasn't nearly as imbalanced. This... more... - Andrew Perry
Re: the pyramid scheme that BH and AP bring up -- I completely agree and want to add one additional point: its not just that an untenable economic situation has emerged which grad schools sweep under the rung -- its that the community itself seems to look down on those who leave academia to join industry/business or publishing or something else entirely. High rates of failure at achieving tenure at impressive school X would be ok if young students/scientists felt they had viable alternatives - Benjamin Tseng
I agree Benjamin - I've noticed that in many academic institutions career options outside that system are rarely discussed openly, and leaving academia is considered failure (even if someone leaves to do something arguable more useful). Granting bodies usually want to encourage collaboration between industry and academia through special funding opportunities (eg, the ARC Linkage grants... more... - Andrew Perry
some more comments here: and I agree with Andrew .. thats why we should fight against even the language that is used (i.e. "quiting science") - Pedro Beltrao
Jonathan Eisen
Cool paper, & winner of "worst new omics word award": Predatosome -
Perhaps authors are now deliberately baiting you in order to get publicity for their paper :) - nlomioni
Yes, sure that would be a good strategy. May have to rethink whether I write about the paper in the future. - Jonathan Eisen
Eisenome: the set of all papers profiled in the "worst new omics word" series... - Andrew Su
Oh man, I can't believe I never thought of Eisenome before --- I am definitely going to find a way to use that - Jonathan Eisen
Liking for "Eisenome". :-) - Bill Hooker
Wouldn't that be the "ironome" ... i.e. all genes involved in iron metabolism? Someone is already researching "you", Jonathan: - Iddo Friedberg
perfect Iddo - my baseball nickname for years was "Ironman" - Jonathan Eisen
Graham - not anymore. - Mr. Gunn
Mr. Gunn you are in deep trouble if that was you - Jonathan Eisen
I was kidding, but is it really not avail. anymore? Could be the evil speculative domain parking stuff practiced by the likes of GoDaddy et al. - Mr. Gunn
Despite my use of twitter for the #scio10 meeting, I continue to be amazed by how awesome friendfeed is --- friendfeed - I am back - Jonathan Eisen
Not that I wont still tweet - but I do love friendfeed - Jonathan Eisen
Make good use of it. It's a rare scientist that can play this trick of a self-named -ome. "Suome" doesn't quite roll off the tongue. "Lindenbaumome"? "Steelome?" "Szczesnyome"? None quite have the same ring. "Hookerome" is close, but I'm sure that's just putting a nerdy spin on a third-grade playground taunt (just a guess Bill)... - Andrew Su
@Andrew "Iddome"? Going back to the hiring and P&T discussion, an inner joke in my department says I was hired only because one of the senior researchers there is working on indoleamine 2,3-dioxygenase (IDO). Hey, it's as good a metric as the ISI impact factor... - Iddo Friedberg
+1 Iddo - thanks for a hilarious discussion Andrew, Graham, Johnathan.... - Mr. Gunn
Andrew, even the judge at our wedding made fun of my name, pointing out that well, of course my wife wasn't going to take *that* name. I'm just wondering how I get a grant to study my own -ome... :-) - Bill Hooker
The Koch a doodle doo -ome is unveiled - Steve Koch
Thank you all for this great discussion. Just changed my name in all public registers to "Nils Reintome". - Nils Reinton
"Lindenbaumome" may not work, but surely it would be the "Lindenbome", which kinda does.. I'm not even going there for my own name... - Simon Cockell
@Steve Koch... is still free... - Iddo Friedberg
Maybe we should do homeopathomics - Jonathan Eisen
@Iddo -- good idea. I snapped it up, and tried to use it for good, not evil :) Maybe someday I'll know what to do with it - Steve Koch
As requested, I'm officially adding the Björnome: - Björn Brembs
Jonathan Eisen
Just submitted my first data set to Dryad - seems like everyone should do this ...
Rufus from the Open Knowledge Foundation was asking for datasets there any coordination on this...? - Noel O'Boyle
All datasets in Dryad are CC0, so he is welcome to any and all data in Dryad, for any purpose! - Heather Piwowar
Alex Holcombe
finally, the Australian Research Council supports open access
If you have ideas of how this should be made stronger for future years, maybe we can sign a letter to the ARC together. It would be good to move towards a stronger mandate - Alex Holcombe
why the limit of 2% of funding to be used for OA? avg ARC DP grant is something like $100,000 a year (actually less I think), and $2000 would only pay for one PLoS ONE paper at $1350/paper or if you prefer the today-announced Nature Publishing Group PLoS ONE imitation journal, Scientific Reports it would cost you... $1350/paper! So you could only do about one, although other OA journals... more... - Alex Holcombe
I was thinking it was reasonable guideline figure but I'd forgotten that ARC grants aren't really paying the full costs so that could be a problem. The other option is to get ARC to pay overheads properly of course. - Cameron Neylon
It's about what Wellcome budget for, for instance in their costing for OA charges in general. - Cameron Neylon
Don't understand the need for a limit. Just budget it in the grant proposal. Done. Was anyone here asked to consult on this? - Matthew Todd
The explanation I heard - about ten years ago - is that the old ban on payment had nothing to do with OA, and was rather due to the ARC simply not wanting to pay author fees, on top of what libraries were already paying for subscriptions. (Different organizations of course, but most of it ultimately comes from the same source: taxpayers.) Admittedly, this was hearsay, but it was from a pretty reliable source. - Michael Nielsen
Andy Maloney
I am making my dissertation writing completely open and based on my open notebook. Here's the first chapter. This is in the rough draft stage but there is more to come.
Another preview of the future of (mainstream) science, imo. Historians and sociologists and philosophers of science, please note and give due credit to such concrete-action early adopters. - Bill Hooker
You kick a ton of ass, Andy! - Steve Koch
Cool, Dude -- will be referring my thesis students to this, especially since I am using a class wiki for some of their work in a pseudo-ONS fashion. In fact, just sent them the link:-). Will also be a good case study for the relationship b/w science and writing which they are discovering is not such a one-to-one kind of thing. - Mickey Schafer
Mr. Gunn
RT @anildash: Really feels like all of the most inspiring work of the early Web 2.0 era is gone. Time to start building again.
delicious is the site that popularized the concept of tags. We owe them all a huge debt of gratitude. - Mr. Gunn
@Neil, I tried following/snooping for suggestions on Simpy and Delicious, and just got overwhelmed. The killer app there is filtering, I think. (Haven't tried on Diigo or Pinboard yet.) - Bill Hooker
I followed a few people in delicious, but found FF to be much more useful for this. - Michael Kuhn
I do. Just following Pete Skomoroch on delicious was worth it - Deepak Singh from iPhone
I found real value in people's delicious bookmarks on friendfeed, less so on Delicious itself but I frequently use a search mode on both delicious and citeulike where I bookmark something myself, see who else has bookmarked it, look for the tags they use, then look for things tagged the same way in their library. Excellent way of checking you've got good literature coverage. - Cameron Neylon
I can't help thinking citeulike (et al) are a much more useful application of the concept because of the expertise of the users and the value of the objects being bookmarked. The metadata generated by their actions is clearly important. The social value comes from the whole web and these type of services win by making everything available as URLs etc. - Kevin Emamy
Agreed, the more focussed content helps surface the value more quickly...tho also the need to do that literature triaging is much more relevant to the research community than the general web - Cameron Neylon
Neil: I do. It's my favorite source of social links. Like Deepak, I find people like Peter Skoromoch fascinating to follow. - Michael Nielsen
I sometimes bookmark something to see who else bookmarked it, how they tagged it, and if they bookmarked anything else interesting. - Mr. Gunn from YouFeed
Cameron Neylon
The Wrong Stuff: NASA Dismisses Arsenic Critique Because Critical Priest Not Standing on Altar -
pq: "Apparently ideas are valid (or not) based not on their content, or even the reputation of the author, but on where they’re published." - Björn Brembs
"She is — to extend the metaphor — a priest. But though Redfield wears the proper robes, Brown wants to dismiss her because she’s not standing on the proper altar." - Andrew Lang
wow - but as frustrating as it is to hear at least they are making their ideology explicit and this is turning out to be a great case for open scientific discussion - I wonder if the authors have responded in the blogosphere - Jean-Claude Bradley
Patricia F. Anderson
Byte Size Biology » A new life form? Not so fast -
RT @OpenHelix: Nicely described. RT @iddux: A new life form? Not so fast - Patricia F. Anderson
Lars Juhl Jensen
Shirley Wu
Get it while it’s hot! 23andMe for $99 -
cutting to the chase: use discount code UA3XJH ( - Shirley Wu
Nice. Found out in time, this time round - but why don't they ship to Maryland? - Rajarshi Guha
@Rajarshi: Certain states do no longer allow this kind of testing. Just ordered mine. - Josef Scheiber
Just tried that code at that link and it is coming up as invalid - it should still be working on Nov 26, right? - Jean-Claude Bradley
I went on tech support and got it resolved with the discount even without the discount code - looking forward to the results :) - Jean-Claude Bradley
Cameron Neylon
Why you may not like your job, even though everyone envies you -
Amen! Although, being a former artist, the blog really only applies to scientists. My art and my music is...(strike that) WAS a pure abstraction from life even though I was making things. As a scientist, I have to say I agree with this post. In the lab I get to tinker and make. But, I see what professors do. 70% or more of their time is spent grant writing. 30% is classes and the last... more... - Andy Maloney from iPhone
Anthony Salvagno
Jonathan Eisen
Cheese seller @ farmers market said sorry 4 strong aroma; I said "it's ok I'm a microbiologist" & was treated like rock star; #scienceiscool
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