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Paulo Nuin › Likes

Euan
CouchDBX — The one-click CouchDB Package for your Mac - http://janl.github.com/couchdb...
Chris Lasher
I need to make a hop from mouse genes to human genes. What's your suggested pre-calculated ortholog database for this?
It seems there's InParanoid (http://inparanoid.sbc.su.se/), roundup (http://roundup.hms.harvard.edu/site...), and TreeFam (http://www.treefam.org/). Any others? - Chris Lasher
Mine, of course. ;-) Berkeley PHOG: http://phylofacts.berkeley.edu/ortholo... See in particular the Downloads page http://phylofacts.berkeley.edu/ortholo... which includes orthologs between human and mouse. We're in the midst of library construction which will greatly expand the number of genes for which we find orthologs. - Ruchira S. Datta
More generally, see this paper: http://genomebiology.com/2009... and references therein for an up-to-date list of methods and databases. - Ruchira S. Datta
@Ruchira I didn't realize you worked with Sjölander. She spoke at the VBI symposium a year or two ago. - Chris Lasher
So I heard! You're at VBI? Please say hello to Reinhard from me. :) - Ruchira S. Datta
I've had a ton of trouble every time I tried to use that phylofacts site for anything. Maybe it's just not intended to do what I wanted... - Donnie Berkholz
@Donnie, I'm sorry to hear that. What did you want to do? - Ruchira S. Datta
I'll let you know next time something comes up, I don't remember exactly what things it was anymore. One example of something I've done recently is, given a residue number in a PDB file, find the sequence, find all homologous sequences (given some cutoff), their % identity to the original, and the equivalent residues (a per-residue mapping of input:result) in an automated fashion. By the way, say hi to John Davidson! - Donnie Berkholz
Yes, I can see how that would be hard to do in the current site. We've been thinking of making per-residue information more evident for the site redesign that's in progress, but I at least had been thinking more about the display rather than doing it "in an automated fashion"--I presume you want to script it? It's good to know what people are interested in, thanks. I'll tell John you said hi! - Ruchira S. Datta
Chris : MGI is providing mammalian orthology information based on literature reports. For example for Myod1, list of mammalian orthologs : http://www.informatics.jax.org/searche... . - Khader Shameer
@Ruchira: Yeah. I had a set of 150 or so proteins I wanted to do that with, comparing each one with all of its homologs. Not reasonable to do it manually. - Donnie Berkholz
Second the MGI resource. Mammalian Orthology: ftp://ftp.informatics.jax.org/pub/reports/index.html#orthology - Walter Jessen
Mike Chelen
"PhyLIS is a user-friendly, free linux distribution for phylogenetics. Install it and you have an instant phylogenetics workstation. No downloading packages or messing with compilers, no configuring software, no worrying about small differences between systems that mess up your scripts. Simply install, sit down, and work. PhyLIS started during a period when I was acquiring several new computers for a large phyloinformatic project and grew tired of installing general purpose linux distributions, and then having to spend an hour or two reconfiguring everything and adding software on each new computer. I began developing scripts that would do some of this work for me, eventually they became overly-complicated, and I still had to carry around thumbdrives full of software or needlessly re-download everything. Eventually it just became more desirable to have an operating system that was specifically geared towards doing phylogenetics. PhyLIS is based on Ubuntu linux, a widely used... more... - Mike Chelen from Bookmarklet
مجتبی
STOP Spamming this room. This is not the place to share your stupid photos
Roderic Page
OMG Java is a pain, jar files that don't run, obscure errors, the need to allocate memory on the command line, need I go on...?
No, you don't need to go on. - Bill Anderson from twhirl
"jar files that don't run"?? ... used to running .so files then? - Egon Willighagen
Jan Aerts
Real Lives and White Lies in the Funding of Scientific Research http://www.plosbiology.org/article...
Reading things like this and meeting old friends (skilled, intelligent scientists most of them) suddenly unemployed or running out of grant money, is what make me glad I opted out of academia. - Nils Reinton
Well, now's as good a time as any to remind everybody of the story of Doug Prasher: http://www.nytimes.com/2008... - Richard Klancer
NPR interview with Prasher: http://www.npr.org/templat... - Nils Reinton
Marco
uBar Makes Mac OS X Into a Windows Transvestite [Apple] - http://gizmodo.com/5352038...
Björn Brembs
How to not apply for a job in science - http://bjoern.brembs.net/news...
Must update the post with this story: http://friendfeed.com/nuin... - Björn Brembs
The key to both Indian and Chinese applicants seems to be a very close knowledge of which institutions have the highest standards and local contacts. I used to try and reply individually to these but now get about ten a week even without positions advertised. - Cameron Neylon
The Onion
Sports: Bill Belichick's Tears Eat Through Podium - http://www.theonion.com/content...
Sports: Bill Belichick's Tears Eat Through Podium
FOXBOROUGH, MA—In a rare show of emotion, Patriots coach Bill Belichick began to cry during linebacker Tedy Bruschi's farewell press conference Monday, shedding a noxious black discharge that burned through the podium and a solid concrete floor before eventually coming to rest deep inside the mantle of the earth below. - The Onion
The Onion
Afterbirthers Demand To See Obama's Placenta - http://www.theonion.com/content...
WASHINGTON—In the continuing controversy surrounding the president's U.S. citizenship, a new fringe group informally known as... - The Onion
Jan Aerts
RT @dgmacarthur Peter Aldhous tracks down alarming errors in his personal genomic data presented by deCODEme: http://www.newscientist.com/article...
Crazy. Any software that recommends medical treatments based on genetics will have to be of the same quality as, say, space shuttle code. That requires slow, deliberate, and methodical development, and insane amounts of testing. Startups and agile web hackers coding into the night have their place, but medicine is not one of them. - Chris Miller
Leonardo Martins
The links series is really good to check out... no one will ever recognize you as a R users from your papers again once you start using these two R packages ;) - Egon Willighagen
Indeed, lattice is amazingly powerful - Rajarshi Guha
This points to the Learning R blog - http://learnr.wordpress.com/. Which, Christina once pointed out, might better be called "learning ggplot2". Regardless, it's a great learning resource with full code and output. - Neil Saunders
Egon Willighagen
great! got an #google #wave invite too now! now just waiting for password...
The Onion
Dog Humiliated In Front Of Entire Park - http://www.theonion.com/content...
Dog Humiliated In Front Of Entire Park
CONCORD, NH—The mortifying scene, which included several heated utterances of "bad dog" and "very bad dog," lasted nearly 20 seconds, according to reports. - The Onion
Marcos de Carvalho
Analysis of Array-CGH Data Using the R and Bioconductor Software Suite. - http://www.ncbi.nlm.nih.gov/entrez...
Egon Willighagen
♻ @nicoadams: Important though it is, I am getting tired of this metrics discussion in science.. It destroys the joy of science... #solo09
That's exactly how I feel. Why do we need metrics, prizes, awards, larger than life egos, etc, etc - Paulo Nuin
distribution of scarce/limited resources? - Christina Pikas
Yes, that's why year after year you see the same groups receiving grants, publishing in the "high impact" journals, etc. - Paulo Nuin
IMHO, resources are not scarce and much less limited. Doing research in a third-world country shows you how to live with limited and scarce resources, and also shows you how money is wasted in world class institutions. - Paulo Nuin
+1 Paulo - Björn Brembs from iPhone
Paulo, well said - Deepak Singh
I don't disagree with Paulo here, but I think Christina is also right. There's a sense in which resources (= funds with which to do science) are limited, and everyone who's ever applied for a grant is familiar with that sense. What metrics -- rich, reliable metrics, not the stupid IF -- might do is level the playing field, so that those oversize egos and usual-suspect labs and their... more... - Bill Hooker
Few people really enjoy the metrics discussions, but if we don't keep having them we are going to be stuck with the present insane system. - Bill Hooker
I consider half of my day job (post-doc) as playing the science game, hunting for grants, boosting my H-index, and getting papers out faster than I can say SCIEN... (and I don't like that) - Egon Willighagen
There's also the Dick Gordon "fund 'em all, let Science sort 'em out" approach. Or we could do away with all metrics and insist on using review panels who would be expected to read all the relevant material. I'd certainly like to see at least some trials of both ideas. - Bill Hooker
A big reason I didn't consider academia as an option was that I didn't want to play that science game - Deepak Singh
+1 Deepak. In many ways industry is much cleaner - if it makes financial sense - funding will be there - go ahead. If not - tough - do something else. For sure, not an approach that will solve all problems, but definitely an option I would recommend for those tired with academic struggle. - Nils Reinton
Ricardo Vidal
Boo! RT @phdcomics: New comic: 'Unemployment vs. Graduate Stipends' http://www.phdcomics.com/comics...
Ricardo Vidal
Death Panel Myth Creator Betsy McCaughey Resigns From Medical Board One Day After Jon Stew // via popurls.com - http://www.pop.ly/2ojc
Jan Aerts
European University Institute - Welcome to the Academic Careers Observatory - http://www.eui.eu/Program...
Comparison of academic careers in Europe: salaries, requirements for positions, ... - Jan Aerts
"Academic careers differ between countries, and across disciplines. See the following pages for info on your discipline: Economics, history, law, political and social studies" :-( - Björn Brembs
I was checking my countries academic career path and noticed they left something out. Something we here call: "Factor cunha" :P - Ricardo Vidal
Lars Juhl Jensen
gReactions shows blog comments right inside Google Reader - http://uk.techcrunch.com/2009...
Brilliant ! Works well too - Nils Reinton
set it up this morning, very nice indeed - Neil Saunders
installed but it didn't find the comments on Iris's post re long essay blogging that I KNOW got comments on her blog and here. Is there a set up step I missed? Msg was "We found nothing on this post in our index!" - suelibrarian
Nothing to set up. I subscribed to Iris' blog RSS and saw the same message, but I've seen stuff from FF for other feeds. - Neil Saunders
Looks like blog comments isn't showing well while friendfeed and twitter mentions shows - Nils Reinton
Lars Juhl Jensen
Global Mapping of Copy-Number Variants in Humans by Next-Generation Sequencing - http://larsjuhljensen.tumblr.com/post...
Kevin Z
Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine - http://www.plosone.org/article...
Lars Juhl Jensen
Applying mass spectrometry-based proteomics to genetics, genomics and network biology - http://www.nature.com/nrg...
Björn Brembs
Climate data spat intensifies : Nature News - http://www.nature.com/news...
"A leading UK climatologist is being inundated by freedom-of-information-act requests to make raw climate data publicly available, leading to a renewed row over data access." - Björn Brembs from Bookmarklet
Andrew Perry
Wagn - a different type of wiki ("Explore, Organize, Thrive") - http://wagn.org/Explore...
Wagn is an opensource wiki engine written on top of Rails. It's main innovation appears to be rather than making the basic unit a "Page" of wikitext, it uses "Cards", which can contain different formatted data types (images, blogs, tickets, forms). One "card" can also be embedded in another, in several places. Other features, such as the JSON-based WQL query language allow Wagn to be used as a structured database with dynamic representations of the underlying data. I'm intrigued ... - Andrew Perry
Intriguing. Install note: if you want to use sqlite3, edit lib/tasks/bootstrap.rake and change now() to datetime('now'). - Neil Saunders
and to get the source "git clone git://github.com/wagn/wagn.git" - Deepak Singh
Cass Johnston
Mr. Gunn
LOL, I see you haven't met our dear PZ yet. http://scienceblogs.com/pharyng... RT @Barbarellaf: It's a shame that atheists aren't as preachy as Christians
Every viewpoint needs an articulate spokesman. - Jack (a.k.a. Jeber)
I agree. Leave the crazy and cult followers follow PZ. - Paulo Nuin
+1 Paulo. The religious nutbags have their blogs (I guess) and the atheievangelists have PZM, and so far all I've had to do to avoid both sets of douchebags is stay away from the blogs they frequent. - Bill Hooker
But PZ is very entertaining - at least to me. The more I think about it, the more Jerry Coin's book review in Science (http://www.sciencemag.org/cgi...) seems to raise an interesting point: educating the US public hasn't really improved scientific illiteracy in 30 years. The polls point to religion as the culprit: "64% said that if scientists were to disprove a... more... - Björn Brembs
PZ is (was) entertaining to me as watching clips of Fox on the Daily Show and Colbert Report. They just sound/seem the same, just on opposite poles. - Paulo Nuin
@BoraZ has some interesting things to say about the role of people like him. Something along the lines of "drawing the fire so that others feel safe sticking their necks out." Kinda makes sense, in a way. - Mr. Gunn
Yes, and they get into the cult and the whole process starts again, atheism or whatever they're preaching there, becomes a "religion" and there will be someone that preaches against it, and the cycle is complete. - Paulo Nuin
c'mon, with zingers like "For the record, though, Stephen Hawking: British. Not dead." are you not entertained?? I laughed my ass off. =) (in case it wasn't clear, I do enjoy reading the pharyngula blog. I just steer well clear of the comments.) - tim
The "atheism is religion" is really old and I don't think Paulo meant to say that. But the more I think about it, the more an open criticism of religion (all religions, really) has its place and is valuable (besides being really entertaining - for me). At least for the few who can be forced into thinking more deeply and beyond their upbringing. Those so dogmatic that nothing will make... more... - Björn Brembs
Actually I agree with Paulo. And religion is not all bad. I know some wonderfully smart people, who are either scientists or engineers (way smarter than all of us) who are deeply religious. But religion for them is a way of governing their life. The problem with the fringe (on any side) is that they want to guide how others live their lives and that's the part that bothers me. And the... more... - Deepak Singh
"I've almost never encountered it" -- you mean hardly anyone has got directly up in your face, right? Well, me neither, but I've certainly encountered the religious fringe: it dominates political discourse in this country by dint of sheer volumee. I don't just mean I see it on TV all the time; for instance, I did a teeny bit to try to promote gay marriage here in Oregon, and it was the... more... - Bill Hooker
I don't doubt it's there and a lot of it, but if it was 50% I'd see it every day, but that's not the case. Yes, when I came to the US, the shock at how conservative the country is was profound, but I do think that it's not as bad as it some make it out to be - Deepak Singh
don't forget the geographic unhomogeneity of USA. It is easy to avoid encountering this in the huge cities on the coasts. Impossible to survive as open atheist in small towns in the middle - they literally kick you out of town. - Bora Zivkovic
this I think belongs here: http://friendfeed.com/search... - Bora Zivkovic
Sally Church
The best analogy for the FriendFeed purchase - http://blindscientist.genedrift.org/2009...
Jeff Habig
@mendeley_com Glad it's getting better, but a marketing strategy that expects users to constantly try/retry your software is a failure.
Processing
Learning Processing: A Beginner's Guide to Programming Images, Animation, and Interaction by Daniel Shiffman - http://www.learningprocessing.com/
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