A room for all the life science types on FriendFeed (and everyone we've co-opted). Topics tend to focus on bioinformatics and computational biology, but discussion from any area in biological sciences is welcome.
Try not to spam and if you are associated with a service (and most don't know that), please say so.
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?
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
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
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
The 3M/Littman 3200 Stethoscope with Zargis Cardioscan is our 2009 Innovation of the Year because of its brilliant simplicity. Detecting heart murmurs can now be done with far greater accuracy by doctors everywhere--from your family internist to those in remote ares bringing treatment to those who need it most. So simple, in fact, that we were able to operate it here in the office with the same diagnostic power as any doctor, with the help of Zargis CEO John Kallassy. See it--and hear it--in action, above.
- Ami Iida
"Web-based technologies coupled with a drive for improved communication between scientists have resulted in the proliferation of scientific opinion, data and knowledge at an ever-increasing rate. The increasing array of chemistry-related computer-based resources now available provides chemists with a direct path to the discovery of information, once previously accessed via library services and limited to commercial and costly resources. We propose that preclinical absorption, distribution, metabolism, excretion and toxicity data as well as pharmacokinetic properties from studies published in the literature (which use animal or human tissues in vitro or from in vivo studies) are precompetitive in nature and should be freely available on the web. This could be made possible by curating the literature and patents, data donations from pharmaceutical companies and by expanding the currently freely available ChemSpider database of over 21 million molecules with physicochemical properties"
- Attila Csordas
from Bookmarklet
Dear LazyWeb, am looking for a list of structural bioinformatics databases with literature curated data (for example Catalytic Site Atlas : http://www.ebi.ac.uk/thornto... .
" The QP-SURF program at UT Southwestern is an intensive summer research training experience which leads to an understanding of the planning, discipline, and teamwork involved in the pursuit of basic answers to current questions at the interface of quantitative science and basic biomedical research. Fellows spend ten weeks (beginning June 7, 2010 through August 13, 2010) pursuing individual research projects in the laboratories of UT Southwestern Graduate School faculty members. Fellows gain experience in modern research techniques, and have a chance to plan and execute an experimental strategy to answer a scientific question. The program introduces students to the sorts of projects encountered during postgraduate research training and leads to an understanding of the planning, discipline, and teamwork involved in the pursuit of basic answers to current questions in the biological sciences. At the end of the summer, fellows present their research in a poster session. In addition to...
more...
- Mickey Schafer
Hi, Mickey. Thanks so much for heads-up. I quickly listed it on ScanGrants: http://www.scangrants.com/grant... I am always looking for neat things like that--thanks!
- Hope Leman
Hi Hope! Then you might also be interested in the SMDEP (Summer Medical and Dental Education Program) -- http://www.smdep.org/ -- this is only for undergrads though, so I don't know how that works for ScanGrants. Also, it targets under-represented minorities. Mickey
- Mickey Schafer
from email
Hi, Mickey--thank you so much. Oh, we definitely include items for undergraduates. I really try to list as many scholarships and academic prizes in the health sciences at all levels as possible. Got to get kids interested in science and medicine! And I have a diversity.underrepresented category, too. Therefore, your suggestion was perfect and much appreciated. I have listed it here--http://www.scangrants.com/grant...
- Hope Leman
attention!! Has The H1N1 Swine Flu Virus Mutated To Become More Like The 1918 Spanish Flu? Dying Patients In Ukraine Are Experiencing The Total Destruction Of Their Lungs
- Ami Iida
Scary... looking forward to Vincent's catch on this...
- Egon Willighagen
"The world's most valued plant database faces extinction because its funding is being phased out by the US National Science Foundation (NSF), and no alternative source is on the horizon. [..] The NSF has suggested that TAIR develop its own self-supporting funding model, based on user subscriptions and other sources of income. But TAIR director Eva Huala told an international meeting on...
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- 'Mummi' Thorisson
Now isn't that a great opportunity to seriously cut subscriptions from journals and invest the left-over funds towards decentralized literature and data databases hosted by the libraries? Two birds with the same stone?
- Björn Brembs
More in editorial: Access denied? - http://www.nature.com/nature... "[..] It is time for a whole new approach. Front-line biology cannot function without these resources, so solutions must be found at both national and international levels. Governments must ensure that at least one of their national funding agencies has money specifically set aside for the long-term support of bioresource infrastructures.[..]"
- 'Mummi' Thorisson
Umm... just make it Open Data and the data is preserved by the community? Why is the *data* at risk? I think they really mean that the *scientists* are at risk!
- Egon Willighagen
Indeed, Egon! Left a comment there. Maybe a bunch of us should contribute to the discussion there, this should raise the profile somewhat. Incidentally, we may think of writing a letter to the editor, if there is some consensus in the comments.
- Björn Brembs
@Björn, I like those ideas... I'll log into my NN account and leave a comment too...
- Egon Willighagen
I think the data is already open - the issue seems to be that TAIR is a centralized resource for the community. If I understood correctly, in the absence of a centralized resource they are afraid of fragmentation. This is not necessarily a bad thing, since over time certain providers may/will become preferred providers
- Rajarshi Guha
Argh... just about to commit my reply, has the page disappeared... nice comment lost :(
- Egon Willighagen
I wonder how their $1.6M budget breaks down (IT infrastructure, curators, admin etc)?
- Eric Jain
If we are going to centralize this as infrastructure we need to take a strong stance on the build quality and compatibility of these databases so we can bring down costs...
- Cameron Neylon
"In his new book, “Reading in the Brain,” neuroscientist S. Dehaene describes his quest to understand an astounding feat that most of us take for granted: translating marks on a page (or a screen) into language. (...) What I am proposing is that the human brain is a much more constrained organ than we think, and that it places strong limits on the range of possible cultural forms. (...)Through its cultural inventions, humanity constantly searched for specific niches in the brain, wherever there is a space of plasticity that can be exploited to “recycle” a brain area and put it to a novel use. Reading, mathematics, tool use, music, religious systems - all might be viewed as instances of cortical recycling.(...) the fact that young children are more competent than we think. Learning is not “the furnishing of the mind's white paper,” as John Locke said. Even for an activity as novel as reading, we do not learn from scratch, but by minimally changing our existing brain circuits, capitalizing on their pre-existing structure."
- Amira
from Bookmarklet
"In the case of reading, very concretely, as I explain in the book, we now have plenty of evidence that the whole-language approach has nothing to do with how our visual system recognizes written words – our brain never relies on the overall contours of words, rather it decomposes all of its letters and graphemes in parallel, subliminally and at a high speed, thus giving us an illusion...
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- Amira
Blatant self-plug here! My response to a number of recent editorials, regarding the importance of making datasets citable to encourage researchers to publish their data and 'data DOIs' being a potential key factor in bringing this about. Comments/criticism welcome.
- 'Mummi' Thorisson
"author can archive pre-print (ie pre-refereeing)" says SHERPA/ROMEO re Nature Biotechnology/NPG - in case your contractual agreements go beyond this, you might be able to enhance the size of your readership, the amount of feedback, and most likely also your citation rates by OA green of the final version - (where) have you self-archived this article? I would like to recommend it to colleagues whose institution cannot afford a subscription of Nature Biotechnology - can you help?
- Claudia Koltzenburg
Claudia - can you give more specific guidance regarding self-archiving? I can't make much out of your comment. I did check the NBT website and according to http://www.nature.com/reprint... I can self-archive 6 months after publication.
- 'Mummi' Thorisson
In any case, if anyone doesn't have access to NBT then by all means contact me directly (FF message) and I'll E-mail the PDF.
- 'Mummi' Thorisson
thank you for the direct delivery service offer, Mummi. Actually, with a paper of THIS topic I would prefer to recommend an open access version that is downloadable from the web by anyone and now :-)
- Claudia Koltzenburg
in more detail: SHERPA/ROMEO http://www.sherpa.ac.uk/romeo/ lists the NPG general license to say (see my quote above) "author can archive pre-print (ie pre-refereeing)" - and adds: "This summary is for the publisher's default policies and changes or exceptions can often be negotiated by authors. All information is correct to the best of our knowledge but should not be relied upon for...
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- Claudia Koltzenburg
Why is it, when I try to download the PDF, that I get Correspondence on "The market value of GM products" instead? :)
- Allyson Lister
Allyson - good one ;) my bit starts near the bottom of that 1st page
- 'Mummi' Thorisson
Claudia - Thanx again. I shall try and sort this out ASAP.
- 'Mummi' Thorisson
@Mummi - I should have trusted the PDF - I didn't even scroll down - just saw the top and figured it was a bum link - my bad! :)
- Allyson Lister
Nature journals' policy is that authors can put their submitted version online eg on a preprint server whenever they want - before, after or during submission. The version that is accepted for publication can be archived in a repository 6 months after publication. The published version stays on the publisher website. http://www.nature.com/authors... and http://www.nature.com/authors...
- Maxine
Quote from first URL above: "Our policy on the posting of particular versions of the manuscript is as follows: 1. You are welcome to post pre-submission versions or the original submitted version of the manuscript on a personal blog, a collaborative wiki or a preprint server at any time (but not subsequent pre-accept versions that evolve due to the editorial process). 2. The accepted...
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- Maxine
@Mummi of course you could have published in an open access journal instead :-)
- Duncan Hull
Duncan - excellent point (was kinda waiting for someone to kick my arse about that...). Honestly, I would have done this, but the backdrop to this is that I was approached originally by the NBT editor about writing a short letter on this topic, following a comment I made on a Nature blog post (http://blogs.nature.com/nautilu...).
- 'Mummi' Thorisson
I *promise* to make an effort to submit to an OA journal next time!
- 'Mummi' Thorisson
For a friend: "I once read about a bacterium which lives only in a single poorly constructed pissoir in a castle. The system didn't drain properly, and when examined, there was a unique species which had evolved there. Do you have any advice on how to track down such a story?"
not quite from the pissoir, but maybe someone peed into the moat: "A bacterial strain capable of degrading chitin, strain SAY3T, was isolated from moat water of Ueda Castle in Nagano Prefecture, Japan." http://www.ncbi.nlm.nih.gov/pubmed...
- Michael Kuhn
I couldn't find anything relevant either, but I did wonder if there could be some form of use for archaeological dating by genetically examining the bugs in an abandoned sewer (or wall painting) for a concestor.
- Alun Salt
Thanks! Donnie, that was my experience, too. I'll pass on the link, Michael - it looks pretty good. Alun, I'd expect that the heterogeneity of dead bacteria would make such an analysis difficult, if not impossible.
- Heather
"Being able to effectively use modern gadgets is necessary in today’s ‘‘high-tech’’ science but to be enslaved and misled by them is not desirable".
- Alejandro Montenegro
I haven´t use it yet, but it claims to include a curated and unique collection of transcription factor binding sites from prokaryotes. http://prodoric.tu-bs.de/
- Nicolas Palopoli