John Eargle - Likes - FriendFeed

Swine Flu Science: First Wiki, Then Publish | The Loom | Discover Magazine - http://blogs.discovermagazine.com/loom...

June 11 from Bookmarklet - Comment - Like - Share

Bora Zivkovic, bifurcafe, Duncan Hull and 8 other people liked this

That's the way it should be done... - Cameron Neylon

a nice fable of openness, IF it's true. I've heard at least one colleague say that the CDC held their swine flu data very close to the chest. what a journalist thinks of as "open" may not be the same as a data-cruncher's definition - Ian Holmes

...although just noticed its a CC-BY-NC-SA licence so should not have been reproduced on the Discover Blog arguably... - Cameron Neylon

yes did wonder a little how much was overexcited journalist. That said there is a Wiki and I believe the sequence data is being posted. Not sure about CDC data but there was a thing last week about someone taking the sequence data and analysing it separately. - Cameron Neylon

The journal Nucleic Acids Research have recently announced that they are OK with publishing stuff that has already appeared on a wiki, for example in the context of the RNA wiki project http://pubmed.gov/18945806 - Duncan Hull

A step in the right direction even if it isn't quite as described. - Jo Badge

Bill Hooker to Bill's feed, The Life Scientists

RRResearch: Can we buy time on a shared computer? - http://rrresearch.blogspot.com/2009...

May 27 from Bookmarklet - Comment - Like - Share

Tom Walsh, Steve Koch and John Eargle liked this

"I'd gladly pay a modest sum to run a few of my simulations on something that was, say, 10-100 times faster than the MacBook Pro I'm typing this on. I tried googling "buy time on fast computer" and other permutations, but couldn't find anything" - Bill Hooker from Bookmarklet

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without reading the post - buy time on EC2? i hear it's pretty cheap, but i guess you need to know how to write things to get it to work. - Christina Pikas

@Christina: yep, this post is a Deepak-trap. I figure he will know if Amazon has anything to offer Rosie. :-) - Bill Hooker

I bet they have something to offer her, but I don't know if she will find the right expertise to run her simulation there. Universities usually have shared clusters that can be accessed by anyone and she could try talking with some of her peers in order to find out. Also, if it's her perl simulations, she won't find anything (at least straightforward-ish) that will make it run 10 or 100 times faster. - Paulo Nuin

Yup. Poke local IT and see if they have "grid computing" services. - D0r0th34

I left a comment on the post: I don't know how your perl script is setup or written, but there are many limiting factors here. One is, if as you say that all 100,000 cycles are dependent on the previous one, running your script on a larger machine won't necessary save you running time. Say your MacBook is a 2.3 GHz machine, even if you run on a cluster with 3.0 Xeons you won't be able... more... - Paulo Nuin

I tweeted that just now--important question, fascinating answers. - Hope Leman

If your calculation is CPU-bound _and_ some input is a collection (e.g. different parameter sets or you call a binary multiple times with different inputs) _and_ you have some lazy computers at your institution PaPy (http://muralab.org/PaPy) will help you to set-up an ad-hoc grid. If the problem is IO-intensive PaPy is still useful on a multi-core machine (you can get a monster at EC2).... more... - marcin

The Life Scientists: Mikael Huss

There is a bewildering number of web-based tools for calculating GO category enrichment in a list of genes: Panther, DAVID, GOStat, GOMiner to name just a few. Which one do you prefer and why?

May 29 - Comment - Like - Share

Lucas Brouwers, fidel ramirez, Pawel Szczesny and 7 other people liked this

DAVID. Never done a side-by-side comparison, but I've never been disappointed... - Andrew Su

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I also like the ease of use of DAVID. I even wrote a simple Ruby API interface, if that's your sort of thing: http://github.com/chrisam... - Chris Miller

I'm partial to ToppGene (http://toppgene.cchmc.org/) It has a few extra bells and whistles too. Recent article on it: http://nar.oxfordjournals.org/cgi... Full disclosure: I work on the project. - Eric Bardes

Most of these tools deal with same statistics (either p-value or bonefferini correction or both), always better to use if they allow you to upload your exclusive list of background genes. I have tried most of those servers, but finally used GO::TermFinder and GoMiner. I would recommend any of the server if requirement is limited, if u need to do enrichment for number of lists better to use a module like GO::TermFinder. - Khader Shameer

Thanks everyone for your input! I'll definitely try out all the suggestions. - Mikael Huss

I've used the Ontologizer a few times. Besides having a cool name, you can run it from the command line (good for batch jobs) and it generates enrichment figures using GraphViz. http://compbio.charite.de/index... - Andrew Warren

Khader's point about allowing users to specify the background gene set is key. Your results will often be gibberish if you don't. Also, I think DAVID has some sort of API for automation, but I've never used it. - Andrew Su

The Life Scientists: Deepak Singh

some solid IRB tips and tricks on stackoverflow: http://stackoverflow.com/questio... (via http://friendfeed.com/igrigor...)

May 29 - Comment - Like - Share

John Eargle, Chris Miller and Neil Saunders liked this

Steve Koch to Steve's feed, Science 2.0, The Life Scientists

Cities and Ambition - http://www.paulgraham.com/cities... (via http://friendfeed.com/steveko...)

May 23 - Comment - Like - Share

Michael R. Bernstein, Ruchira S. Datta, John Eargle and 8 other people liked this

My friend Richard Yeh linked this on facebook. A fascinating essay, especially for someone like me who never lived in a big city and always wondered why big city people think nothing else in the world compares with where they're from. I guess I believe it more now. - Steve Koch

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From the essay: "Great cities attract ambitious people. You can sense it when you walk around one. In a hundred subtle ways, the city sends you a message: you could do more; you should try harder." - Steve Koch

Also from the essay: "Maybe the Internet will change things further. Maybe one day the most important community you belong to will be a virtual one, and it won't matter where you live physically. But I wouldn't bet on it. The physical world is very high bandwidth, and some of the ways cities send you messages are quite subtle." - Steve Koch

I, personally, would bet on it. Not replacing cities altogether...but I feel that this community on friendfeed that I lucked into about 6 months ago is by far my most important one. Most of my friendfeed contacts are in the Science2.0 and Life Scientists rooms (I think). The messages sent are very strong. In the essay, New York's message is "you should be richer." Cambridge's is "you... more... - Steve Koch

Slightly off-topic, but I really like this essay (from the same author): http://www.paulgraham.com/love... - Michael Nielsen

Steve: I agree, you could just about replace the word "City" by "Community" throughout the "Cities and Ambition" essay. The message you get depends on the circles you walk in. - Michael Nielsen

Michael, thanks for linking to the "do what you love" essay -- I just finished reading it and very much enjoyed it! - Steve Koch

Especially in response to Michael's suggestion, see drugmonkey "Science is just another profession" http://tinyurl.com/mlvr4b but especially the comments. A commenter called "becca" (#29) sets off a particularly interesting set of exchanges (starting at #32 and onward) that made for great reading (if you're sensitive to bad language, then skip this!) -- comment thread is also a kind of... more... - Mickey Schafer

Hey Mickey -- that looks pretty interesting. I only made it through becca's question and then a couple responses...a lot more reading in there! - Steve Koch

laura to laura's feed, The Life Scientists

Dear Lazyweb, what's the quickest way to find out if a given single base change has already been documented as a SNP or mutation and what its effect on protein expression/structure/function might be?

May 27 - Comment - Like - Share

Daniel MacArthur, Christopher Harris, Chris Cotsapas and 5 other people liked this

in an ideal world I would make a custom track annotating all documented variants and just compare it against my own sequences, but I'm not sure if that's the easiest way or even how you do it. Just know that looming deadline is impacting on problem-solving skills. - laura

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You probably looked here but: http://www.ncbi.nlm.nih.gov/sites... - Bill Hooker

Good place to ask your question: http://www.openhelix.com/blog/ They have a regular "what's your problem" post for questions from readers, but I'm sure they'd be happy to help out if you just emailed them. - Bill Hooker

Thanks, I've been using dbSNP information but I find it hard to believe that manually checking if the SNPs in my particular gene are also in my samples and vice versa is the way to go. Maybe I'm just lazy but there ought to be a more efficient way. - laura

invent it? - Christopher Harris

in less than a week and with no knowledge of databases/informatics? - laura

i'd wait till this particular project is done. cmo, just fill up on coffee and do it manually - Christopher Harris

actually, it's too late for coffee - Christopher Harris

Might help: a few weeks ago I wrote a tool called 'consequences' (see http://plindenbaum.blogspot.com/2009...) . Given a set of mutations mapped on the genome, this tool finds the consequences of a mutation. and the name of a known SNP if it exists. - Pierre Lindenbaum

can't get it to work, and it might not be exactly what i had in mind. but at least a step in the right direction - thank you. - laura

laura, feel free to tell me if you need help with running this tool. - Pierre Lindenbaum

thanks, that's okay. it's close but not exactly what i was after. now i'm wondering, how long does it take to learn how to write scripts like that? *wishes she had studied bioinformatics* - laura

Probably not very long if you're familiar with a computer language. Python appears to be the language of choice these days. Find a computer science grad student and throw some money at him/her :) - Brian Krueger - LabSpaces

hmm, i'm not familiar with any programming languages (yet) and have no money. maybe i should put up a sign on my door: "will cook for code" ..? - laura

If writing code is not an option, dbSNP at NCBI has to be the best starting point. The main issue is: how to search dbSNP effectively? The link provided by Bill provides examples of fields on which you can search. If you know the chromosome and base position for your base, search on [CHR] and [CHRPOS] is a good option. There are also batch search options at NCBI Entrez (upload list of... more... - Neil Saunders

Looking up SNPs, as others have suggested, involves interfacing with dbSNP in some way (a web browser, in your case, I'm guessing?). The problem is that for most SNPs there is no definitive evidence of their effect on anything, including RNA levels (and certainly protein levels or structure) unless someone has actually studied that polymorphism in some detail in a relevant... more... - Chris Cotsapas

Second part of your question is rather more complex. Effect on expression requires sequence analysis (e.g. does SNP affect reading frame, cause truncation etc.) Effect on structure can only be guessed at using e.g. homology modelling. Effect on function - who knows, unless the gene/protein in question is extremely well characterised experimentally. No way into these questions without programming, I'm afraid :-) - Neil Saunders

@neilfws - or even with programming, in many cases... - Chris Cotsapas

Chris, very true. At least with a little code, you can quicker learn that we know nothing :-) - Neil Saunders

Absolutely - I can now discover I know nothing about something in minutes. Used to take days of back-breaking labour to do that before. Ah, progress :-) - Chris Cotsapas

Laura - you could adapt Brian's suggestion and throw food at the CS grad student. But not poo. Never that. - Chris Cotsapas

Hey, thanks guys. Trouble is I'm trying to figure out the rs #'s myself, got a whole bunch of variants in my sequences, most of which are probably just artifacts (but I'm not very good at eyeballing that kind of stuff yet). For now, I shall just do what I've been doing all day: go back and forth between dbSNP, UCSC, Expasy and my list of putative variants. I was just getting frustrated... more... - laura

I will certainly work for gorgeous german apple cake. - Neil Saunders

that makes two of us - Chris Cotsapas

Ultimately, I'm afraid there is very little in the way of answering the second part of your question with extant resources. This is something we are looking at very hard right now (think rare variant detection through sequencing) and it's really not clear there is an answer... - Chris Cotsapas

"go back and forth between dbSNP, UCSC, Expasy and my list of putative variants" Laura, can you describe more precisely this process ? May be we can help here. - Pierre Lindenbaum

i can try, after another 2-3 coffees. - laura

The Life Scientists: Wladimir Labeikovsky

Protein sequencing gone awry: 1 sample, 27 labs, 20 results - Ars Technica - http://arstechnica.com/science...

May 18 from Bookmarklet - Comment - Like - Share

John Eargle, Heather, Neil Saunders and Andrew Clegg liked this

The Life Scientists: Jan Aerts

Science Outreach Program: http://xkcd.com/585/

May 18 - Comment - Like - Share

Rob Syme, John Eargle, Jason Stajich and 7 other people liked this

c.f. http://www.youtube.com/watch... - Andrew Clegg

The Life Scientists: Antony Williams

It was announced this morning that ChemSpider has been acquired by the Royal Society of Chemistry. See here: http://www.chemspider.com/blog...

May 11 - Comment - Like - Share

Pawel Szczesny, Paul Bacchus, John Eargle and 3 other people liked this

Congrats! - Victor / Mendeley Team

Terrific news! Congrats. - Michael Nielsen

Nice one, Antony. - Graham Steel

Deepak Singh to Deepak's feed, The Life Scientists

As usual people underestimate the balance that biology provides/needs. Drug design is artifically changing biology and it is fraught with danger. We are seeing proteins as monomeric standalone entities in these arguments and this is limited thinking http://crnano.typepad.com/crnblog...

May 4 - Comment - Like - Share

John Eargle and Rajarshi Guha liked this

I agree that it's limited thinking and putting the cart before the horse. We still don't fully understand the physics and we don't fully understand enzyme evolution. Enzyme design has a long way to go; the design in the Baker paper "resembles primordial enzymes more than they resemble highly refined modern-day enzymes". I'm skeptical of "higher performance than biological machines" but generally a protein design optimist ;-) - Adam Kraut

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Likewise. It's just that the nano-crowd really gets to me when it comes to this subject - Deepak Singh

"We've been making flies here for thousands of years and we've never had any complaints"... until Drexler - Wladimir Labeikovsky

That's not only nano-crowd - wherever I look I see the same putting the cart before the horse. From bioinformatics to synthetic biology - artificial labels of a research area people put in front of their eyes block their ability to see see certain parts of a big picture. - Pawel Szczesny

DIYBio: Mackenzie Cowell

Biology's next revolution by Nigel Goldenfeld and Carl Woese - http://arxiv.org/abs...

February 3 from Bookmarklet - Comment - Like - Share

John Eargle liked this

"The interpretation of recent environmental genomics data exposes the far-reaching influence of horizontal gene transfer, and is changing our basic concepts of organism, species and evolution itself." (Dyson cites Woese and this paper in "Our Biotech Future") - Mackenzie Cowell from Bookmarklet

DIYBio: Mackenzie Cowell

A New Biology for a New Century -- Woese 68 (2): 173 -- Microbiology and Molecular Biology Reviews - http://mmbr.asm.org/cgi...

February 3 from Bookmarklet - Comment - Like - Share

John Eargle liked this

"Biology today is at a crossroads. The molecular paradigm, which so successfully guided the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision of biology now realized, the molecular paradigm has run its course. Biology, therefore, has a choice to make, between the comfortable path of continuing to follow molecular biology's lead or the more invigorating one of seeking a new and inspiring vision of the living world, one that addresses the major problems in biology that 20th century biology, molecular biology, could not handle and, so, avoided. The former course, though highly productive, is certain to turn biology into an engineering discipline. The latter holds the promise of making biology an even more fundamental science, one that, along with physics, probes and defines the nature of reality. This is a choice between a biology that solely does society's bidding and a biology that is society's teacher." (Dyson cites Woese and this paper in "Our Biotech Future") - Mackenzie Cowell from Bookmarklet

The Life Scientists: Eric Jain

Public Data Sets on Amazon Web Services - http://aws.amazon.com/publicd...

December 4, 2008 - Comment - Like - Share

Attila Csordas, John Eargle, Jill O'Neill and Deepak Singh liked this

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