Andrew Su › Comments

it's bizarre, scripps has two vpn modes. one gives access to the journals, but makes *all* web browsing then go through scripps (slowing things down significantly). The other doesn't interfere with other web browsing, but also doesn't allow access to journals. Haven't dug into it much. Was actually thinking of setting up a web proxy on one of our lab servers. Argh, who has time for that? Things should just work! </rant> ;) - Andrew Su

oh, and thanks for sending the article, Björn! - Andrew Su

That is bizarre indeed, Andrew.. - Graham Steel

no chance... but sometimes I see a link to a PDF (to which I don't have access) - Michael Kuhn

It wants me to buy PDF (none of my host institutions is a subscriber) - I guess it's there. - Pawel Szczesny

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

Eisenome. Brilliant !! :-)) - Graham Steel

Liking for "Eisenome". :-) - Bill Hooker

@Jonathan The geek element in me can confirm that http://eisenome.blogspot.com is freely available. Just sayin' ;-) - Graham Steel

Wouldn't that be the "ironome" ... i.e. all genes involved in iron metabolism? Someone is already researching "you", Jonathan: http://www.chem.tamu.edu/faculty... - 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

"It Wasn't Me" - Shaggy :- http://www.youtube.com/watch... - Graham Steel

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

I am now the proud owner of http://eisenomics.blogspot.com/ and http://eisenome.blogspot.com/ - - Jonathan Eisen

1 Gazillion points to Mr/Dr./Prof J. Eisien for creating these soon to be, infamous Eisenome and Eisenomics blog sites via this humble FriendFeed thread !! - Graham Steel

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, I think we all have to hand this one to you for coming up with the idea in the first place :-) - Graham Steel

@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 http://kochadoodledoo-ome.blogspot.com/2010... - 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... kochpostulates.blogspot.com is still free... - Iddo Friedberg

To keep the fun/discussion going, I have commenced http://prionomics.blogspot.com/2010... - Graham Steel

Maybe we should do homeopathomics - Jonathan Eisen

Absolutely :-)) Now't on goog so far in that regard !! - Graham Steel

@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 http://kochspostulates.blogspot.com/ - Steve Koch

Thanks for the links and info. But ugh... IANAL, and for good reason... </glazed_eyes> - Andrew Su

As RR says, the E.U. states and many other countries do have IP rights for databases, and sometimes for straight-up facts. Sometimes these are part of standard copyright, sometimes they're separate pieces of law. What the law does, and what most scientists and academics act like it does, are two totally different things in the U.S. Most scientists do act and think as if they have... more... - N. Ansi

Andrew, the problem is exactly that glazed eyes effect. Likely result of using copyright is that some of your data will not be "protected" somewhere, people get confused, good people then decide they can't use out and the nasty ones will use it anyway. Basically you aren't doing yourself any favors. If you must restrict uses then at least use a license designed for data - Cameron Neylon from Android

What Cameron says... See http://www.opendatacommons.org/license... and if that doesn't seem suitable enough, all you can do is to produce data _access_ agreement (which needs to be signed by someone, even via web form). I don't think you can effectively "own" the data if you decide to share it. - Pawel Szczesny

Very good suggestion, especially as a way to find genes to test. But short term, I'm hoping to find a published example that I can just cite. (Edited the post to clarify that.) - Andrew Su

Heterozygous lethal mouse strains in JAX, about 50 genes, vascularization and imprinting. - John Hogenesch

What are the axes? - Bill Hooker

The downward trending curves are the %attendance vs days from the start of the term. The upward trending curves are RSS subscription numbers. At the end of each term the % attendance was in the 10-20% range but the students who attended vs. those who just watched the lectures online performed statistically the same. - Jean-Claude Bradley

Interesting... I wonder what those curves would look like if you _didn't_ provide the screencasts... I imagine that attendance drops in most classes. Or said another way, I wonder if you have enough data to segment the performance of non-attenders who did or didn't watch the screencasts. - Andrew Su

Andrew - I wasn't able to easily identify who watched the lectures and who didn't. When I didn't provide screencasts attendance did drop but not as much - don't have any hard numbers though. Now that I don't repeat lectures and do workshops instead I don't get that curve anymore. - Jean-Claude Bradley

JC, thanks for the info. I really like the idea. One follow up question. Do you ever get feedback from your students that they miss the interactivity of a traditional lecture? For example, suppose a student has a fundamental question at the very beginning of a lesson. In a lecture they could ask for clarification immediately, whereas viewing a screencast would mean they'd have to wait... more... - Andrew Su

This is fascinating. As a terrible swot who never missed a single lecture in three years' undergrad, I'm astonished at the dropoff in attendance. What was the pattern of repeats -- and what does the curve look like with workshops instead of repeats? - Bill Hooker

Andrew - the lack of interactivity in the traditional lecture format was a big motivation for me to change. I simply don't have the time to stop lecturing and spend 30 min on a student question if I have to cover a certain amount of material in class. With 4 hours a week of workshops there is time. Some students watch the lectures with headphones during the workshops and pause to ask questions. - Jean-Claude Bradley

This is today's talk for #rluk10 First time in living memory I've got the slides up in advance! - Cameron Neylon

I may or may not be live streaming at: http://www.livestream.com/cameron... I aim to be live tweeting but that depends on how well tweetdeck scheduling works... - Cameron Neylon

During my Phd I went to the physical library once, only because the printers were located in the basement and I had to get my thesis bound. - Frank

I used to go every Thursday morning. With my pencil and paper cause I couldnt always photocopy the articles .... (and I had email at the time!) oh how times have changed! - Kubke

S4-6 http://friendfeed.com/cameron... - S9 http://friendfeed.com/cameron... - S12 http://friendfeed.com/cameron... - S13... more... - Kubke

S26 http://friendfeed.com/cameron... - S28 http://friendfeed.com/cameron... - S31 http://friendfeed.com/cameron... - S36 http://friendfeed.com/cameron... - S39... more... - Kubke

S54 http://friendfeed.com/cameron... - S57 http://friendfeed.com/cameron... - S60 http://friendfeed.com/cameron... - S65 http://friendfeed.com/cameron... - S67... more... - Kubke

S71 http://friendfeed.com/cameron... - S73 http://friendfeed.com/cameron... - S77 http://friendfeed.com/cameron... - S81 http://friendfeed.com/cameron... - S83... more... - Kubke

S87 http://friendfeed.com/cameron... - S89 http://friendfeed.com/cameron... - S94 http://friendfeed.com/cameron... - S98 http://friendfeed.com/cameron... - - Kubke

Great slides, Cameron. I made very similar points in a talk I gave last spring titled "We are all curators now: Envisioning new roles for research libraries in an era of information abundance, social networks, and digital ephemera" (slides here: http://www.duke.edu/~paulm...) and even quoted you in one of my slides. I also referenced the Shirky quote, and... more... - Paolo Mangiafico

I love slides 59-61. I'm definitely going to steal (and adapt)... - Andrew Su

Like @kubke, I am old. I remember (as in, I actually used) Index Medicus... on paper. - Bill Hooker

I wonder if someone would be interested in automating the edit/editor counts. The numbers in the old spreadsheet were filled in by hand, but one can imagine writing a simple program using the MediaWiki API to get that info. Might even be a cute application note (BMC Research Notes, PLoS One) that creates a historical and continuously-updated report of wiki activity... - Andrew Su

Thanks for pushing this! Ewen - ewencallaway from email

Ewen -- Hah! you overestimate my ability to "push". Lots of smart people lurking here, so I'm just throwing out a random thought to see if it sticks. Usually an effective filter for good ideas... - Andrew Su

Why would we do free work for Nature? - Bill Hooker

Bill, only if you thought it were personally interesting or beneficial I suppose... - Andrew Su

Eh, sorry, ignore me, that was uncalled-for. The benefits of maintaining such a list are obvious and if Nature is promoting it that's even better. My bad. - Bill Hooker

I agree the list is worth maintaining, but it's just a pain to keep current. (The numbers there now are almost two years old.) Anyway, perhaps a fun little project (for those around here who like that sort of thing)... - Andrew Su

Neil, are you sure a Wiki is the right tool for this? ;-) - Cameron Neylon

Hi, Dan Bolser has kindly created a wiki to collect data on biological wikis: http://nettab.referata.com/wiki..., so if you have anything to add, please put it there! Ewen - ewencallaway from email

Ideally the maintainers of these wikis could supply this info. Perhaps the thing to do is to write/find a mediawiki plugin that would expose this data automatically - then the source wikis would simply have to install the plugin and everything would/might/might sometimes 'just work'. - Benjamin Good

I agree: Build and promote didn't work very well. The public SEED (http://theseed.uchicago.edu/FIG...) allows anybody to annotate anything; yet, there is almost no outside contributions. Workshops slightly work better, but they're expensive and their effects fade two days after the workshop. Why do people spend time evaluating books, rating movies, etc. but not tagging/annotating genomes? - Ramy Karam Aziz

So you think that genus/species-based efforts are better than pathway-based ones? The problem is that they introduce inconsistencies - Ramy Karam Aziz

Interesting, I wasn't aware of the pseudomonas database. But it appears that they are no longer accepting community annotations? http://www.pseudomonas.com/quickSu... I wonder if that's true and if so why... - Andrew Su

I agree with Su and Ramy that scientific altruism is overestimated. Here a talk and model that might make it work http://nubes.esof2010.org/stored... - joergkurtwegner

And I remain completely in awe of DE Shaw - Deepak Singh

Wow, what would you do in science if you had that amount of money available? - joergkurtwegner

Shaw is not doing this for commercial reasons. He has the money, which gives him the luxury to try interesting problems that don't make commercial sense. Although as Vijay Pande says, even Shaw acknowledges that Anton only goes so far - Deepak Singh

Anyone done an Anton vs. Folding@Home comparison? - Matthew Todd

I am still not convinced software should be funded the same way as research, especially infrastructure software - Deepak Singh

Or just the people using the software. Sometimes I am not sure they appreciate it, or is that cause they always use crummy software - Deepak Singh

Andrew, I agree. There has been some recognition, and both Francis Collins (NIH) and Eric Green (NHGRI) seem to get that computational analysis is a big bottleneck as we try to move towards genomic medicine. Progress is being made, but I still think there needs to be more funding and more recognition that robust and polished software is an important product. - Chris Miller

Deepak, I'm curious what you mean by "not convinced software should be funded the same way as research". Do you mean different funding mechanisms, or different criteria by which they should be evaluated? - Andrew Su

Different funding instruments and different evaluation criteria. The lifetime of software projects and cadence are different than research projects. It also depends on the nature of the software project. Is it infrastructure? Is it algorithms (which is science first, software second)?, etc - Deepak Singh

+1 for importance of software, and for appreciation of the importance of people working on it. But I can certainly see where Deepak is coming from: the history of software development funded by large organizations isn't exactly stellar. By contrast, the Silicon Valley development ecosystem has a lot of great features: a lot of risks are taken, there's a lot of support for people from... more... - Michael Nielsen

@Deepak, your statement can be expanded to, "I am still not convinced research should be funded the way research is." :) - Steve Koch

I've got to say a first page like that have me reaching for the bin. No pictures? No colour? It's like I'm expected to be wowed by the science or something...seriously tho a picture if allowed that grabs reviewers attention is a good thing in my book. - Cameron Neylon

Cameron, interesting comment. A figure on the Aims page seems perfectly reasonable and logical. Having said that, I've never done it (neither on the two successful proposals nor the one unsuccessful one) and from my time reviewing for NIH, I can't recall ever seeing it done either. Anyway, if you do it, it better be a frickin good figure! - Andrew Su

@Andrew if you look a bit at the blog, you'll see more posts on Significance, etc. - Iddo Friedberg

ahh right, it's a whole series of posts. Nice! (Still think it's good to have a full, non-redacted grant to work from. At worst, you can FOIA one... ;) ) - Andrew Su

@Andrew - the whole thing better be top notch or your're wasting your time. Goes for any pictures as well. But presentation is also an issue, my objection to that redacted version is that its basically pretty ugly. Not even really nicely laid out text, too close to margins, looking like it's squeezed in. Also no short summary. All of those would put me off - and they do have an effect, whether conscious or not on reviewers. You need snappy, clear, and detailed, which is a hard balance to strike. - Cameron Neylon

@Cameon grant applications are generally very formulaic, and any deviation from the format prescribed by the funding program will have your application triaged. This is especially true for US Federal grants. There is no room for creative aesthetics in the Aims page. And caught between page constraints and the reviewers tendency to pick at every detail, it is very hard to make an... more... - Iddo Friedberg

give me 5 minutes :-P - Pierre Lindenbaum

see also http://davidrothman.net/categor... - Bill Hooker

I saw the corlan.net one, but it stops at 2008 unfortunately. And if I had to think of the _ideal_ solution (hint hint Pierre), I think it would be great if there were a tool that was hooked up to some slick visualization (e.g., google charts)... - Andrew Su

Heh, "ask Pierre to build you one" was going to be my next suggestion! - Bill Hooker

I have a prediction... XSLT! - Andrew Su

java : http://gist.github.com/596106 - Pierre Lindenbaum

just a ~ copy-n-paste of a previous program - Pierre Lindenbaum

BTW, yes, I got a XSLT stylsheet for this, processing a set of PubmedArticles in XML format : http://code.google.com/p... but it wouldn't work if your XML file is too big. - Pierre Lindenbaum

You used to be able to do this at hubmed.org, but I can't see how to do it anymore. - Mr. Gunn

thanks all, much appreciated... (Also tried to play around with my pubmed2wordle code to do this. currently works just okay...) - Andrew Su

GoPubMed.org does that among other things - look into the "statistics" section of search results - Yaroslav Nikolaev from Android