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Jean-Claude Bradley › Comments
ChemAxiom – An Ontological Framework for Chemistry in Science - http://www.citeulike.org/user...
Jean-Claude Bradley, Dan Hagon, Cameron Neylon and Egon Willighagen liked this
We present ChemAxiom as the first ontological framework for chemistry in science. ChemAxiom enables discourse about chemical objects in a computable language and is useful for the management of chemical concepts and data, the retrospective typing of resources, the identification of ambiguity and supports chemical text mining.
- Duncan Hull
That is very interesting - would it be possible to represent the solubility data in our recent book using this framework? http://usefulchem.blogspot.com/2009...
- Jean-Claude Bradley
@Jean-Claude this is Nico Adams work, I've pinged him about your question....
- Duncan Hull
Thanks Duncan - I was hoping Peter was checking FF too
- Jean-Claude Bradley
Inconvenient truth for Al Gore as his North Pole sums don't add up - Times Online - http://www.timesonline.co.uk/tol...
Jean-Claude Bradley and Khalid Mirza liked this
"'This is an exaggeration that opens the science up to criticism from sceptics,' Professor Jim Overland, a leading oceanographer at the US National Oceanic and Atmospheric Administration said."
- Andrew Lang
This could be a positive thing if it encouraged people discussing it to look at data more closely - but alas notice this article has zero references.
- Jean-Claude Bradley
Starting a new post doc at NKU - http://www.michaelbarton.me.uk/2009...
Piotr Byzia, Bill Hooker, Cameron Neylon and 5 other people liked this
good luck, and enjoy it
- Frank
Very cool. Wish I'd stayed with the microbial genomics. Happy to discuss it anytime!
- Neil Saunders
All the best at new place.
- Pawel Szczesny
Good luck!
- Martin Fenner
congratulations Michael!
- Jean-Claude Bradley
Classroom rewards 'do not work work' - http://www.telegraph.co.uk/educati...
Jo Young, Peter Miller, beatrice cherry and 2 other people liked this
Reward schemes reduce intrinsic motivation.
- AJCann
from Bookmarklet
Curious -- how many children are born with "intrinsic" motivation? Or is this something that is environmental?
- Mickey Schafer
Intrinsic versus extrinsic.
- AJCann
yes, learning can be both intrinsically and extrinsically motivated--and I believe this is true for everyone with variation depending on what has to be learned. But I've also encountered the terms as personality dimensions, and it isn't clear in the article which one was being used.
- Mickey Schafer
Yesterday, I overhead a very interesting conversation during which a school counselor was advising a parent with a failing child to remove all things of value to the girl and make her earn it back by achieving passing grades. This included _everything_ the girl liked from clothes and shoes to electronics to time with friends. She quipped after that she frequently has to teach parents how to be parents since today's generation was ill-informed. I found her horrifying.
- Mickey Schafer
@Mickey: that sounds like a recipe for leaving home at 16 and never going back to me. Horrifying indeed.
- Bill Hooker
There is some truth to this - when I have students play games for prizes, the reward (usually a chemistry book) is not the central motivation but it does make it more fun for the very best students to compete a bit. Similarly, with our ONSChallenge where students do labwork, the cash prize is small enough to not be the primary motivation but again it makes things more interesting.
- Jean-Claude Bradley
Jean-Claude, I agree that external motivation is quite useful. Nor does it have to be a big deal! I have premed students who once commented with enthusiasm that they would like get smiley stickers on their papers -- I was amazed. Didn't invest in stickers, but have thought about why this would be the case. In writing, the work is very personal and I get to see so many different sorts of...
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- Mickey Schafer
I also suspect we over-romanticize the intrinsic nature of learning in children. Yes, they do like learning, and they are curious, and the natural process of hypothesizing and testing that occurs can be rewarding (to a normal child). But this isn't the same process being used in school. And getting a kid to study for something like a spelling test in the first grade has very little to...
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- Mickey Schafer
Mickey good points. I experimented with different rewards and didn't find that much difference between a $5 reward and a video ipod - there is a type of student that responds to this type of competition so why not make their experience more enjoyable even if not all students respond?
- Jean-Claude Bradley
Doesn't this relate to Dan Pink's TED talk where tasks requiring significant thought were indeed adversely affected by a reward system?
- Peter Miller
That's a good point, Peter. And it gets at a real conflict in public education. Tasks that require significant thought are often intrinsically rewarding; James Paul Gee makes this point about computer games that are really quite complex, require hours of play to finish, and which kids readily engage in. In the public sphere, especially a test-driven one like the U.S., such tasks don't...
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- Mickey Schafer
People, remember that we need to be attracting more people to the benefits and rewards of making the effort of deep thinking and problem solving. We could and should considering using a reward system to draw young people (and by 'young', I mean from pre-school to college) into situations where they need to challenge themselves by thinking deeply. When they are at that place, we can...
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- Jason Miller
Very interesting point, Jason, but figuring out how to draw a young child into complex activity, especially in a public school setting, is damned difficult. My kids are in a science/tech magnet precisely b/c the educational tasks are deeper and often collaborative. This particular program also screens more for motivation to learn than sheer "IQ" -- the academic requirements for selection are "B" grades and above, but the clincher is whether the kid wants to work.
- Mickey Schafer
And while I agree that drawing a greater population in is really important, my observations after a year of volunteering is an unpleasant truth: kids are not equally talented. They are not all cut out for complex work whether b/c of personality or ability. I would argue that bribing the talented is a crucial undertaking since many of those will not pursue careers in STEM b/c those jobs...
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- Mickey Schafer
Mickey - I agree with what you're saying. One think I'm sensitive to (and it sounds like you are, too) is where and how we look for talent. If we're looking for talent in white-bread communities, then we're doing something wrong. If we're looking for talent in _all_ communities, especially in those that have historically been underrepresented in STEM, then we're doing something right. This will bring new challenges and frustrations, but that is a Good Thing. Don't you think?
- Jason Miller
Absolutely -- I spend summers working with under-represented populations and have been puzzling for years about how to get these students more connected to all the possibilities out there. The difficulty that most vexes me, and which I've never found/read/overheard a way to counter is the cultural differences. And this isn't just about color: it's more a factor of education and SES. As...
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- Mickey Schafer
What should social software for science look like? - http://blog.openwetware.org/science...
Ruchira S. Datta, Meryn Stol, suelibrarian and 32 other people liked this
FF doesn't meet all your requirements but it does seem to work well compared to the specialized services - at least in some fields
- Jean-Claude Bradley
Well I guess that's not surprising given my biases - at some level I'm more interested in what people think I've missed than my own predjudices though. FWIW I think a clever combination of DropBox, FriendFeed and some of the elements from StackOverflow, with perhaps a bit of the coordination ability of posterous would go very close to the mark. Still need better network and filter management tools though - somehow they need more configurability but less configuration...
- Cameron Neylon
OpenWetWare is looking to make a major overhaul in the next couple months, and has a bit over 1 year of funding left. I feel like this is an opportunity to at least try to do some of the things that most people think are necessary for SS4S. Not perfect, but better so that we'd have a better idea of what is really needed. I think the time frame (now; already funded) makes "not perfect" a...
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- Steve Koch
I really like what you said in point 10. It's something that I've seen far too many scientists being cavalier about. Federation, open protocols and specifications, along with open source, are very important to science.
- Christopher Granade
Might be worth seeing how far sourceforge meets your criteria. Certainly it's totally based around objects, i.e. software projects, and there are lots of high quality open source science projects whose code is hosted there. Although it has community/social networking tools I've personally never really used these and most visits I've had to sf have either been fleeting (to download...
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- Dan Hagon
Steve, absolutely we need to keep evolving with the resources available. OWW is a great place to do that.
- Cameron Neylon
Dan, there was a conversation around using Github in a similar way some months ago and I think these things have a lot of potential as a back end. I think federation is important enough that you'd want to use a DVCS rather than SVN as a back end though.
- Cameron Neylon
Sourceforge has several DVCS options in addition to svn these days. Although github is great I would be wary of anything that requires scientists to learn the intricacies of git. hg and bzr are much more friendly to non-developer types that don't need the full flexibility of git. I've had some success using them to collaboratively author LaTeX documents.
- Matt Leifer
Matt, ok, I'm behind the times (nothing new there!). The intracies are less of an issue as this would only be a back end. No SS4S that any significant proportion of scientists use is going to look _anything_ like a code repository. To start with your average scientist is never going to touch a command line. If you're dealing in Latex you're already talking about a minority I'm afraid....
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- Cameron Neylon
There are several wikis that use DVCS as a backend. This could be a starting point for developing the type of thing you are interested in.
- Matt Leifer
LaTeX isn't the minority in whole areas of math, CS, physics....I guess that brings up the same old complaint: "science" is defined as all biomed, all the time. I'll try to come up with some more substantive comments though
- Christina Pikas
Christina, didn't mean to say it should be excluded just that a non-command line system is non-negotiable so most online VCS aren't going to be good enough as a front end. Support for Word, Excel, video, images, XML and Latex are all non-negotiable characteristics of any such system.
- Cameron Neylon
Matt, not sure that a wiki is the right starting point - the document model doesn't seem right to me, although I'm way behind on the most recent developments in Wikis so I may be out of date on that as well. What is in my head is a DVCS back end with APIs providing access from e.g document authoring systems, databases, publishers, whatever. A feed system that looks a bit like friendfeed...
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- Cameron Neylon
I wasn't suggesting actually using one of the wikis, just that they have already done a reasonable job of abstracting the version control functionality (in fact, some of them support more than on DVCS in this way) so there may be some things in the codebase that are useful. It is also an example of taking a command-line DVCS and giving it a more user friendly interface. In addition, if...
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- Matt Leifer
Ah good to know - which do you think are the best examples of these wikis? I should take a look. In any case at this stage I'm just throwing ideas out. Have no resource to actually a build anything at moment.
- Cameron Neylon
Is there actually a need for social software for scientists? Or should scientists use and customize the existing social networking tools (FriendFeed, Facebook, LinkedIn, etc.)?
- Martin Fenner
I'm beginning to think the main issue will be that business models for consumers services are incompatible with what researchers need. So yes, customise might be better than build but if we have to go down that route we may as well have a good idea of whats required. One person's customisation is another person's build.
- Cameron Neylon
I'd be curious what you think of HubZero, Cameron.
- D0r0th34
Depends a bit on server setup. For Mercurial I like Hatta, but it requires persistent python processes, i.e. no good for most shared hosts that only allow CGI. There is a list of RCS backed wikis here: http://hatta.sheep.art.pl/Similar projects
- Matt Leifer
Cameron, I love and absolutely agree with the necessity of "scientific objects". If you lack those, then (as Martin points out) just use the general purpose sites. In that principle, I think there are some viable networks -- DVCS systems around scientific code, Mendeley around scientific publications, (eventually our BioGPS around genes). But I think we should be developing specific networks appealing to specific groups of researchers, rather than trying to serve the needs of all scientists...
- Andrew Su
Andrew agreed, but if these are federated then they can all still talk to each other. I'm thinking more framework than site or single service. Ideally all of these things can be plugged in or wired up together...my concern with general purpose sites is primarily that they don't provide the level of trust and stability that we would expect for "research enterprise"
- Cameron Neylon
Just one comment. There are protocols out there that allow different social networks to talk to each other. There are protocols out there that allow web resources to talk to each other. It's not really that hard if everyone supports some basic standards. RESTful API's, OAuth, OpeniD/Facebook Connect/Friend Connect, etc. IMO what's more important is that any sites we design have the...
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- Deepak Singh
@D only really had a chance to have a quick look. First impressions are that it is very slick but looks as though everything has to be on the inside - I don't see much mention of pulling stuff in and out. The multimedia talks are nice but why not pull them in from e.g. slideshare to pick an example.
- Cameron Neylon
completely agreed, federation through standards...
- Andrew Su
Twitter is far from perfect, but look at the infrastructure that has evolved around it e.g. 3rd party apps, services). You don't get that kind of traction around a social networking site just for scientists. Imagine what email or the WWW would look like if there were separate versions just for scientists.
- Martin Fenner
from iPhone
Absolutely but that actually means we can build something better, and as long as it hooks into Twitter (RSS/OAuth...Deepak's list basically) we get all the benefits and all of the functionality we want - as well as a way of drawing people in. Assuming this framework is any good of course. Imagine PubMed if it had been built for the consumer web (actually maybe not such a good example...
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- Cameron Neylon
Sort of responding to Deepak a few comments earlier. Something like a social network is useful for at least one reason: recruiting scientists who aren't ready for open science, or cannot communicate openly for one reason or another. So, a reasonably secure way of making data private and shared with a limited network is a good thing, I think. I think ultimately that will lead to much more open science (my own lab started out with a private wiki before doing ONS)...
- Steve Koch
Steve, but does it have to be a social network per se, or a site for say sequencing geeks (I am looking at you SeqAnswers) with the appropriate features built in. Social networks don't have to be all in the open. Facebook is a social network. 90% of my communication on there is private and you should see how much of my Twitter usage is DM's
- Deepak Singh
Deepak, I think I was just using terminology incorrectly. I was assuming Facebook = social networking.
- Steve Koch
What would research funding look like if it were invented today? Let's start collecting materials. (via http://friendfeed.com/danielm... ).
joergkurtwegner, suze, Meryn Stol and 7 other people liked this
The basic structure for this part iii of the "what would X look like if invented today" series is in the mind map at http://www.mindmeister.com/3016825... , with background via http://friendfeed.com/search... . Main points: More flexibility in the models of funding, more attention to technological shifts in the way people (including scientists) communicate. Such has also been argued at http://ff.im/9GGRn and http://2020science.org/2009... .
- Daniel Mietchen
Just noticed that we used different notions of "public funding environments" in the mind map so far. What I had in mind was to have "funding environments" in public, much like what fundscience.org plan to do. Some of the added comments seem to have used the term in the sense of environments for "public funding". Both notions are certainly valid, and we should think of ways to keep them apart.
- Daniel Mietchen
good point re making this difference clear(er) in the map
- Claudia Koltzenburg
I would like to see a lot more funding of contests
- Jean-Claude Bradley
Yes, Jean-Claude, contests and prizes with a competitive element are definitely on the list. If you have good examples from the recent past, please post them here.
- Daniel Mietchen
"More money for science is always good. Or is it? Six experts tell Nature what concerns them most about the US stimulus spending and suggest ways to ensure that it benefits research and society in the long term." - http://www.nature.com/nature...
- Daniel Mietchen
Daniel -for a recent example of a contest for research: http://onschallenge.wikispaces.com/
- Jean-Claude Bradley
Thanks, Jean-Claude. It is noted along with http://www.claymath.org/millenn... and http://www.xprize.org/ as an effort to make the chain from achievement to award both shorter and more transparent than currently usual.
- Daniel Mietchen
Daniel - the thing I like about contests is that barrier to participation is orders of magnitude lower than traditional funding - there is no need to convince anyone that what you are attempting will actually work before doing anything. Of course this limits the type of projects that can be run but it still applies to a large number.
- Jean-Claude Bradley
Has there been any recent follow-up study to "Activities, costs and funding flows in the scholarly communications system" at http://www.rin.ac.uk/our-wor... ?
- Daniel Mietchen
The Wellcome Trust weighs in on reforming science funding: http://www.timeshighereducation.co.uk/story... - see also http://ff.im/bljS1 .
- Daniel Mietchen
thanks for the pointer, Daniel
- Claudia Koltzenburg
Let's not forget that http://www.submeta.org/ provided funding for http://onschallenge.wikispaces.com/ - certainly a "basic research" funding model that looks promising
- Daniel Mietchen
One more: http://ff.im/cHoa5 on HHMI's focus on "people, not projects" - http://pazoulay.scripts.mit.edu/docs... .
- Daniel Mietchen
Daniel, not that I have anything against HHMI, but that mantra is not exclusive to them. For example Max-Planck Society has exactly the same approach (and I would say that at 10% of HHMI's budget and having twice as much Nobel prize winners, MPG looks a bit more effective ;) ).
- Pawel Szczesny
Didn't mean this to be exclusive, and I am well aware of MPG approaches (been there for a while).
- Daniel Mietchen
"I wish there was a universal format for submitting grant proposals; authors could post proposals (once!) & then the funders bid on them." (rephrased from http://ff.im/5VwEI ). I would add that the process should be public. fundscience.org plan to go this way.
- Daniel Mietchen
How do funders and scientists rank "more attention to technological shifts" against the "scientific expertise they have"? One says "change" the other "keep doing what you know"! Are those two things not disagreeing each other? In other words, who would you fund first, the "crazy new idea" or the "conservative stuff"?
- joergkurtwegner
I would think funders should have (as they do now) the liberty of choosing their priorities, and in many cases this will be a mixture of many incremental projects and some revolutionary ones. The main shift in the system would thus be to have just ONE avenue for proposals, and to make it public.
- Daniel Mietchen
On the role of rules in creativity and innovation: http://ff.im/cRs7K .
- Daniel Mietchen
The US gov is inviting comment on the Public Access to Science and Technology. http://friendfeed.com/mrgunn... I know we have some comments, can we draft a quick letter?
Kubke, Bora Zivkovic, Alejandro Montenegro and 7 other people liked this
I assume international input is welcome.
- Mr. Gunn
Don't have much time to help draft but will try -- and will certainly sign.
- Bill Hooker
ditto Bill
- Jean-Claude Bradley
ditto Bill, too
- Graham Steel
Will be happy to contribute and carry work load. Would it be worthwhile to write an 'international' letter that could be forwarded to individual govts (a letter that would be put forward globally, and simultaneously, with signatures from around the world).
- Kubke
Can look over drafts and do tinkering if it is useful...or just sign if it isn't
- Cameron Neylon
Cool, I'll start something on Etherpad.
- Mr. Gunn
question is: should we have 2 letters - one from US residents (whether citizens or whatever) and one from interested international folks? I don't know if they get sorted into different piles or what.
- Christina Pikas
I dont see a need for two letters. The signatures could be separated into US scientists and international support.
- Kubke
#ahm09 interesting, scientists are afraid to share data because others might mis-interpret the data, though this hardly ever happens.
joergkurtwegner, Heather Piwowar, Sarah and 10 other people liked this
Has there been much research into this (i.e. quantified "hardly ever")?
- Sarah Kendrew
I think a bigger reason is they don't want people seeing errors - every experiment has some kind of "error" - especially an unmeasured quantity that turns out to be important in the end
- Jean-Claude Bradley
As I said on twitter, really think this is just an instance of the control imperative. Scientists are for the most part very uncomfortable with relinquishing direct control over anything that affects them - they want to make every decision as far as possible and the idea that for a framework to scale you have to give up control over thing seems very alien. But I too would like to see some data and analysis on the issue - a fair bit of high profile data misinterpretation going on at the moment.
- Cameron Neylon
scientists concerns can help be addressed by advancing methods and best practices, and by describing case studies to provide confidence. accuracy is an inherent purpose of knowledge sharing, it is a testament to the high level of skill that it is usually accomplished
- Mike Chelen
Well, the imperative to 'show your work' can make people very uncomfortable. I see this all the time in the Open Source world, where developers sit on their code polishing it instead of releasing.
- Michael R. Bernstein
Mike, I'm with Michael on this one - in principle what you say is true, in practice it involves a huge change in attitude, psychology, and culture. You know that slightly nauseous feeling you get when pressing the button to submit a paper or grant? It's the loss of control - the worry that someone will find something you haven't - or tell someone else you're an idiot that leads to that....
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- Cameron Neylon
I'm with Cam, Jean-Claude and Michael on this -- scientists are terrified of being "found out" in an error, or of having someone see something they missed. This is a fundamental issue: ideally, what we want is a culture that values willingness to take those risks as much as (or maybe more than) it values demonstrations of brilliance. It's the emphasis on the latter (science as a career is basically a lifetime of "look how smart I am") that leads to the fears that block cooperation.
- Bill Hooker
Sarah, great question. I haven't found any research quantifying how often misinterpretation (or scooping, or error-finding) actually happens when scientist share their data, but it would be fascinating and important.
- Heather Piwowar
Can anyone post more details, links, information? Actually, I find it quite amusing that some people might find 'the (scientific) interpretation' more important than 'the (raw) data'. Should we start listing the examples in which people have published wrong interpretations, and how long it took for others to reproduce the data and come-up with the 'right' conclusion? For me it looks more like keeping people busy with reproducing data, even if not needed? What a waste in such resource limited times !
- joergkurtwegner
In astronomy data are re-used all the time - scientists often re-use archival data, although there is a certain etiquette to doing this. It's led to new discoveries years after the data were taken, e.g. reprocessing of Hubble images from 1998 led to the retroactive discovery of an exoplanet, see this paper by Lafreniere et al '09 on arxiv http://arxiv.org/abs/0902.3247. Many publicly...
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- Sarah Kendrew
Project H.M., Phase I - http://scienceblogs.com/neuroph...
Peter Miller and Daniel Mietchen liked this
It is ironic how the whole brain of a human being is made public - "like Google Earth for the brain" but making the NMR spectrum of a routine compound open data is controversial
- Jean-Claude Bradley
Data-sharing culture has changed - DATA SHARING - Research Information - http://www.researchinformation.info/feature...
Björn Brembs, Rafael Sidi, Graham Steel and 3 other people liked this
Simon Hodson of JISC examines how technology and funding policies have changed the ways that researchers share data Tags: opendata Posted by: cwhooker
- Bill Hooker
Love the intro "Scientists would rather share their toothbrush than their data!"
- Jean-Claude Bradley
iLabCentral Polymer Crystallization Experiment at MIT - http://ilabcentral.org/4.php
high school students can control temperature and observe crystallization remotely
- Jean-Claude Bradley
This is a notebook entry of mine that is trying to use an "atomistic" approach that links recipes I use to run the experiment. http://www.openwetware.org/wiki...
Mickey Schafer, Jean-Claude Bradley, Cameron Neylon and Steve Koch liked this
I understand that the context will be lost without more introduction but I'm still constructing the how and why I do experiments for each notebook entry. Hopefully this will generate a template for my notebook entries that will allow anyone to be able to reproduce what I do if they want.
- Andy Maloney
(My comment on your notebook page): Oh man, I'm dying to know the answer!!! Larry and I discussed possibilities of making his tracking software output a velocity, so that you could manually find out these kinds of answers in a matter of minutes. Not sure how long it will take him to do that. The long-term answer of how to fully automate everything is still a puzzle. Also, in terms of...
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- Steve Koch
Steve's point about instances is a good one here. Let's say the anomaly turns out to (perhaps) be connected to a specific bottle of D2O which is (say) contaminated with magnesium or something. I think the key point about "atomistic" approaches is that whatever the implementation, as far as possible the user shouldn't have to worry about creating the atoms - it should be done for them....
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- Cameron Neylon
That certainly makes it a lot clearer Andy. So what you are saying is that your protocols are so standard that you never vary anything? In our work that just doesn't happen - but it would be nice if it did :) Maybe I missed it but what is the type of microscope you are using and what is the magnification?
- Jean-Claude Bradley
To follow up on Cameron's point we did try to modularize at one point but from a practical standpoint we were never able to do so without removing too much information necessary to understand exactly what happened in each experiment http://usefulchem.blogspot.com/2008...
- Jean-Claude Bradley
Andy I don't know how deep you want to get into the concept of an experiment as an instance of a protocol but you might find some useful info and refs here (from the dark ages of closed notebook science) http://www.jalajournal.com/article...
- Jean-Claude Bradley
Yep, and the message to me is that with an atomistic approach it either all has to happen automatically while you're writing a higher level description or you have to accept that you end up doing both (the high level and the low level description). The atomistic/modular approach fails faster in JC's lab I believe because experiments are more clearly defined than in our work. Because our...
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- Cameron Neylon
JCB: I've tried very hard to make the setup for experiments mind numbingly simple and repetitive. So yes, my standards are all the same. I find this makes my life easier because I don't have to think about the setup, I just do it. This leaves me time to think creatively about what I am doing and what I want to look at in an experiment. It also works when something goes wrong. I can easily back track to find mistakes if I make everything the same.
- Andy Maloney
JCB: I have not made a page for the microscope setup yet. I actually completely forgot to do that so thank you for reminding me. Just for right now, I'm using an Olympus IX71 microscope with a 60x objective and a rhodamine filter cube that has filters from Chroma.
- Andy Maloney
CN: I'm not 100% sure but I think I have done this "low level" description with a very crude "high level" description in my most recent notebook. Or, at least I'm starting to implement it. There is still a lot of low level stuff that I need to make, such as the suggestion from Jean-Claude about making a page describing my microscope setup, so it's still a work in progress. It would be...
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- Andy Maloney
There's an interesting point around these cases where you "always do the same thing" its a classic case of tacit knowledge. Even if you were forced to write it down you'd probably miss the one thing that three weeks/months down the line you wish you knew. I suspect its a good case for just videoing proceedings, or having a tape of the user just narrating what is happening along with a timestamp
- Cameron Neylon
Hi, Andy. So first, let me clarify that I could in no way intelligently comment on the science itself. I'm looking at the page simply as a reader, and with the intent being to use such pages as examples to undergrads of what is meant by "open science". What I am curious about from a reader's point of view is whether the notebook has the "significance" or "research question" stuff...
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- Mickey Schafer
BTW, one of the things I really like about the OWW, and other wiki-like objects, is that I can use Diigo to take notes. Diigo cannot see inside .pdfs and some kinds of html, so it's neat to be able to use it here.
- Mickey Schafer
Andy, I suspect that's exactly what you're doing - and don't take any of this as a criticism or even an expectation that you shoudl dall all of this stuff. No-one does this perfectly and its interesting just to have a good example to talk about that is different to what's gone before. The problem as I see it is that this record is serving all sorts of different purposes to different...
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- Cameron Neylon
To get funded, aren't there narrative portions of grant applications? Those would funnel nicely into a lab's OWW page, with the projects doing the work branching off without the need for further explanation. Or, since OWW hosts blogs, that would be another option, though one that might require more upkeep than is ideal.
- Mickey Schafer
Also, Andy, just in case, I want to chime in with Cameron that I meant no criticism at all. Rather, I was visualizing a future class, where I bring this up, and one of my generally brilliant neurosci students asks "And what is the project all about?" especially b/c I've been harping at them to be able to explain their own work. And I, of course, would have no intelligent -- or even unintelligent -- answer to give!
- Mickey Schafer
Mickey: Writing down the broad context of this experiment is a big thing that I need to do. It would be nice to have a purpose spelled out for each new experiment, and relate that purpose to an old experiment. That way, there is a sort of logical evolution behind what is being done, not to mention the broad picture as well. Ultimately, I'm hoping that what I write in OWW will be the...
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- Andy Maloney
Mickey & Cameron: No worries about criticism since it is all constructive. Actually, I encourage it because it has made me think more deeply into what I want my notebook to look like and how other people can read/will it.
- Andy Maloney
Open objects take on a life of their own -- or something like that. I need to figure out a way to say it, but I think it's rooted in Cameron's observation that readers will bring so many different needs. The creator is not responsible for answering all those needs, but it is helpful, IMO, to have a stage like what you're going through where we all get to see what happens when open...
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- Mickey Schafer
Mickey the grant is a good start when one exists and it bears some resemblance to reality. But these are the case much less often than you might think
- Cameron Neylon
from Android
Andy thanks for the info on the microscope - how does that translate into a scale bar in the image? You'll probably need that when it comes time to publish. It wasn't clear to me what you were saying about how you handle changes in the protocols - if you find an error or make a small improvement will you just create a new protocol page on the wiki and link to that? You can't edit your current protocol page because it would misrepresent what you did in older experiments that link to it.
- Jean-Claude Bradley
Jean-Claude, it's an imperfect system now, because it takes a lot of clicks to create instances of things (as discussed above). However, in terms of preserving information, the "history" feature of wikis is nice. Andy and I discussed whether we can create a system that makes it very easy to link to the "permalink" for a protocol. That way, if the page evolves, the lab notebook will...
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- Steve Koch
Steve - I guess you would have to make it clear to a naive user that they must check the wiki history when they click the link for the protocol. But doing it that way how could you add more detail to an old protocol - whenever I read a lab notebook I'm thinking - is there enough information to publish without needing to contact the student? - so more details get added to our experiment pages over time. The other issue is wiki pages in the history don't get archived on Google.
- Jean-Claude Bradley
Steve - what you are talking about reminds me of the "snapshot" approach we are trying to use. Where an archive contains a copy of every document as it existed on that day. Andy Lang has already written some code for this - if you want it could be modified slightly to work on any similar systems: http://onsarchive.wikispaces.com/
- Jean-Claude Bradley
Dogs vs cats: The great pet showdown http://www.newscientist.com/article...
cats bond with their owners in much the same way that dogs do - if only he could persuade them to take the test
- Jean-Claude Bradley
And then there's the confused giant rabbit who thinks he's a dog. I think he'd come in third in this race. http://www.dailymail.co.uk/news...
- Abigail Maley
that is one big rabbit Abi
- Jean-Claude Bradley
A PLoS ONE Success Story--Taxol Crystals Masquerading as Microtubules - http://stevekochscience.blogspot.com/2009...
Peter Binfield, Mr. Gunn, Bill Hooker and 8 other people liked this
This is my review of a recent PLoS ONE article I read. I think people on FriendFeed will be most interested by how well the PLoS commenting system worked for me. I love it! Also, this is my first stab at a "Research Blogging" post, and if you're interested in microtubules, the results of the paper are pretty interesting.
- Steve Koch
from Bookmarklet
Science2.0 at work - beautiful
- Jean-Claude Bradley
All STM publishers everywhere please take note, this is the way it's supposed to work in the 21st C: any journal that does not have this functionality is a glamor magazine, not an instrument of scientific communication. Reading Steve's post gives me a happy that I don't think I can describe in words.
- Bill Hooker
If you had three full days to get from Raleigh, North Carolina to Gaithersburg would you a) barrel straight to DC and do the monuments/museums or b) stop off at something interesting along the way? In...say...January
Hm. You're kind of in the boring areas of NC and VA vis-a-vis natural beauty -- neither the coast nor the mountains. I don't know what there is off that drive for historical interest; the state tourism orgs probably have websites (I'll dig 'em up in a sec). If it were me, I think I'd go straight through, but on back roads rather than the interstate, keeping my options open if I saw something interesting.
- D0r0th34
If you want to go a little further north and give a talk in Philadelphia let me know
- Jean-Claude Bradley
Jean-Claude, coming to Philadelphia in late February - http://www.nfais.org/page...
- Cameron Neylon
BTW, on the interstate it's not a hugely long drive. Around six hours.
- D0r0th34
cool - if you want to talk at Drexel again you would be welcome
- Jean-Claude Bradley
That would be great if it were of interest. I arranged to fly out on the Monday evening so have the whole of Monday available I think. Maybe expand on the NFAIS talk to relevant people? Current working title is "Thankyou Mr Shirky, now where's my ******** filter?"
- Cameron Neylon
Barrel to DC and eat :)
- Rajarshi Guha
I could set you up on March 1 at 11:00 - it would be in the chem dept but I'll make sure we advertise to bio, IT, library and local universities
- Jean-Claude Bradley
Most Ugly & Useless Infographic Competition: The Winners - http://infosthetics.com/archive...
Khalid Mirza, Rajarshi Guha and Jean-Claude Bradley liked this
To me, this shows a need for quantitative literacy across the disciplines.
- Andrew Lang
I have some ugly chem data to highlight after my class is over...
- Jean-Claude Bradley
Citemine - a prediction market for academic papers (via @michael_nielsen) - http://citemine.com/
Richard Akerman, Rafael Sidi, Björn Brembs and 3 other people liked this
is anyone an active member?
- Alejandro Montenegro
I doubt it :-)
- Neil Saunders
I signed up a while ago and invested in Jean-Claude's paper. I just revisited and couldn't figure out how to even find more papers to invest in :) I guess it remained "very beta."
- Steve Koch
in the category of try anything once
- Jean-Claude Bradley
Proposal for Science 2.0 lectures - http://freelancingscience.com/2009...
Piotr Byzia, Berci Mesko, MD, Steve Koch and 7 other people liked this
I think the compatibility of IP and ONS is a very interesting topic - Steve Koch has an agreement with his research office that might make it partially compatible
- Jean-Claude Bradley
Jean-Claude, thanks for the pointer. I need to look into that. Also, Paulo Nuin commented on the blog that I could (and I will) mention data attribution.
- Pawel Szczesny
That's a great list. And data attribution and citation, maybe data management in general would be good additions. Paulo on the ball as always...
- Cameron Neylon
Agree with Jean-Claude that IP / ONS is interesting. Happy to provide any info on our very narrow and limited experience with the issue here at U. New Mexico.
- Steve Koch
Steve - hopefully we'll discuss that a bit at the ONS session in NC
- Jean-Claude Bradley
EtherPad Blog: Google Acquires AppJet - http://etherpad.com/ep...
Nany, Dan Hagon, Richard Akerman and 3 other people liked this
"We are happy to announce that AppJet Inc. has been acquired by Google. The EtherPad team will continue its work on realtime collaboration by joining the Google Wave team."
- Daniel Mietchen
from Bookmarklet
"If you are a user of the Free Edition or Professional Edition, you can continue to use and edit your existing pads until March 31, 2010. No new free public pads may be created. Your pads will no longer be accessible after March 31, 2010, at which time your pads and any associated personally identifiable information will be deleted."
- Daniel Mietchen
OK, now I have to start using Wave?
- Peter Miller
Etherpad was immensely more functional for realtime collaboration than google docs . This development was predictable..considering that wave is still so hard to grock
- Hari
I think the key for casual users of wave is that robot that email you when there is an update - Cameron gave me that trick. It was broken for a few days last week but seems fine now. Otherwise it is hard to keep checking wave for updates as part of your workflow. BTW - is there a way to get email alerts when wikipedia pages change?
- Jean-Claude Bradley
What is the address of that robot? Strange, though, that the supposed replacement of email doesn't work without it - let's hope this is just transitional.
- Daniel Mietchen
Daniel the robot can be added to any wave as wave-email-notifications@appspot.com
- Jean-Claude Bradley
There's also an XMPP jabber bot that sends you an IM when a wave is updated, that's what I use.
- Mr. Gunn
Thanks, Jean-Claude; put it on some waves and will see what this gives.
- Daniel Mietchen
Noticed that the bot was already on most of the waves I have been on for weeks, but not a single notification reached me so far. Back on topic: Etherpad will remain operative until at least when they release their source code. http://etherpad.com/ep... .
- Daniel Mietchen
Daniel - if the bot is working it shows up at the very top of the Wave - it might be set to OFF and it will give you a link to activate it. If you see a broken image it is not working at all
- Jean-Claude Bradley
Thanks - got the activation links in some waves, though not in others. No broken image.
- Daniel Mietchen
Got my first notification. Thanks, Jean-Claude.
- Daniel Mietchen
Submitted CAREER proposal & posted to Scribd: http://www.scribd.com/doc... Open proposal for an open science project!
mkz, Michael R. Bernstein, Graham Steel and 20 other people liked this
Thank you to everyone who helped and encouraged on this and offered future support! Among many things, one thing I'm a bit embarrassed about is the lack of details in the "broader impacts" and open science parts of the proposal. Definitely it needs more planning and better writing, and the panelists are going to point that out. Hopefully you all understand that it's a product of spending all my time trying to make the research parts as good as I could.
- Steve Koch
good luck Steve!
- Jean-Claude Bradley
A small step for a team, but a giant leap for #science .
- Daniel Mietchen
Good luck!
- Brian Krueger - LabSpaces
Thanks everyone! I sort of dropped off the map after submitting the proposal. One of my most successful attempts at actually vacating during a vacation.
- Steve Koch
Bummer! Just found out tonight that the proposal was not funded. I have done one read-through of the reviews. First of all, I am once again amazed at the time and effort the reviewers put into reviewing my proposal. There were 6 reviewers in total and they all had a page or more of feedback. And they all pretty much agreed on the main points: (a) interesting proposal that is worth...
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- Steve Koch
Thank you Jean-Claude, Andy, Cameron, and Drew for the Open Science support letters! I am sure that was key to the very positive reviews for Open Science. Thank you to everyone else on friendfeeed who supports me and our other lab members. We now have 7 months to obtain the preliminary data and get a couple publications, and indeed we are now poised to do so. I am confident the lab members can do this, and by eliminating (b) and (c) above, all signs point towards this being a very strong proposal next time.
- Steve Koch
well done all 'round! next time you'll knock 'em dead.
- D0r0th34
for the CAREER third time is often the charm - good luck for next round
- Jean-Claude Bradley
Thanks, Jean-Claude and Dorothea. The CAREER "3rd time's a charm" effect is part of the reason I submitted without strong preliminary data. (But I also thought we'd be able to generate the data in time for the 2nd submission. Now, though, I'm SURE we can before July :) )
- Steve Koch
After thinking about it for a couple days now, I am still very happy that they viewed the open science so positively. I think that's a big deal.
- Steve Koch
absolutely Steve - very good feedback about OS being a positive to the funders
- Jean-Claude Bradley
Steve, this looks really really promising. If you can come up with interesting data for the next resubmit, I think you have a great chance to get funded. Congratulations!
- Bill Hooker
Thanks, Bill!
- Steve Koch
IBM: Computing rivaling human brain may be ready by 2019 http://news.cnet.com/geek-ge...
Yaroslav Nikolaev, Piotr Byzia, Naz and 3 other people liked this
According to IBM, 'BlueMatter, a new algorithm created by IBM researchers in collaboration with Stanford University, exploits the Blue Gene supercomputing architecture in order to noninvasively measure and map the connections between all cortical and sub-cortical locations within the human brain using magnetic resonance diffusion weighted imaging. Mapping the wiring diagram of the brain is crucial to untangling its vast communication network and understanding how it represents and processes information.'
- Ami Iida
"some of the world's most prestigious universities have already managed to simulate the computing complexity of the feline cortex" - gotta be hype
- Jean-Claude Bradley
as a cat owner, I know that's a very low bar to clear.
- Mark A Jensen
They've known the connectome of C. elegans for 20 years and still can't make a model work like the real animal. We will still learn a lot from failure, though, as usual in science.
- Björn Brembs
Bjorn - that really is the point - the connectome is not enough. Even is simple species like elegans is there not hormonal and other modes of communication besides synapses? Is it understood why the models don't work well?
- Jean-Claude Bradley
A Presentation to Students at Drexel University Via Webex and Skype - http://www.chemspider.com/blog...
Alexey, Peter Miller, Graham Steel and 3 other people liked this
It was an inspiring talk Tony - thanks for taking the time. In all the talks we had at U of Ottawa 20 years ago I don't think we could have guessed that this what would be happening to chemical information today.
- Jean-Claude Bradley
I like the way you can click on different parts of the InChIKey and have it do searches automatically - I didn't know that before - very cool.
- Andrew Lang
JC...if you'd asked me almost 20 years ago whether I'd be working on a project like ChemSpider the answer would be a big no. I certainly wouldn't have envisaged the progress that we have seen in computer-based chemistry....the internet wasn't even a term we had heard back there in Ottawa!
- Antony Williams
yes we actually physically went to the library back then :)
- Jean-Claude Bradley
It's somewhat amusing that I still recognize almost all the names in current issues of Proteins: Structure, Function, Bioinformatics? Are no new people doing structural bioinformatics? And we really need a good "open" journal in this space
Pedro Beltrao, ElijahBailey-Zu of FF <0,, Nir London and 5 other people liked this
nothing close enough in the BMC group Deepak?
- Jean-Claude Bradley
It doesn't suprise me that its tough for new people to get into these kinds of fields. High entry costs and high project burn rates looking for the big hits. Really tough for new entrants.
- Cameron Neylon
Jean-Claude - Not quite although I haven't been tracking content that closely
- Deepak Singh
Cameron, agreed. The field hasn't really progressed that much either for a while, which really bugs me
- Deepak Singh
Also the concern that has certain pathways become standard and it is too expensive to rebuild those they limit the way people can think about the subject
- Cameron Neylon
from twhirl
A. Deepak: I disagree that the field hasn't really progressed (frowning smiley) it keeps progressing all the time. B. Is "Proteins" really considered such high-end publication target for structural bioinformatics ?
- Nir London
Nir, with few exceptions (and your stuff is in that short list), it hasn't. I find it difficult being drawn in and the improvements have been painfully slow. I should add that my bias is towards more "physical" methods
- Deepak Singh
from IM
Well, you could say I'm somewhat biased ;) I actually revisited a poll I published a while ago (http://bit.ly/617Geh) regarding the prefered journal for computational structural biologists and was amazed to find that indeed proteins ranks much higher than, let's say "Structure", and by the way PLoS CB ranks as high as proteins..
- Nir London
I think a relevant question is how to define "structural bioinformatics" nowadays. There are a lot of gray areas that result from different reasons: 1) there are a lot of relevant papers to the field (as I see it) that come from people in CS or Chemistry. Many of these people don't think they are doing "structural bioinformatics". 2) There are no conferences that bring the majority of...
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- Mickey Kosloff
@Nir. "Proteins" might not have the highest impact factor of the relevant options, but it's a very good journal that is read by many people in the field (with the caveats of this definition as I wrote above). As for your comparison with "Structure", what percentage of the papers there do you find *really* relevant to your research vs. "Proteins"? For me Proteins is one of the very few...
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- Mickey Kosloff
I'm going to do a round of looking at some of the Science Social Networking sites again. Is anyone active on ResearchGate, Epernicus etc. and interested in testing functionality?
John Delacruz, Jack H. Pincus, Dan Hagon and 24 other people liked this
I'm interested in joining the testing. Need to agree on criteria for comparison before starting, though.
- Daniel Mietchen
I'm willing to keep an open mind but so far FF surpasses these in terms of networking and ease of use. But if you want to experiment I have accounts in many of these and I would be willing to try.
- Jean-Claude Bradley
I'm really just looking to make sure that things haven't moved on and improved significantly, particularly in the light of the NIH projects.
- Cameron Neylon
I tend to migrate to social networking sites based on "pull" - virtually the only time I go on LinkedIn or Facebook is when I get an email alert to something relevant to my interests. I would assume that if there was anything really cool going on in these new sites I would get these alerts generated by actions by you and my other friends.
- Jean-Claude Bradley
BTW Cameron - that is one of the issues I'm finding with Wave - I tend not to check it because I don't get alerts that there are updates - is there a way to get an email alert for Wave updates?
- Jean-Claude Bradley
Yes, there is an email alerter. I'll add you and it to Wave...
- Cameron Neylon
Agreed to the general point though - if there isn't a pull, I'm not going there really. And I think that is a big issue with Wave - people just aren't checking in.
- Cameron Neylon
@Jean-Claude I don't think there's currently a way of doing this with the current interface without adding a robot but I saw there's a robot on the Haskell public wave which has similar support http://wave-xmpp.appspot.com/public...
- Dan Hagon
I'd be interested in testing (I recently started looking over Epernicus for an article on NGS). Where is the email alerter for Google Wave? Currently, I'm using Waveboard (Mac), which alerts you when there's activity. However, it needs to be running in order to do so.
- Walter Jessen
Just added you to a Wave with the email notifier Walter...
- Cameron Neylon
New SNS from American Institute of Physics, got email invite today: http://www.aipuniphy.org/
- Andrew Lang
I have accounts on Epernicus, SciLink, Laboratree, and maybe could consider BenchFly a social networking site too, but like JC, I don't go to any sites besides FF and Twitter (and those are typically through 3rd-party apps), not even Facebook or LinkedIn, unless I get some alert. But I would be happy to see if anything's changed in those science-oriented sites I mentioned
- Shirley Wu
from twhirl
I do get alerts that new people have joined the organic chemistry group in Research Gate but there is no discussion and my questions have not been answered there by anyone so not much motivation to check in.
- Jean-Claude Bradley
I have accounts at NN, Epernicus, BioCrowd and SciLink. I have begged for account deletion at the latter for months, to no avail and have not visited most of the others for as long as I can recall. So: active - no, interested - no. It's all FF/Twitter for me.
- Neil Saunders
It's alright - this is a benefit of the doubt exercise - making sure that things haven't changed or that we've missed something. My brief look around yesterday suggested that nothing much has but I wanted to make sure I'm not missing something.
- Cameron Neylon
What about the criteria for comparison other than some "pull" functionality (which they all seem to have, to different extents)? Does usability boil down to feed import/ export and (hierarchically) threaded conversations ordered by novelty and importance, as at FF?
- Daniel Mietchen
When considering the usefulness of the individual platforms, perhaps discipline-specific ones should also be on the list? Besides http://polymathprojects.org/ (maths), these would include, for instance, http://openanthcoop.ning.com/ (anthropology), http://www.apecs.is/ (polar research), or this very life science group at http://friendfeed.com/the-lif....
- Daniel Mietchen
It would be worth doing a compare and contrast - also things like Math Overflow and even some of the chemistry blogs act more like community sites. Seems particularly apposite with respect to Pawel's blog post yesterday about the idea to set up a next generation sequencing community site.
- Cameron Neylon
I have a ResearchGate account but don't actively use it. I currently do some FriendFeed, Nature Network (where my blog is hosted) and Google Wave, but mostly Twitter.
- Martin Fenner
The last issue (November 23) of the German computer magazine c't has an article on social networking for scientists. They like ResearchGate and Mendeley, but also include ResearcherID, Scholarz (a German network), Nature Network, SciLink and Scientist Solutions: http://www.heise.de/ct...
- Martin Fenner
That c't article (which shall come out in some OA fashion soon) may serve as guidance but I found the choice of networks therein rather arbitrary, and the comparison between sites was done on a more general level rather than on the basis of specific criteria.
- Daniel Mietchen
The article makes two obvious omissions: a) no mention of CiteULike (or Connotea), b) no mention of the recent $12 Mio social networking NIH grant to U of Florida/Cornell University. There are some more things in it I don't like, so I wrote a letter to c't magazine.
- Martin Fenner
Cameron, what criteria were you thinking of using?
- Mr. Gunn
Key questions: a) What is the immediate impression on signing up? Is there a pull for people to come back? b) What functionality is being offered? Is it immediately available? How dependent is it on having a network in place? c) Funding model and stability d) User numbers, ideally active users and accounts, but whether we can get those is another question. Those aren't very objective criteria and they are built on my biases but nonetheless
- Cameron Neylon
Sorry if this is slightly tangential to the discussion, but I was imagining a new kind of social network for publication of research results here: http://virtualchrisleonard.co.uk/blog...
- Chris Leonard
Chris - when you talk about "credit" are you expecting tenure and promotion committees to count it or do you have some other system in mind? If you set something up I have content that might be suitable to play with. As for citability - in our last few papers we have used blog posts and wiki pages as references and have not had any problems with that - so I think the system is quite flexible and can accommodate the types of activities you are proposing.
- Jean-Claude Bradley
I think Chris means system credit or karma. The idea as I understand it is somewhere between Friendfeed and Stack Overflow
- Cameron Neylon
Thanks Cameron, yes, that's what I meant by 'credit' - however, by quantifying and metricising that credit, there is a possibility that one day tenure and promotion committees may want to use it as another measure of a scientists influence in a field. Apologies to Cameron for hijacking his thread. There is another discussion on this blog post here: http://friendfeed.com/chrisle...
- Chris Leonard
That's fine, it's not my thread, it the communities thread :-) Pointers are good, they link up the information.
- Cameron Neylon
Blog postings to replace (journal) papers and (in-depth) peer review a luxury that can only be acquired if paid for and to be replaced by blog comments instead? Weakening both readability and certification? That does not sound like a healthy idea.
- Wobbler
Wobbler: why should blogs lack any aspect of peer review? the standard of any publication depends on how editorial powers are used
- Mike Chelen
...and we already pay for peer review. It just isn't a cost transferred as actual cash.
- Cameron Neylon
But blogs do not have any editorial powers? What advantage do blog postings have over (journal) papers? They lack format = lack of consistency = lack of efficiency = lack of scalability. Are you seriously suggesting that blogging/blog posts have the potential to replace journal publishing/ (journal) papers as the primary scholarly communication model/channel? Upgrading the traditional...
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- Wobbler
@Cameron: that's true, but now peer review is at least mandatory for the primary scholarly communication model i.e. scholarly publishing. Replacing that with something else and having peer review only on request/payment is a very different story.
- Wobbler
Wobbler - there is a difference between requiring the peer review to be performed before making some information public and allowing it to take place after that. I do not see why the latter option would generally fare worse than the former. In fact, we already practice it here at FF, with numbers of likes and comments roughly indicating the popularity of a topic, while the quality has to be sought in the individual comments (and of course the source item that started the thread).
- Daniel Mietchen
... it isn't a cost transferred BY YOU as actual cash. Yet. It should be, in my not-terribly-humble opinion, however, because the market disconnect in the current system has proven ridiculously unsustainable. Wobbler, some of my blog posts have had more measurable impact than anything I've ever written. Sure, it's a lightning-strike sort of thing, and most of my blog posts languish in...
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- D0r0th34
@Daniel: I'm not talking about post-"publication" peer review. That's still different from random blog commentary on blog posts. There's no evidence that what we're doing here isn't just a "niche" thing that works well because we're a niche. There's certainly no consistency in quality in our blog postings (well, at least not in mine :p ). Not to mention a lack of consistency in...
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- Wobbler
@D0r0th34: No, we should absolutely not ignore lighting strikes. But we should see them as lightning strikes and consider them to be an exception more than a rule and focus our attention on something that provides that level of quality more as a rule than an exception. Blogs as a complement to (journal) papers is great. But once you start to see it as a primary source, a replacement for...
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- Wobbler
We don't know about our OA bets. As for slow-and-steady, a well-run blog isn't? Lightning strikes aside, building a reputation and a readership is hardly an immediate thing.
- D0r0th34
@D0r0th34: That's one more reason why blogging as the primary scholarly communication model is a broken idea. "Popularity" and "building a readership" will be important for blogs (and other post publication peer review models) to be visible/significant. But aren't we going after journals for using their JIF to attract peeps to read their stuff? How is "blog (poster) popularity" to get a...
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- Wobbler
I think the most important property of non peer-reviewed scientific communication is that the content be easily indexed and searchable. Relying on comments and rankings can be very misleading indicators for utility in long tail systems. For example we get over 100 searches a day for our solubility data via Google and Wikipedia but we have never had a comment or any type of feedback from the people who searched for and found information.
- Jean-Claude Bradley
Shrug. System-gaming goes on everywhere; there are a number of studies of citation-impact gaming, if you look. Also, why is connectivity a bad thing? We are talking about scholarly *communication* after all, right? Restricting "what counts" only to what goes through the baroque serials-publishing process is IMO an extraordinarily blinkered and limiting view of how knowledge really advances. Sure, it's not easy to come up with more inclusive views -- but that doesn't mean it's not worthwhile.
- D0r0th34
The problem is that I'm not sure we can talk about "gaming the system" rather than "an intrinsic part of the system that everybody will be forced to play or greatly risk invisibility" when it comes to blogs and other models relying on postpublication "peer review". PLoS ONE is, intentionally or not, already trying to stake their claim on an as large a readership/community as possible....
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- Wobbler
@D0r0th34: And connectivity can be unfair if your serious/scientific works are getting more attention than others simply because you've managed to draw a bigger crowd through non serious/scientific stuff. On a slightly more personal note: for someone who occasionally complains about the (lack of) readability of (journal) articles, I had expected that you, of all people, would appreciate...
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- Wobbler
I have to say reading down this I am unsure of whether the complaints apply to blogs or journal articles. Consistent structure and copy editing would be nice but it is rare for both blogs and journal articles. Quality is an issue across the board. Going back to peer review - it's only mandatory for the author, refusal rates for reviewers are going through the roof and unless we acknowledge that cost the system will collapse sometime soon.
- Cameron Neylon
@Cameron: Consistent structure and copy editing are rare for journal articles? They are? Not entirely sure about copyediting, but surely most, if not all, journal papers have a recognizable structure? And I don't think they're as rare or rarer than for blog postings. I also think the issue is with peer review, and not with the (journal) paper (format). As such, we should find ways to...
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- Wobbler
Of my recent papers, only one received close copy editing by anyone but me. And that was the Nature piece for which to be honest I would have been happier if the editor had got a co-credit. And formats are all over the place - maybe consistent for a single journal but that's not use to me. The costs of both peer review and publication are so high we need to find a way to lower them -...
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- Cameron Neylon
@Cameron: I'm not sure that's a convincing enough argument for me. Maybe your other papers were written clearly enough already? You're a prolific blogger/writer, Cameron. It's not weird to assume that your ability to communicate concepts clearly is higher than the average scholar. Maybe high enough to not warrant copyediting (in a lot of journals)? My impression of journals is that...
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- Wobbler
Well others can pitch in but perhaps a different anecdote. Until I started getting into arguments with Maxine Clarke I didn't even realise that journals might do copy editing. Nature and similar are very different beasts to the average of course.
- Cameron Neylon
So, generally speaking, only the high profile/impact journals provide copyediting services? Hmm, that is definitely not what I expected. If you had to estimate the % of journals that provide copyediting services, what % would that be? The (top) 10% of all journals?
- Wobbler
I have the same experience as Cameron - the only time my manuscript was copyedited was when I published in Nature
- Jean-Claude Bradley
So far as I'm aware, no-one here wants to replace peer-reviewed journals entirely by blogs. Yet that seems to be what you're arguing against, Wobbler. For some functions, journals are a lot better than blogs. But for other functions, blogs are a lot better than journals. At the least, I really can't imagine how, say, DHJ Polymath or Galaxy Zoo or the Open Dinosaur Project or [fill in...
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- Michael Nielsen
Most of this is as a response to an FF comment by Chris Leonard on the 23th of November in this thread, who is arguing for exactly that.
- Wobbler
Cameron, any progress on the roundup? Is there any information I can provide from Mendeley?
- Mr. Gunn
Right - getting there slowly! Have set up a wiki page (ignore the state of the rest of the site I am working on it!) at http://wiki.cameronneylon.net/index... You should be able to login with openids, any problem give me a yell. I would suggest a week by week schedule to dive into and try and use a specific site, give it a good shot and then report as we go. I...
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- Cameron Neylon
Cameron, what do you mean by "stability" - things like a service being bought/shut down vs. server outages? What about one week to agree on parameters and sites to check? I added data portability.
- Daniel Mietchen
I was thinking more of medium to long term financial stability - but technical stability is a good criterion in terms of functionality. Data portability is a good point!
- Cameron Neylon
Cameron, I spoke with Drew Endy, Bill Flanagan, and a couple other PIs that use OpenWetWare (Maureen, Pam) last week about the future of OWW. There are two major issues (a) funding and (b) overhauling the platform. I think funding will work out, if we can figure out what is the best way to do (b). Bill and Drew have some good ideas at this point, but in my gut I think we're still not...
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- Steve Koch
I guess my easy question for everyone who's familiar with OWW: Do you think with the resources we have (one full-time excellent lead developer) we can transform OWW into a killer openscience resource for many more people going forward? One thought that keeps coming to me is that something could be (needs to be) done to tap into the energy of the user base. I.e., obsessed students who...
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- Steve Koch
Another thing that keeps coming into my head since the conference call last week: FriendFeed is quite possibly very similar to what many people need for OpenScience. As far as science goes, we generate information from all kinds of different sources (Machine-specific data; gel photos; microsoft word; evernote; scratch paper; blogging; etc.). This needs to be aggregated and shared in a...
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- Steve Koch
Oh, and to clarify a bit: I don't want to replace FriendFeed with OWW. I want to use the FriendFeed model as a starting point for the new OWW. As an OpenScienceAggregator / Networking tool. As others have pointed out, much of the value of friendfeed is that it's not limited to scientists generating data.
- Steve Koch
Steve, that's a great way of asking the question. I'd go one step further and say how can we make it the framework in which we can integrate all the other things we do on other services. It's never going to be a no-brainer to move from what you use to something else - there is always the simple problem of the activation barrier to change - its a question of the balance. But my guess is...
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- Cameron Neylon
Cameron, I agree with you exactly: I don't want people to switch, and indeed I want to think "one level above." Do you think there's a real possibility for doing that?
- Steve Koch
If we could coordinate a series of activities and get proper funding then yes. Quite a lot of interest in the pieces of this (including the grant I'm currently rushing to finish), Chris's ideas further up this thread, OWW obviously, Mendeley/Citeulike/Zotero. But coordination is the hard bit - and getting agreement that its what enough of us want. Do I think we have a clear idea of what...
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- Cameron Neylon
Should we include some discipline-specific ones or are we going for general-purpose only?
- Daniel Mietchen
Molecular Representation, Similarity and Search - http://www.scivee.tv/node...
Peter Miller, Khader Shameer, Deepak Singh and Andrew Lang liked this
Rajarshi Guha presents at the final fall 09 Chemical Information Retrieval class at Drexel University on December 3, 2009. The audio for the first 45 seconds is a little off but the rest is fine. Implicit and explicit molecular representations in 1D, 2D and 3D formats are introduced. Approaches to quantifying molecular similarity using fingerprinting are discussed, such as the Tanimoto index. The relevance of these methods to drug design in terms of virtual screening and QSAR is explored. The concept of scaffold hopping is presented as a way of speeding drug discovery. Finally, ways of comparing the similarity of molecule libraries are detailed, stressing the importance of generating diversity.
- Jean-Claude Bradley
patient HM's brain microtomy live http://thebrainobservatory.ucsd.edu/hm_live...
Mike Chelen and Jean-Claude Bradley liked this
that is pretty cool
- Jean-Claude Bradley
About « Experimental Turk - http://experimentalturk.wordpress.com/about
Peter Miller liked this
About The goal of this blog is reporting evidence concerning the reliability of Amazon Mechanical Turk as an online subject pool for experiments in economics, psychology, and social sciences in general. Using AMT to run web-based experiments allows researchers to obtain large quantities of data in a cheap and efficient way. However, there is lack of evidence regarding the actual reliability of AMT’s workforce as a subject pool; as any new instrument, AMT requires to be tested thoroughly in order to be used confidently. This blog aims at collecting any individual effort made in order to validate AMT as a research tool. It reports results from experiments that increase or decrease the reliability of AMT as an online subject pool, as well as general guidance for running experiments through this service. Tags: mechanicalturk x-phi Posted by: cwhooker
- Bill Hooker
I do think the Turk can be useful for scientific apps - but you need a community of people that you have trained.
- Jean-Claude Bradley
Being Scientific: Fasifiability, Verifiability, Empirical Tests, and Reproducibility - http://www.openscience.org/blog...
Dan Hagon, Mike Chelen, Steve Koch and 6 other people liked this
Great post on what science is supposed to be.
- Egon Willighagen
Looking at logic charts made me grin - we have so many experiments that ostensibly falsify hypotheses we currently hold likely to be close to what is going on. The problem is there are a large number of ways an experiment can be misleading due to errors (human or not). If you apply fuzzy logic you can muddle through to some approximation of the way things work - but if you start thinking about any measurement as a "fact" that's asking for trouble. Remember NaH oxidation?
- Jean-Claude Bradley
Agree. The second chart was illuminating (both being deductively invalid). I'd say I often see cases where "T" (Theory) is ruled out when the "A" (Assumptions) are nowhere near rock-solid. I like this quotation from the article: "Contrary to Popper, there really is no asymmetry between falsification and verification. If we cannot verify theoretical statements, then we cannot falsify them either."
- Steve Koch
I also really like the ending two paragraphs, "computational science and reproducibility," with good arguments for necessity for open source and open data in the case of very complex computational science.
- Steve Koch
Of course the part about reproducibility in computation is very important to many people here.
- Jean-Claude Bradley
kaplanmyrth: If you haven't seen Metropolis on the big screen yet, next week is your chance at the Bytowne! http://bit.ly/5epzvw #ottawa #film - http://twitter.com/kaplanm...
kaplanmyrth: If you haven't seen Metropolis on the big screen yet, next week is your chance at the Bytowne! http://bit.ly/5epzvw #ottawa #film
- Richard Akerman
that was a favorite theater of mine - they often had oddball movies - something to do while reactions running in lab
- Jean-Claude Bradley
Public Terabyte Dataset Project - http://bixolabs.com/dataset...
Richard Akerman, Pierre Lindenbaum, Michael R. Bernstein and 3 other people liked this
interesting - I left them a message to see if they could help with our archiving challenge http://onsarchive.wikispaces.com/
- Jean-Claude Bradley
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