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Colin Archer › Likes
Programming cells by multiplex genome engineering and accelerated evolution - http://www.nature.com/nature...
Colin Archer, Ruchira S. Datta and Pierre Lindenbaum liked this
Engineering prokaryotic gene circuits. - http://www.ncbi.nlm.nih.gov/entrez...
Colin Archer liked this
A fast, robust and tunable synthetic gene oscillator - http://www.nature.com/nature...
Colin Archer and Roland Krause liked this
Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy - http://www.nature.com/nbt...
Colin Archer and Pawel Szczesny liked this
Dani Rodrik's weblog: Why the econ-blogosphere is here to stay - http://rodrik.typepad.com/dani_ro...
Meryn Stol, Colin Archer, Richard Akerman and 6 other people liked this
"one of the unexpected scholarly benefits of having a blog is that it is like keeping an intellectual journal. You get an idea, you jot it down in your blog. Some months later, you vaguely remember having had the idea and you google your own blog to recover it. I am not kidding: I google my own blog all the time... "
- Michael Nielsen
It's true and again it's the "me first, social later" effect. I started a blog more or less as a journal to remind myself of useful stuff that I'd learned. If other people like some of it too, great, but it's as much a resource for me as others.
- Neil Saunders
Similarly at this end. I can't read my handwriting, so my blog was essentially my moleskine notebook, filled in as I ran from one hotel room to the next. At least in the beginning.
- Deepak Singh
I started a blog because I did not know how to build a website to deposit my essays ;-) When people started commenting, I started writing more and understood the community aspect of blogging that I missed in the beginning.
- Bora Zivkovic
I started initially because I was a very prolific reader and commenter, and wanted to link together various things I had read in different places. I guess that's a kinda hybrid approach.
- Mr. Gunn
[Computer_Science] Stochastic hybrid modeling of DNA replication across a complete genome - http://www.pnas.org/content...
Pawel Szczesny and Colin Archer liked this
PLoS ONE on FriendFeed - http://scienceblogs.com/clock...
Colin Archer, Todd Harris, Deepak Singh and 5 other people liked this
Genomics of cellulosic biofuels - http://dx.doi.org/10...
Colin Archer, Deepak Singh and Thomas Lemberger liked this
Functional genomics: An array of bacterial interactions - http://www.nature.com/doifind...
Colin Archer, Jason Tsai and Thomas Lemberger liked this
Genetic variation in an individual human exome. - http://www.ncbi.nlm.nih.gov/entrez...
Colin Archer, Arash, Berci Mesko, MD and Jason Tsai liked this
[SPECIAL/Perspective] Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems - http://www.sciencemag.org/cgi...
Colin Archer, Neil Saunders and Mitchell J Stanton-Cook liked this
Some of the feedback from my CV has been: "So are you a internet/programming guy or a bioengineering guy?" Why? Can't be both?
Colin Archer and Neil Saunders liked this
Clearly those responders lack imagination; you don't want to work for them :)
- Neil Saunders
Waiting and looking for more "understanding" responders :-)
- Ricardo Vidal
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism - http://www.biomedcentral.com/1752-05...
Colin Archer and Andrew Perry liked this
Top 10 Best Presentations Ever - http://www.knowhr.com/blog...
Daniel Jurczak, Michael Kuhn, Colin Archer and 5 other people liked this
(via Jamie McQuay)
- Jen Dodd
great link but it didn't come from me...
- Jamie McQuay
Not a single TED talk? Hmm.
- Chris Lasher
if you look at the "readers choice" it's full of TED talks
- Deepak Singh
The Hans Roling/Gapminder TED talk has got to be the best talk ever.
- Nick Lothian
Jamie: You're right - it came from a link on a page you bookmarked.
- Jen Dodd
Paul Collier's TED talk on "4 ways to improve the lives of the bottom billion" is a great presentation - not as fancy as some, but really striking. I also like Robert Fuller, Stewart Brand, John Doerr, Freeman Dyson, and Bill Stone. (Yes, I have watched way too many TED talks...)
- Jen Dodd
[Biophysics] Using noise to probe and characterize gene circuits - http://www.pnas.org/cgi...
Pawel Szczesny and Colin Archer liked this
Sorry, it's in Dutch, but here's a cool online multiplayer metabolomics game (yes, no kidding!)... have not started, but says it will take me 10 hours to finish it... so, afraid it will kill my productivity this week... damn cool! - http://www.metabolaspel.nl/
Cameron Neylon, Euan, Colin Archer and 3 other people liked this
Oh, this is so cool... two teams, fighting against each other by playing the metabolome: one team converting sugars into fats, others fats into sugars... let the organism suffer in agony!
- Egon Willighagen
It's even better *because* it's in Dutch!
- Todd Harris
Harnessing the power of multicore - http://computationalbiologynew...
arek, Colin Archer, Jason Tsai and 4 other people liked this
My brain seems to work much better in the morning ... after years of neglecting my limited Perl skills, I can actually read this code ! Except chomp. Can't remember what chomp does, but I'll look it up :)
- Andrew Perry
As long as you remember how "push" works.
- Deepak Singh
I have to give this a try
- Pedro Beltrao
Be sure to subscribe to Animesh's blog too.
- Paulo Nuin
The importance of stupidity in scientific research - http://scienceblogs.com/clock...
Michael Kuhn, Colin Archer, Flemming Funch and 2 other people liked this
ScienceDirect TOP25 Hottest Articles - http://top25.sciencedirect.com/
Jason Tsai, Colin Archer, Martin Fenner and 4 other people liked this
"Now you can keep track of the latest trends and developments in your speciality with ScienceDirect's Top 25 Hottest Articles. The Top 25 is a free service which provides lists of most read articles counted by article downloads on ScienceDirect."
- Pedro Beltrao
from Bookmarklet
Stem cells stem cells stem cells....boring. EDIT - RUNS FROM Mr. GUNN! ;)
- NatBlair
Don't worry, NatBlair, Alexey is waiting just around the corner. ;-)
- Mr. Gunn
sure, for someone who is not in to stem cell research it seems boring, i understand, but it's just shows relative scientific interest to the topic, it's still new still hot - http://hematopoiesis.info/2008...
- Alexey
Exactly, it's a little faddish at this point. And I don't think it's boring, though it's not my interest. It's just I have the feeling many of the claims being made regarding stem cells are likely to be overblown.
- NatBlair
Hey, that is pretty cool. Didn't notice you could limit the scope. Any info on their ranking? I presume views/downloads/whatnot, but I don't suppose they specify.
- NatBlair
I think it is based on the number of PDF downloads. I don't really get why publishers don't provide these values alongside other metadata for the article. This would allow anyone to build sorting tools or simple to test different metrics of evaluation of paper impact.
- Pedro Beltrao
Is the number of PDF downloads a reliable metric? I suppose it's better than number "hits" ... and it would be interesting beside citation data. For example, what sort of article might be downloaded often, but not cited?
- Jere
@Jere : number of PDF downloads correlates with citations but as for any metric there is debate on its usefulness. See here: http://network.nature.com/london... My view on this is that having several indicators is better than relying on one (impact factor of the journal) and that by making these public the publishers would allow people to study them.
- Pedro Beltrao
Hottest articles are the most downloaded articles in specific subject or journals for the specified period of time. Thanks for the feedback that you have provided here.
- Rafael Sidi
I switched it to Biochem/Genetics/Mol Bio and every link was for Cell bar the last one.. hehehe..
- Colin Archer
It occurs to me that since citing an article isn't necessarily evidence of having read the article(because some lazy/busy people recycle sets of citations) that some sort of ratio between the number of downloads and number of cites(especially cites published after download) would provide a "usefulness" index.
- Mr. Gunn
@Mr. Gunn - The problem is that number of downloads is much easier to game than citations. All metrics have problems but economically it is not viable to evaluate everyone by a sufficient number of peers so we do need some form of numerical (semi)-automated metric to help in the evaluations. Since all metrics have flaws the best would be to have access to many different metrics at the same time.
- Pedro Beltrao
Sequence-based prediction of protein-protein interactions by means of codon usage. - http://www.ncbi.nlm.nih.gov/entrez...
Mr. Gunn, Colin Archer, Ricardo Vidal and 4 other people liked this
Results are not groundbreaking, but the idea is obvious (now, when it's published ;) ) and simple.
- Pawel Szczesny
"Although we did not test the power of PIC for prediction of direct physical interactions between proteins, it is possible that it can be used for that purpose as well" -- I'd like to try this; if anyone is interested I have some test cases available (unpublished biochem data to test against predictions).
- Bill Hooker
Interesting idea. Looking forward to reading the paper in more detail.
- Colin Archer
Founders at Work: Stories of Startups' Early Days - http://www.amazon.com/dp...
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Colin Archer, Dimitar Vesselinov, Nick Lothian and 4 other people liked this
Pawel - Personally, I found this a terrific book. Almost every interview is very good.
- Michael Nielsen
Thank you Michael. After such recommendation, the only thing I can do is to pull out credit card :)
- Pawel Szczesny
I can already see that Friendfeed is going to cost my wallet dearly :)
- Dave Bacon
Dave - If you like this kind of thing, you really should buy "Hackers and Painters" as well!! (What's it worth for me to stop? :-)
- Michael Nielsen
Michael, I have "Hackers and Painters" on my shelf and surprisingly I found it rather weak book. There's not much content that's not present on the Graham's page, and the main idea of similarities of hacking and painting is not deeply explored. I like a lot Graham's essays, but I hoped the book contains much more new ideas.
- Pawel Szczesny
Pawel - The book is just a collection of some of the essays on his webpage, so it's not surprising you were disappointed. I probably should have mentioned that fact above, to save others disappointment. I still like my copy a lot - having it in book form lets me write all over the essays. Incidentally, Founders at Work seems to be original content.
- Michael Nielsen
Beginning to wonder if "the way science is done" really is changing. Seems sometimes there's a small cohort of early adopters / technology enthusiasts and a large majority just doing what they've always done.
Chris Lasher, Aarthy, Deepak Singh and 11 other people liked this
Agreed.
- Walter Jessen
from Alert Thingy
ALA Kuhn's "The Structure of Scientific Revolutions"
- Todd Harris
from twhirl
I've been wondering that for years. It's actually probably more prevalent in academia.
- Deepak Singh
and that's ok - success should not be defined as "practiced by the majority"
- Jean-Claude Bradley
hard to talk on "science" in general, there are scientific fields and niches and you can define your niche by this adopter community as a reference point
- Attila Csordas
I'd say it's not changing at all -- has barely even responded to the web. To me, that's what the biogang/open (notebook) science collective (BONSC?) is all about: we're out to change all that.
- Bill Hooker
my next job decides whether I am able to find the niche of my taste or not in which I am not an early adopter anymore because everyone else is along those lines
- Attila Csordas
What surprises me is that scientists inherently should be curious folks. Somethings gone wrong somewhere. It's not just technology, it's how you approach science and how aware you are of the ways of doing science. I'd argue that things aren't as bad as it sounds, but e.g. in structure prediction/molecular simulation, not too much has changed in the past decade (well not as much as I would like)
- Deepak Singh
instead of the AAAS let's establish the WWWS :)
- Attila Csordas
My feeling is that it's a generational change. Once the people who do science the "new way" gain more and more positions of influence, there will be a cooperative effect. As it is, there seems to be a lot of talk and a general agreement of the direction to head, but not as much movement among the majority of scientists as I'd personally like to see.
- Jason Winget
the question is whether the new generation needs new institutions or the deinstitutionalized web collaboration forms will be enough to bear the burden of a radical change
- Attila Csordas
Science has always been like this. If you check papers from basic science journals (ie phylogenetics journals) you will see people working with the same methods, software, etc of 20 years ago, even though new things are available for quite some time. I think it takes a little bit of time for the new guard to replace the old one, in a slow process. And for some people, new things are frightening.
- Paulo Nuin
@Paulo: yes, but scientists should not be among those for whom the new is frightening! Or at least, so I would have thought -- but it seems I'm wrong in many cases. I never have understood this.
- Bill Hooker
Me neither Bill, but that is what I feel from reading some journals. Some methodologies are quicker to be accepted than others, but overall the process is slow. And it shouldn't be.
- Paulo Nuin
Don't forget, some people study science because they need to know what is out there, endangering their world. Others study what is out there that can enrich their world. '
- dK
My take here is more than just using the web. I am talking of methods and approaches to problem solving as well. Scientists often take the "if it is not broken, don't change it" approach. Like Bill I think that inherently scientists should take the, if it works, let's try and break it approach
- Deepak Singh
My approach to "break the approach" is to try new programming languages, new APIs, anything that will make me think with a different perspective and angle.
- Paulo Nuin
Also in science the emphasis is more on the acquisition of knowledge rather than the tools. People just go in the lab and follow protocols, to get the data out so that the "fun part" begins. Again to praise my own house, difference in bioinformatics is that you bring all new sorts of tools in, and see how they alter your knowledge generation.
- Ntino
The phrase "punctuated equilibrium" comes to mind. arXiv adoption by physicists in the mid-1990s was frighteningly fast. In 1994, nobody I knew used it. In 1996, nobody I knew didn't.
- Michael Nielsen
Danny Hillis has a great quote that I think is relevant to any process of social change: "There are problems that are impossible if you think about them in two-year terms --- which everyone does --- but they're easy if you think in fifty-year terms."
- Michael Nielsen
Natural Selection May Not Produce The Best Organisms - http://www.sciencedaily.com/release...
Jean-Claude Bradley, Colin Archer and Deepak Singh liked this
I've always felt that evolution did not optimize unless required. There has to be some evolutionary pressure to do so. And how do you define "best possible". One that is physically optimized? Functionally?
- Deepak Singh
I read that as "may not produce the best orgasms."
- Tad
myExperiment - http://larsjuhljensen.tumblr.com/post...
Duncan Hull, Colin Archer, Jason Stajich and 2 other people liked this
http://myExperiment.org/ is indeed a rather interesting approach to make ones work reproducable. I have two metabolomics workflows on that side, and just wondered if it also supports storing input data (pointers, at least)... should explore that...
- Egon Willighagen
There isn't at the moment the facility I think for doi ng this. You can store 'blob's or at least there is a plan to let you. I'm not sure whether non-workflow stuff shouldn't really be elsewhere. That's my 'do one thing and do it well' philosophy
- Cameron Neylon
The impact of online publishing - http://blog-msb.embo.org/blog...
Michael Kuhn, Björn Brembs and Colin Archer liked this
It seems the main way people search for information, at least from what I've seen/heard, is via directed search but I think as more people become aware of the usefulness of RSS, we'll see more people coming across articles they find intersting but wouldn't necessarily search for, moving the equilibrium back towards content skimming a little.
- Colin Archer
I have the same impression as Colin. I have a handful of PubMed search alerts for fairly general terms (like "DrugBank") and also ISI WOS citation alerts for some basic papers. So in the end, to stay with the example, I receive TOC from the "Journal of DrugBank-based analyses". Thus, I am exposed to a manageable slice of the literature (and hopefully a large section of the relevant literature).
- Michael Kuhn
Visualizing genetic loci and molecular machines in living bacteria. - http://www.ncbi.nlm.nih.gov/entrez...
Colin Archer, Dan Kaplan and Pawel Szczesny liked this
[REPORTS] Electronic Publication and the Narrowing of Science and Scholarship - http://www.sciencemag.org/cgi...
Michel Roland-Guill, Michael Habib, Rafael Sidi and 3 other people liked this
"What is the effect of online availability of journal issues? It is possible that by making more research more available, online searching could conceivably broaden the work cited and lead researchers, as a collective, away from the "core" journals of their fields and to dispersed but individually relevant work. I will show, however, that even as deeper journal back issues became available online, scientists and scholars cited more recent articles; even as more total journals became available online, fewer were cited."
- Thomas Lemberger
Ideally. Shouldn't matter where good work is published as long as it can be found, with relevance driven by some metric
- Deepak Singh
I agree. But there is not only the problem of finding 'good' work but also to be aware of 'diverse' research. Searching and browsing are complementary strategies in this regard. Apparently online publishing favors 'search' versus browsing and thus restricts the scope of citations/knowledge. Probably a good reason to promote RSS aggregators!
- Thomas Lemberger
I cannot help but wonder if this has anything to do with electronic publication, or if it is simply an effect of sheer volume. If researchers have to search through ten times as many articles (because of the exponential growth of the literature), is it really surprising that they don't make it as far back into the past as they used to do?
- Lars Juhl Jensen
Combinatorial engineering of microbes for optimizing cellular phenotype. - http://www.ncbi.nlm.nih.gov/entrez...
Colin Archer and Thomas Lemberger liked this
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