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Science and Web 2.0: Talking About Science vs. Doing Science - http://scholarlykitchen.sspnet.org/2010...

February 8, 2010 from Bookmarklet - Comment - Like - Share

Patricia F. Anderson, !lker yoldas. )°(, Georgie Bestie and 16 other people liked this

In fact too many talkers and evangelists! - Abhishek Tiwari from Bookmarklet

This hits me right where it hurts! All I do is talk about these ideas, never put them into practice. Crotty, you bastard, I'll get you for this. :-) - Bill Hooker

Well the OS glass will never be full - it isn't even half-full but there is water - lets keep adding more drops as opportunities arise http://en.wikipedia.org/wiki... - Jean-Claude Bradley

I am conflicted. After all I did the complaining, but not sure I agree with everything in there :) - Deepak Singh

I am very curious on how "doing" is defined - Deepak Singh

And I'm looking at all the cool stuff from Galaxy, and all kinds of collaborative apps that may not quite be public - Deepak Singh

If "doing" means randomly selecting and reading scientific articles then this is easily done. If doing means listening to my fellow friends and scientists in various networks for allowing me to rank scientific articles, then this is better. In this case "doing" requires communication, one form is talking, and the major goal is increasing knowledge by reducing information overload. BTW,... more... - joergkurtwegner

"Tools for Work: Every journal is looking for a leg up on the competition, looking for offerings that make them more attractive than other journals. Instead of offering yet another suite of communication tools likely to be ignored, we need to instead focus on the priorities and needs of our readers. Can we create new resources that support communities or that aggregate information in... more... - Daniel Mietchen

Neil - if the question is "are Web2.0 tools good enough to allow people to do Open Science" then the answer is yes - at least for applications like sharing solubility data. It might not work as well for applications with massive amounts of data - but we have to evaluate that on a case by case basis by at least trying with existing tools first. My concern is that people who might be... more... - Jean-Claude Bradley

JC, that's where I disagree. If there's one area where modern web technologies do very well it's handling massive amounts of data. It's just that no one is building the tools or (based on what I've seen), the best ones are either commercial or internally focussed. I am talking about data managements, etc. Why is there no Flightcaster for genomic data or platforms like Twilio? - Deepak Singh

I'm not so sure, Deepak. If nothing else, transferring massive data sets is a blocker in many cases. Or do you mean web based interfaces/applications to massive datasets? - Rajarshi Guha

Deepak - with the docking work that Rajarshi did for our molecules the massive (relative to what I'm used to in organic chem) amount of data was hard to share on free hosted platforms. I was very hopeful about Google Research Data Service - we got some early accounts at SciFoo and Rajarshi did upload a large number of conformations from our virtual library. But that didn't pan out. We... more... - Jean-Claude Bradley

@JC, your last point is what makes me think that web tech is not necessarily a panacea for large datasets. The situations you describe are basically all ways to avoid transferring large datasets. Furthermore, they lead to some extent of "implicit" vendor lock-in. Not 'explicit', since you can pull the data down - but if it's so massive would you really want to pull it down? And of course there's the issue that code then needs to run on the storage system. - Rajarshi Guha

Rajarshi, I mean the latter. You should not be sending data sets to multiple locations, but shared dataspaces accessible by multiple people spinning up ad hoc compute resources or using APIs/services to pull in required data is the way to go (and being done today across any number of fields) - Deepak Singh

JC, Gmail isn't meant to front end compute. The design point for those storage systems is write few, read occasionally, so that's not surprising per se. - Deepak Singh

Jean-Claude makes a good point here: "IP and collaborator issues were." That is why people like John Wilbanks, Heather Joseph (both of whom are speaking at Science Commons Symposium – Pacific Northwest http://sciencecommons.org/events...) and Victoria Stodden (see her papers here http://www.stanford.edu/~vcs...) are so important. You guys all need to talk more to the Open... more... - Hope Leman

Reading Jean-Claude's comments 5 posts up: Replace "Google" or "Amazon" with The Library sounds like the future to me. Libraries have the advantage of sharing the same mission as the open researcher (i.e., eliminates need to make it profitable for Amazon). Disadvantage is they don't kick as much ass yet (as far as I know). Have libraries across institutions begun collaborating on this... more... - Steve Koch

Steve, well we made a small step forward with our library this weekend by having them host our notebook archive on DSpace. There is a chance they will agree to do more sophisticated hosting in the future- we'll see. - Jean-Claude Bradley

Great to hear, Jean-Claude. Maybe we're about a year behind you (no data hosting till at least the fall), but hopefully can catch up some day. - Steve Koch

Steve, as to your last point. Libraries cannot and will likely never be able to manage infrastructure at scale and really shouldn't even try. They should (and are) leveraging 3rd party infrastructures today. It's up to them to figure out the models around it. (example: http://duraspace.org/duraclo...) - Deepak Singh

Steve I would be curious to know if it is possible to export your whole notebook from OWW or is that code that needs to be written? - Jean-Claude Bradley

That code seems not to exist yet - I had posed Steve the same question by email, and here is what he replied yesterday: " OWW does provide data dumps. It is described here, http://openwetware.org/wiki... and supposedly the most recent data dump is here: http://openwetware.org/dumps/ Presumably you could write a script that would download the data dump daily to back... more... - Daniel Mietchen

thanks Daniel - it would be nice if you could export your pages and data only - Jean-Claude Bradley

Bill (developer at OWW) could probably write these scripts relatively easily (and perhaps already has). I've been unable to reach him lately, though. - Steve Koch

Steve if you end up using lots of Google Spreadsheets to store data Andy has written some nifty code to make archiving them with the notebook fairly painless. - Jean-Claude Bradley

Thanks Jean-Claude -- I've been noticing that. Anthony uses google docs almost every day, so I've been thinking about it. There's talk of "OWW 2.0" (with that kind of thing integrated), so I've been holding off a bit. - Steve Koch

Chiming in late. Quick reply to Steve & JC's thoughts on libraries as partners for data archives/curation thru lens of UMich. Library reporting structure is thru Public Goods Council http://www.provost.umich.edu/publicg... , includes partnerships with institutional data repository. I did a couple blogposts on this with loads of links. Data plans: http://is.gd/jCiSet & data sharing http://is.gd/3FEirR Perhaps a model for other schools? - Patricia F. Anderson

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, 2009 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. - pn

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... - pn

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, 2009 - Comment - Like - Share

fidel ramirez, Pawel Szczesny, Chris Lasher and 6 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, 2009 - Comment - Like - Share

John Eargle and Chris Miller 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, 2009 - Comment - Like - Share

Michael R. Bernstein, Ruchira S. Datta, John Eargle and 7 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

The Life Scientists: Wladimir Labeikovsky

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

May 18, 2009 from Bookmarklet - Comment - Like - Share

John Eargle, Heather and Andrew Clegg liked this

The Life Scientists: Jan Aerts

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

May 18, 2009 - 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, 2009 - 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, 2009 - 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, 2009 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, 2009 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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