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Rebecca Holz › Likes
Problem Market Places (PMP) versus Social Networks for Scientists (SNS). What do we really want ?
Martin Fenner, Björn Brembs, diego morelli and 6 other people liked this
Reading various articles and discussions on social networks tailored for scientists (SNS), I realize that what I really would like to have is a searchable online marketplace for scientific problems and solutions (PMP). The central units of the marketplace would be well-defined problems and solutions (or methods), not so much the people. Here some of the dream-features: There is a searchable, browsable and rate-able list of problems, looking for solutions, and a list of solutions, looking for applications. Everybody can post new problems/solutions and comment on others. One can subscribe to any number of problems/solutions in order to receive alerts whenever new comments have been added. In contrast to STREAM-like feeds, which disappear into nothingness after a short time, the problems/solutions in the list would be persistent. It would be nice if at least on person (or a group) assumes responsibility for every problem/solution feed. The responsible person could occasionally clean up the feed or wrap it up. I think I don't expect much more. Shouldn't be so difficult to realize, or is it ?
- Claus Metzner
I would like to add to my list of dream-features what Michael Nielsen suggested in his great article "Doing science in the open" (http://physicsworld.com/cws...): "An ideal collaboration market will enable just such an exchange of questions and ideas. It will include metrics of contribution so that participants can demonstrate the impact that their work is having....
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- Claus Metzner
Claus: A lot of this is already being done in other domains, of course - StackOverflow is a nice example, and many open source forums achieve much of the functionality you're talking about. But socially it's not so obvious scientists will want to contribute. With that said, two communities that do seem to be on their way are the iGEM people, and the Tricki. It's interesting that in both cases, the main focus has been community-building, not so much tool-building...
- Michael Nielsen
I've had a tiny bit of experience with PMP and with SNS, and I'd have to say that I much prefer SNS -- it's much friendlier.
- Nathaniel Thurston
Nathaniel - Yeah, I've noticed the same thing. I'll be interested to see how the tricki turns out. At least early on, when most of the participants know each other, I expect it'll have a friendly, collegial atmosphere. But as it grows that may change.
- Michael Nielsen
... I guess the SNS effectively create lots of small overlapping communities, where there's a lot of incentive to play well with others. On the PMPs that's not nearly so true. Reminds me of the explanations for why people are ruder to one another in cities than in towns.
- Michael Nielsen
Michael, Nathaniel: If the community aspect is so important for a pleasant atmosphere, shouldn't we think about a clever combination of the two ? Actually, if it just would be a little easier in FF to find again (and occasionally to wrap up) a certain discussion feed after a longer pause, I would already be happy to use it for problem-oriented scientific collaboration. (OK, in my case,...
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- Claus Metzner
Claus: For some of my work, I've found FF works really well in this way already. E.g., http://friendfeed.com/michael... was very useful to me. Is there a large enough community of people on FF in your research area for it to be useful in this way?
- Michael Nielsen
Michael: So far, I couldn't find any people in FF working in my specific sub-field of systems biology and cell mechanics. Even the much broader field of complex systems theory seems not to be very well represented yet. But another good feature of FF is that it provides us with opportunities to participate in discussions on many fascinating topics outside our direct professional scope. A great way to counterbalance professional specialization. Very stimulating.
- Claus Metzner
Claus - I don't think it would be too hard to build such a thing but the problem is critical mass of community. Which is I guess what you mean about being clever in mixing SNS and PMP. My suspicion is that we haven't yet figured out how to give problems the right level of granularity to make them appealing to academics to solve in general. Innocentive seems to appeal to a certain type...
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- Cameron Neylon
Cameron, you are right that mixing PMP with an already existing SNS might also help to reach the critical mass quicker. My original motivation for the mixed concept was that, as I learned from the comments above, purely problem-oriented services generally seem to create anonymous, heterogeneous and increasingly larger "working" groups, in which the people eventually don't feel...
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- Claus Metzner
Claus: I didn't mean to be too negative about PMPs. StackOverflow, for example, works astonishingly well. But they do have, as Nathaniel says, some downside.
- Michael Nielsen
Claus: Starting a field-specific room and then feeding it good material seems to be a good partial solution to the problem of building a community. E.g., http://friendfeed.com/lecture... is a room on a very specialized topic that has grown very nicely in the few months it's been operating. That's part of the extraordinary power of the "like" button: it makes...
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- Michael Nielsen
Another interesting model somewhere inbetween PMPs and SNS is issuetracking / bugtracking software.
- Michael Nielsen
As for existing scientific PMPs, Innocentive is indeed the only working example I know. However, this is not really a collaboration tool in the sense that several people are working together on a single project and try to solve it by combining their individual small contributions, as it is the case in open software development projects. For me, Innocentive is more a self-organizing task...
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- Claus Metzner
Claus, people have tried a few times, but the right set of eyeballs never seem to be in the right place. Also resourcing these little bits of work is difficult outside of computational and theoretical science. That said I have a dream that we could create a marketplace for problems that could be solved in educational settings. That is they could be picked by instructors and assigned as...
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- Cameron Neylon
migrating from endnote / pdf folder to mendeley today...
Björn Brembs, Thomas Brox Røst, Rebecca Holz and Ricardo Vidal liked this
imported folder of 122 PDFs, looks like it got about half unambiguously...
- Andrew Su
... wait, just noticed all of Pierre's activity with zotero... hmmm...
- Andrew Su
Pierre gives everything ago. Always looking for the next thing to hack :)
- Ricardo Vidal
Do you notice any trends to the ones it didn't get? I've found it does much better with newer papers.
- Mr. Gunn
@Mr. Gunn, only done a few so far, but science magazine is clearly a problem since they continuously flow from one article to another. so page 1 contains the references from the previous articles. I'll try to look for other trends too. So far, it hasn't been too difficult to google the title, copy-and-paste the pmid, and then hit "lookup"...
- Andrew Su
PNAS seems to be a difficult journal too... and letters to the editor
- Andrew Su
yeah, but with PNAS you have a DOI so you can easily populate the info from that
- Mr. Gunn
mendeley bookmarklet is fantastic... word plugin also fixed in the latest release (word 2007, vista 64). Nice...
- Andrew Su
I'm glad it's working well for you. Can I ask a favor? Would you be able to forward the details about my Social Media for Scientists workshop to the SDBDG? The info is here, and there's a PDF flyer as well.
- Mr. Gunn
to SDCSB, you mean? I'm not sure we have an active mailing list, but I can check. Maybe we can post it on the events section of sdcsb.org. can you send the link again (didn't show for me in your comment...)
- Andrew Su
Whoops, yes, that's what I meant. Acronym soup doesn't taste so good. Yes, I would appreciate that. The link is http://sdbn.org/may
- Mr. Gunn
Watching "Little Miss Sunshine".
Rebecca Holz, Bill Hooker, Piotr Byzia and 2 other people liked this
thinks the best thing about TL ChunkIt! is the rap video: http://www.youtube.com/watch.... I especially like the part where he ghost rides the whip.
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Rebecca Holz liked this
New AWS Public Data Sets - Anthrokids, Twilio/Wigle.net, Sparse Matrices, USA Spending, Tiger - http://aws.typepad.com/aws...
Rebecca Holz and Richard Akerman liked this
I give up. will no longer pretend to try and read every item in my reader feed. just killed 800+ unread items. my apologies to sharers.
Chris Lasher, Rebecca Holz, Pierre Lindenbaum and Karoli liked this
Would there be an audience for a Beginning Ruby for Bioinformatics blog?
Khader Shameer, Carl Fulp, george and 10 other people liked this
Perhaps it's worth finding out! I'd be interested in trying - any other volunteer authors?
- Matt Wood
I would help out, even though I am no Ruby expert.
- Paulo Nuin
I wonder if something along the lines of the Peepcode or Gitcast screencasts would be cool?
- Matt Wood
Gitcasts lite would be nice. Essentially a world in which the examples are about bioinformatics-related topics and not blogs and shopping carts :)
- Deepak Singh
That's the sort of thing I had in mind - teach Ruby from a bio perspective: define classes with biological relevance, using ActiveRecord in biology, show use of @jandot's Ensembl API etc. Perhaps some podcast discussions too.
- Matt Wood
Stands in front of line. I saw go for it
- Deepak Singh
I'd be interested in learning some Ruby, especially if it's bioinformatics-related.
- Walter Jessen
This is a great idea.
- Michael Barton
Yep. And I'll try to find time to contribute :-)
- Jan Aerts
That would be great - It would be great to help introduce the rest of my lab to ruby and programming. -r
- Rob Syme
I'm in a ruby bioinformatics lab - I may be able to contribute a guest post or two, and I'd definitely read the blog.
- Chris Miller
Don't know about a blog, but I'd love to help write a wiki book. We could start by demonstrating every bioruby method by example.
- Neil Saunders
The ruby_for_bioinformatics site could be a repository on github, written in the format of Tom Preston Warners blog engine. That way everyone can contribute sections via git. The site could then be automatically hosted on github at ruby_for_bioinformatics.github.com.
- Michael Barton
Explanation of TPW's blog engine http://bit.ly/rVdl
- Michael Barton
As nice as github is, a wiki has a lower barrier to entry, which, in theory, means more contributions.
- Chris Miller
Rebecca Holz liked this
JoVE finally got in to PubMed!!!! - http://www.ncbi.nlm.nih.gov/pubmed...
Rebecca Holz, Cameron Neylon, Duncan Hull and 12 other people liked this
COOOOOOOOOOOOOOL - this is major !!!!!!!!!!!
- Graham Steel
How cool also that I/we found out about this via something like FF. I can't do it today, but tomorrow, I'll post something about this over at the Official JoVE Blog e.g. http://jove-blog.blogspot.com/2008... Unrelated to this news (PubMed) JoVE t-shirts etc. will be available in the coming weeks.
- Graham Steel
i feel so happy for JoVE team, they are incredible!
- Alexey
purely out of interest Alexey, how did you find out? For more JoVE background (for those unfamiliar), check out Bora's excellent interview with JoVE's CEO, Dr Moshe Pritsker:- http://scienceblogs.com/clock...
- Graham Steel
I was just browsing my PubMed trough RSS feed by key words "stem cell" and found like 3-4 abstracts, Moshe (JoVE CEO) told me that they applied for PubMed, so i was waiting when they get approval.
- Alexey
Neat. Just heard back from Moshe and he's confirmed "Yes. This is true". JoVE has just landed firmly and permanently on the global STM publishing landscape.
- Graham Steel
Great news!! thanks for letting me know.
- JWS
Very cool
- Deepak Singh
Facebook for Scientists: Requirements and Services for Optimizing How Scientific Collaborations Are Established - http://www.jmir.org/2008/3/e24
Michael Habib, Rafael Sidi, Rebecca Holz and 4 other people liked this
Review on requirements from a biomed perspective. originally posted by Berci Mesko
- Cameron Neylon
"The world is awash with large datasets, how do we give life to them?"
Björn Brembs, Marco(aureliusmaximus), Sally Church and 6 other people liked this
How do we data mine all the information in the universe in an integrated way? What can we do with the output?
- Sean McBride
The context of that statement was that, e.g. our GPS systems know where were are, but not why we are there and things along those lines
- Deepak Singh
One can easily see data mining systems inferring our intentions from GPS data linked with other data.
- Sean McBride
Agreed
- Deepak Singh
The sky is the limit on this stuff -- there are no limits.
- Sean McBride
From a bio perspective: we can find the location of a SNP, but need overlayed data to see the context wrt genes, other SNPS, other individuals, protein expression, etc.
- Matt Wood
That's what Eric Schadt has been arguing for a long time. GWAS by itself does not give you the answer
- Deepak Singh
Annotation metadata
- Walter Jessen
Towards a unified data mining science: the entire cosmos consists of a set of linked, data minable objects. Distinctions among the sciences, social sciences and humanities are artificial. Everything is related to everything else.
- Sean McBride
I see Google Adsense being location sensitive. Different adverts at home, and at work based on the search history for each location.
- Michael Barton
Better visualization. That's where it starts. Maybe I'm looking at this weirdly, it wouldn't be the first time, but I kinda see machine learning as a visualization technique first; equations are graphics too...
- Andrew Walkingshaw
What Andrew said (+ Matt, for that matter) - need to contextualize and visualize the data we already have better.
- Euan
Andrew you're right on target. It's why I like Freebase, even more so after seeing what they're up to these days
- Deepak Singh
A bit of an Open Science roundup - http://www.plausibleaccuracy.com/2008...
Rebecca Holz, Roger Chen and Michael Nielsen liked this
Science in the YouTube Age - http://www.slideshare.net/Cameron...
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Pedro Beltrao, Andrew Perry, Michael Kuhn and 13 other people liked this
bug in slideshare : I cannot see the slides from 7 to 30 :-(
- Pierre Lindenbaum
getting the same bug Pierre reports...
- Bill Hooker
Yeah, me too. I have to sign in to download the file. By the way, great stuff. :-)
- Ricardo Vidal
Precedings has a SlideShare type viewer now - maybe try that too
- Jean-Claude Bradley
It seems that the flash conversion doesn't work with the transparency of that image. WIll work on it when I have a minute. Currently supposed to be doing an experiment at ILL
- Cameron Neylon
Feel free to download if that works better obviously - can anyone do me a favour? Looks like the quickest way to solve problem is convert to pdf and upload that - online pdf converters are failing me for some reason and I don't have any working converters on this laptop. File is at http://dl.getdropbox.com/u... Could someone convert to pdf and either email it back to me at C dot Neylon at rl.ac.uk or just post it somewhere I can get at it? Need sleep now.
- Cameron Neylon
Cameron, you must be tired - getting an error message from that Dropbox location
- Sally Church
Sure thing, Cameron. The PDF is here: https://dl.getdropbox.com/u.... Great talk.
- Matt Wood
Thanks for that. @Sally, yeh its been a long week, but I think in this case it was just still synchronising. Hopefully things will be improved now. Slidshare just converting the pdf version now
- Cameron Neylon
aarrggh! Same problem. Think I will have to re-do the image...
- Cameron Neylon
after much faffing Ii've got a version up and running but the url is now different try http://www.slideshare.net/Cameron... (I can't edit the link above)
- Cameron Neylon
Came across Google Mashup Editor which I had never seen before but tickled my interest - http://code.google.com/gme/
Todd Harris and Rebecca Holz liked this
Thinking of organising a workshop on scientific software development.
arek, Rebecca Holz, Thomas Brox Røst and 12 other people liked this
That message was from a while ago, but it's a fascinating idea!
- Victor / Mendeley Team
like the sound of that.
- Colin Ashe
Cool - some interested folks - will think some more!
- Matt Wood
Just throwing in another 'me too'. I'd attend.
- Euan
Ace - have in mind a small 10-20 person workshop covering techniques, approaches and case studies for modern development of scientific software.
- Matt Wood
It's a great idea. Would definitely attend - if in Australia :) If it happens, maybe you can share the experience so we can copy and do it here too.
- Neil Saunders
Sounds like a great idea!
- Michael Nielsen
Me too. On a weekend would be best so I don't have to take time off.
- Michael Barton
Great. Chad Fowler organises 'charity workshops' around some of his Ruby conferences. Grassroots prices to cover costs, with the rest going to charity. I like that idea.
- Matt Wood
Given your area of influence I guess there will be more than 20 people willing to come :) Count me in if it's in Europe.
- Pawel Szczesny
@Pawel - cool, maybe we can do two!
- Matt Wood
Might even be possible to synch multiple workshops -- Second Life, skype...?
- Bill Hooker
We could have people joining in from Second Life, that might be fun. Do people still use Second Life?
- Matt Wood
Proposed Life Science Room logo. - http://picasaweb.google.com/lh...
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Rebecca Holz, Pawel Szczesny, Nils Reinton and 11 other people liked this
LS Room needs a logo. How about this?
- Chris Lasher
I don't know why we need it, but I like it. :-)
- Bill Hooker
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
- Paulo Nuin
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-... 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
OMG! Friendfeed added User Profiles! - http://userscripts.org/scripts...
Rebecca Holz and Czar liked this
Video Archive from Workshop on New Communication Channels for Biology - http://scienceblogs.com/clock...
Rebecca Holz and Deepak Singh liked this
Quick check: I haven't found the voice and the stream was far from being perfect, but maybe my stronger Mac will manage it.
- Attila Csordas
This is great; I don't have any problems viewing the videos
- Adam Kraut
I haven't had any problems with the videos either.
- Michael Nielsen
Public domain, copyright licenses and the freedom to integrate science — JCOM - http://jcom.sissa.it/archive...
Graham Steel, Jill O'Neill, Rebecca Holz and 4 other people liked this
A must read!!! PDF somewhere in there
- Deepak Singh
from Bookmarklet
"The future of the scientific paper" by Bora Zivkovic - http://jcom.sissa.it/archive...
Ricardo Vidal, Rebecca Holz, Mr. Gunn and 4 other people liked this
Science commons announces launch of Health Commons - http://sciencecommons.org/weblog...
Patricia F. Anderson, Yaroslav Nikolaev, Rebecca Holz and 3 other people liked this
Of particular note to J-CB and colleagues: "Science Commons welcomes your interest in the Health Commons. If you’d like to collaborate with us to accelerate drug discovery, we encourage you to contact us."
- Bill Hooker
Looks like the consortium for the post below (would science profit from a non-profit?) is already beginning to take shape.
- Paul Bacchus
That would be very cool - JC, can we combine our current proposals at this stage into a two page coordinated thing? It would be great to take this to John and Kaitlin in Barcelona. Possible SciFoo session?
- Cameron Neylon
Citation Sensor - http://www.nlm.nih.gov/pubs...
Rebecca Holz, Deepak Singh and Andrew Perry liked this
Pubmed improves the search by identifying citation searches. Nice addition.
- Pedro Beltrao
The Citation sensor is a great addition. They must have noticed all my lazy PubMed searches which follow that "author year" (without using [au] etc) format and decided to make them work better. Hurrah for giving the users what they want !
- Andrew Perry
Took me a while to get it, but I like it.
- Neil Saunders
Community Sites for Scientists and Physicians: The List - http://scienceroll.com/2008...
Rebecca Holz, Bill Hooker and Sally Church liked this
Hey Berci, good to see you on board the good ship friendfeed
- Cameron Neylon
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