“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.”
I've been wondering that for years. It's actually probably more prevalent in academia. - Deepak
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
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. - PauloNuin
@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. - PauloNuin
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. ' - dekay
I agree with generational change. The generation that *actively* used the web in high school as part of their regular learning is only just starting grad school now. They're probably the most eager to try new things. And right behind them is a generation of undergrads who have always put everything they do on YouTube. They don't know any better. - Eva
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
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. - PauloNuin
"I am a Miller Fellow at the University of California, Berkeley, in the lab of Adam Arkin. I am also the lead developer of the arXiv.org API." - Attila Csordas via Bookmarklet
“Dear life science experts of the FriendFeed-o-sphere: Does anyone know of a good program for producing clearly annotated maps of circular genomes; ideally for mitochondia ?”
I have used A Plasmid Editor (ApE) -- http://www.biology.utah.edu/jo... which is platform independent. If you have the genome annotated in Genbank format, it will generate a graphic with the structures annotated. Here's an example of a plasmid that I made and used ApE to make a graphic out of: http://kamrani.net/kambiz/file... Let me know if you have any questions, I can provide a more detailed set of instructions (kambiz@anthropology.net) - Kambiz Kamrani
Ideally it would take a Genbank format (or similar) file with gene annotations, and produce a nice (publication quality ?) picture. Maybe one of the programs for drawing plasmid maps would be good also for this purpose ... I've never seen one I liked but I'm sure it's out there. I'm also familiar with MitoWheel (http://mitowheel.org/mitowheel...) ... it's pretty but only does the human mitochondria, and has a sequence window obscuring the diagram. We want to display various other mitochondrial genome maps. - Andrew Perry
I see, Andrew. Do give ApE a try. I just updated my previous comment with an example of a plasmid graphic I made using ApE. - Kambiz Kamrani
Being part of the Mitowheel developer team I can connect you with the real guy behind, called Gabor Zsurka. Your problem does not seem to me the toughest coding challenge comparing to what Mitowheel already knows. - Attila Csordas
Kambiz: Yes, I'll check out ApE .. my first comment wasn't actually in response to your initial one, it was just extra info .. you were too quick in responding for me ! Thanks ! - Andrew Perry
Attila: That would be great .. I have intended to email him about it anyway, since I think mitoWheel would have far greater utility if it could do any (or many) mito genomes. Unfortunately I'm actually asking for a student in the lab who needs a solution rather ..err.. quickly, so I figured Gabor wouldn't be able to meet her deadline :) In the long term, however, an updated mitoWheel would be excellent. - Andrew Perry
I actually remember trying ApE years ago now ... it's really improved, and I'll probably use it to assist my cloning in the future. Unfortunately, there are too many features (ie ORFs) on many mitochondrial genomes to display everything neatly with ApE ... I need to be able to enlarge the circle, and only display the short gene names (Genbank /gene, not /product) written around the circle, basically the way mitoWheel does it. It might fit if we hand edit the features and tweak the ApE source a little ... - Andrew Perry
"Question: Are you as obsessive as he is?
Bale: Listen I think that you know I get obsessive, but over shorter terms you know. Obviously a movie lasts a few months and then you're done with it. With him it's life long of this single obsession. This one particular trick that he knows will make him immortal. So I have an obsession, but it's a different kind of obsession. It's more kind of short term obsessions." - Attila Csordas via Bookmarklet
I do keep my text books and do read or refer to them regularly. - Kambiz Kamrani
I hadn't had money to buy many textbooks. I keep the few I have. - PauloNuin
I sold pretty much anything I could get a reasonable amount of money for. I still ended up keeping quite a few and rarely, if ever, refer to them. - Chris Miller
I kept them all, but only brought five with me when I moved: Biochemistry, Organic Chemistry, Human Physiology, Chemical Principles (Zumdahl) and Introduction to C. - Eva
Books (unlike the previously discussed papers) I love to keep around. I also make a habit of picking up old textbooks (especially genetics ones). Have a couple of great early 1900s books. It's such a great way to capture a snapshot of the state of 'condensed' knowledge at the time, the fact the information dates just part of the charm. Mind you I'm hte kind of person who would desparately like to turn one of their bedrooms into a fully fledged library ;) - Daniel Swan
I really like the PDF and Book deals that have arrived recently: book to read on the plane, PDF to search later. Perfect. - Matt Wood
Daniel, I still have most of the classic books in the field. They look good :) - Deepak
I have some, not all. Like Daniel said, I keep classics, but I sell or donate others. I go digital (much easier to find something that way) - Andreas Matern
I used to keep all of my textbooks, but as a lifelong student, that became unwieldy. Now I keep only books that might be considered seminal in the field, or ones I particularly like, or ones that are less than 5 years old...actually, come to think of it, I end up keeping most of them anyway. :-) - Timothy Driscoll via Alert Thingy
and if I want a real approximation of 'new handshakes' just for the people who are not familiar with each other, we have to take the number of all handshakes minus the number of handshakes made by people already acquainted with each other - Attila Csordas
I also get 4950. (Every person shakes the hand of 99 others, but divided by two because it's one handshake per two people.) - Eva
I like empirical tests: what if we actually measure the number of new handshakes at BBCamp? - Attila Csordas
X - 99 handshakes, Y - 98 handshakes, Z - 97 handshakes... (cut out due to Friendfeed comment limit) ... XXX - 2 handshakes, YYY - 1 handshake. 4950 together or my Perl installation is broken. - Pawel Szczesny
"A small group of researchers is meeting in Birmingham, UK, later this month to plan a free digital library of mathematics.
All the mathematical literature ever published runs to more han 50 million pages, with around 75,000 articles added each year. Over the past decade there have been several attempts to make this prodigious body of work accessible in a single digital archive, but so far none has succeeded." - Attila Csordas via Bookmarklet
Hi all, just got into the idea of using Sourceforge's marketplace (link above), to get together a mini-group of people interested in offering bio-it support (for-profit). The concept of how this works for open-source software support through the Sourceforge marketplace platform, is explained at the "Take a tour" link on the right of webpage above. We can maybe get together a list of available expertise of interested people on a Biogang wiki page? I'm thinking we can offer support for anything from setting BLAST databases to scripting for data file mashups. It'll be tricky to advertise and get the message to potential buyers though, given the fact that bioinformatics researchers who might need support, probably not forage much in sites like Sourceforge marketplace. But still this site offers the structure to get something like that going. - Ntino
I think there should be a virtual science marketplace. Not sure if sourceforge is the right place necessarily http://bit.ly/4mKm0e - Deepak
"freelancing project in bioinformatics" is probably among top phrases people get to my blog, so I would assume that there will be more than a few people willing to participate. Something like a year ago I tried to to build a marketplace for freelancing scientists similar to Elance or Rent-A-Coder, but amount of buyers for such services was too small (I still plan to launch such service). Organised group looks much better for potential buyers than single freelancing scientists, so... - Pawel Szczesny
... so I think your idea has better chances to actually be profitable for providers. - Pawel Szczesny
Deepak, I've just seen your comment. Do you think now it's the best time to launch such marketplace? :) A year ago it was definitely too early... - Pawel Szczesny
Pawel,I think the best way to find if any beat exists on the marker for selling bioit support, is to initially write up an offering (at low price for start) in Sourceforge, Elance etc.Then advertise it around the bioit circles and see if people buy it.If there's demand, then the startup cost for implementing a site similar to Elance would be justified.I'll make a page on Biogang once I get my openwetware passwd,and you guys can pitch in your expertise if want to join the initial service offer at sourceforge - Ntino
Intrigued, but not yet convinced, by this idea... Who's the target market? Industry/academia/government? I might be able to give some industrial perspective. We are half-way through our first outsourcing project -- a flex app that we will embed in our web app. Attractive as an outsourcing project because it had well-defined specs, so benchmarks/milestones could be easily evaluated and it wouldn't need lots of iteration with our team. Also, Flex is a newer technology and ... - Andrew Su
... we didn't have in-house expertise. As for your use cases... don't think we'd ever pay for BLAST database set up. Not only do we already have that expertise, but more generally, it requires some maintenance so developing the in-house skill set would be important. Scripting I'm a bit skeptical of -- so much of that requires constant iteration (either in one's own brain, or with other team members). Would be hard to do with someone off-site. my 2 cents... - Andrew Su
very good comments Andrew. The BLAST / scripting were two examples. What I see in my workplace is a huge gap in knowledge of "power tools / latest techs" (see definition below) of people coming from biology background and getting into bioinformatics. People know Perl, some R, SQL, maybe some REST via NCBI e-utils but that's mostly it. I define "power tools / latest techs" as full fledged web-service programming, unix/linux wiz scripting, in-depth SQL and db administration. I've found myself offering this.. - Ntino
... this type of services / support to my group more than once. Of course you have IT guys, but they're specialized in one each of these techs, and it's difficult to get them talk to the biologists. What I see as offered as pay services as I mentioned already are data file mashups,setting a SQL db for mining some data etc.Useful for groups where they have some data and might not want to divert people to learn and wait 6months for the learning curve Rather, pay someone and have it ready in couple of days - Ntino
Pawel ... I think still too small for a formal marketplace and existing buyer behavior. Andrew raises some important points, although I think there are so many good developers out there now, more should happen. Companies like PivotalLabs required in LS space. Not too many boutique firms to solve software challenges and most in house software SUCKS (with a few notable exceptions) - Deepak
Is it useful to consider the difference then between research bioinformatics and bioinformatics tool development? The former (e.g., analysis of microarray dataset, combining with protein interaction data, and then gene set enrichment analysis) I think is almost never appropriate for outsourcing. There's just too much iteration that needs to go on. The latter I think is *sometimes* appropriate for outsourcing. For me to consider it, it's got to be a well-defined unit of work, ... - Andrew Su
... and the interfaces to the other tools in our environment also have to be well defined. It took a full day for one of our developers to define the specs for our outsourcing guy -- not an insignificant investment. To take another of your examples, I fear there are too many details in how an SQL db is set up (schema, indexes, etc.) that it would be difficult to communicate all the considerations to an off-site person. Anyway, FWIW... - Andrew Su
Andrew, definitely the discussion here on probably more on the Tools side, but I've seen big pharma begin to outsource a good chunk of informatics/modeling out to boutique players or service providers, esp in areas where they have no core expertise. They are happy trying to do the biological interpretation of the data - Deepak
Also, I think most developers at companies tend to be limited in their scope (most just get stuff to a "good enough" condition and then they are asked to move to the next project). I definitely come from a, there are a lot of smart people elsewhere, especially when it comes to software engineering - Deepak
1 supporting reason it is worth convincing a Nobel laureate to blog: yo has probably enough time to blog. But by blogging even the Nobel laureates will quickly lose their "exclusive celebrity status" and this is a trend I really like: being transparent on the web solves the interpretation problem of the "big man from the point-of-view of the footman". - Attila Csordas
Gary Becker (economics) blogs. And, as I write in the comments on Martin's blog, at least three Fields medallists blog (Terry Tao, Tim Gowers, and Alain Connes). The Fields medal is a much more exclusive prize than the Nobel - I'm guessing about 10 percent of the living Fields' medallists blog! Not sure why prominent mathematicians are so much more likely to blog than people in other areas. - Michael Nielsen
Economists do tend to blog don't they. Not quite at a Nobel level, but you can add Tyler Cowen, Alex Tabarrok, Dani Rodrik, etc to that list as well. - Deepak
Somebody loves us at GT: "Time to get psyched — and sign up! BioBarCamp is a mere three weeks away, and there are only 45 people registered to attend, with room for 55 more. At Pimm Attila Chordash lists all the attendees so far, including some from the systems biology community of scientist bloggers like Pedro Beltrao, Jason Bobe, Cameron Neylon, Deepak Singh, Ricardo Vidal, and Andrew Yates." - Attila Csordas
Did you know that you are part of the 'systems biology community of scientist bloggers'? - Attila Csordas
Should there be a field of systems blogging? :) No-one's ever called me a systems biologist before... - Cameron Neylon
Is there a central resource/recommendation list for finding accomodation etc nearby? I'm not sure I can make it but I'd like to scope out possibilities (with, as you can see, minimal effort on my part :-) ). - Bill Hooker
"Personal genetic knowledge is sort of like knowing your blood type: Important to know but far from sufficient." Depak already hunted down this post: http://is.gd/Spz - Attila Csordas via Bookmarklet
It's funny to see how this Wired founder, Kevin Kelly and fellows like him (Tim O'Reilly) are finally paying a big chunk of attention to biology due to personalized genetics. We should come up with The Biotech Geek Guide in time! - Attila Csordas
Kelly is a longtime fan - he wrote a book with biological ideas at its heart about 15 years ago. "Out of Control" - well worth reading. - Michael Nielsen
You are right about Kelly, I knew about that book, just ignored. - Attila Csordas
If memory serves, I think Aldhous Huxley and H G Wells explored some of these ideas, too, in fictional settings. - Maxine
I invited Kelly to BioBarCamp, he knows IFTF well. - Attila Csordas
May I like stuff on which I hardly have any idea?: "An algorithm is presented for graphics processing units (GPUs), which execute single-precision arithmetic much faster than commodity microprocessors (CPUs), to calculate the exchange-correlation term in ab initio density functional calculations" - Attila Csordas
One of the cooler things I got a chance to see was a GRAPE card running all the force calculations for MD, and then interacting with the actual simulation using a haptic joystick. Too cool!!! - Deepak
say at the end of every session there is some time for 1-2 web based questions. I don't expect a big online audience but that's not the point. The point is to make it possible but I cannot guarantee this right now. - Attila Csordas
might be logistically hard, but any plans to post session videos on youtube after? I suspect a lot of people are interested, but just don't know about it - Daniel Kluesing
I would guess enough of us will be carrying web cams, key question will be connectivity and platforms. But it worked pretty well at the North Carolina Science Blogging meeting earlier this year. - Cameron Neylon
1 tricky thing about FF is that all forms of all my tweets are here and so you can see that I am a perfectionist and working on an inforich tweet a lot :) - Attila Csordas
Moshe Pritsker:"1) I put the word “basic” in BIG quotes because: is there anything in biology today that can be considered “basic”? Biological research is becoming more and more fragmented, and researchers become more and more focused on their specific areas. Typically, as I observed in many labs, a neurobiologist would not know how to do a Western blot, and a biochemist would not know how to perform a simple cell staining. These are very “basic” techniques." - Attila Csordas via Bookmarklet
True, Attila. It's always been hard for scientists from different fields to communicate on the same level. - Mr. Gunn
"Bowie is marvelous as Tesla, who appears as a quiet, calm genius, one all-too painfully aware of the dangers of obsession.
For that matter, most of the cast is truly top notch. Particularly, Bale and Caine, reteaming with their Batman Begins director, Christopher Nolan. Jackman also delivers great performances as both Angier and his drunken doppelganger.
Surprisingly, the weakest link in this magic trick is Scarlett Johansson as Olivia, the lovely assistant who serves both Borden and Angier on stage and at home. Normally a solid performer who’s comfortable in foreign territory (as in Girl with a Pearl Earring and Scoop), she seems a little out of place amidst the fine-tuned talent of her cast mates; her faux British accent frequently does its own disappearing act. That’s not to say she’s terrible, but she has done better." - Attila Csordas via Bookmarklet
I liked the movie. I actually like the Illusionist better for some reason. Scarlett's accent is pretty bad isn't it :) - Deepak
Haven't seen the Illusionist yet, problem is that don't really like Edward Norton. But will watch it. - Attila Csordas
Bale and especially Nolan are both extremely gifted in their respective lines of work. Can't wait for Dark Knight. - Daniel Jurczak
And I haven't seen the American Psycho yet (just some scene at HBO) which made Bale famous. - Attila Csordas
Just thought it would be nice to have one instead of the default smiley faces logo. I figured since we spend so much time here, we might, y'know, spruce the place up a bit. - Chris Lasher
It's a glider from the Game of Life! Great idea! - Michael Nielsen
which part do you suggest? It won't show both - PauloNuin
ideas: superimpose the two, or replace the dots with helices, or just stamp the helix on every dot. - Bill Hooker
If I make it symmetric, will it display both? Currently it's ration is 2:1 for W x H. - Chris Lasher
I would go with one or the other - less is more. The left hand side has a certain nerdy charm. - Matt Wood
The left hand is indeed the Glider http://www.catb.org/hacker-emb... flipped horizontally; together with the helix, it's supposed to be the initials LS, and signifies that we're all bio hackers of some sort--in silico, in vitro, in vivo, or combinations thereof. Well, that's the thought at least. - Chris Lasher
If the glider is "L", perhaps lose the grid? Or de-emphasize; pale grey maybe. - Neil Saunders
"Most important, the future of open access probably does not lie in journal publishing models. The huge success of online literature databases such as arXiv (http://arxiv.org), free to publish and access, is significant. Such databases currently host mostly non-peer-reviewed preprints, and so are of little value for career building. But academic organizations throughout the world could, if they wished, build an equivalent archive of peer-reviewed papers." - Attila Csordas via Bookmarklet
Tedious -
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nature.com > Journal home > Table of Contents - Graham Steel
This is a very short Correspondence letter in Nature that itself is a comment on an earlier Correspondence letter. I will post the whole thing on Nautilus blog at some point when I have some time (as I did the earlier letter). I tend to post the full text of Correspondence letters and other bits of short journal content, when they are published, that relate to authorship on that blog, if you are interested. Today, for example, there is a brief news item up there. - Maxine
PS whatever one's opinion of the letter itself, the title isn't useful. Attila's extract is basically the writer's point. - Maxine
I'll need to go back through the correspondence but, putting aside the fact that arXiv is not free, the extract as quoted seems to be based on the idea that peer review can be carried out for free. The 'journal model' is not what costs money; its the peer review process and the brand management associated with it. Financially viable Open Access publication would clearly benefit from (I still don't agree it requires) cheaper modes of peer review. And we still haven't really worked out how to do it. - Cameron Neylon
Going back to the earlier letter and the main body of the response which is about third world access. I think the first letter makes a good point. Access for third world scientists is a compelling argument for OA but a strict author pays model is clearly not consistent with this. What I found interesting talking to some scientists is that even if they can get the fee waived they find having to ask this embarrassing and even the comments that they can to be paternalistic. There is more to it than just money. - Cameron Neylon
Protocol buffers have many advantages over XML for serializing structured data. Protocol buffers:
* are simpler
* are 3 to 10 times smaller
* are 20 to 100 times faster
* are less ambiguous
* generate data access classes that are easier to use programmatically - arek
Don't see much benefit for large files that are streamed (gzip does a good job there)? But could be great for storing or transferring large quantities of small bits of data -- e.g. when using Google's App Engine datastore! - Eric Jain
My first reaction. Not another data interchange format :) - Deepak
I am shocked how underutilized the undergrads are at mostly-graduate institutions. They're like a second class. I went to a PUI, and we weren't treated as menial labor there. - Donnie Berkholz
This was discussed here sometime ago when someone linked to a PR article that appeared online. - PauloNuin
Here's the structural proteomics example I mentioned previously: http://www.nature.com/nsmb/jou.... "All cloning and initial expression, purification and HSQC/crystal screens were performed at the Ontario Cancer Institute (OCI) over a 12 month period by A.D., D.C. & A.Y. with the help of one FTE technician and (for 4 months) six summer students". - Neil Saunders
On the topic of under-utilisation: we once had a plan to set up something like Condor on machines in the undergraduate computer labs, for number-crunching during vacation. Faculty IT was not impressed, naturally :) - Neil Saunders
I know the people that published the Nature Structural Biology paper. - PauloNuin
"I read recently about the cease and desist letters sent to 23andme and other personal genomics companies selling tests directly to consumers. 23andme has responded, saying that they agree with the ultimate need for regulation, but that harnessing the consumer internet for personal genomics is a really valuable scientific tool.
I have to say I find myself doubtful about the urgency of this regulatory move. It smacks more of the hand of the AMA, an entrenched industry trying to make sure that the new tools of genetic testing remain under the thumb of doctors, than of true consumer protection. You have only to walk into Whole Foods to encounter a multi-billion dollar industry of supplements making all kinds of dubious health claims, which is completely unregulated. Why pick on personalized medicine, which has way more substance, and at least so far, way more care in the types of claims it makes?" - Attila Csordas via Bookmarklet
