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Alexey › Comments
Fwd: Increasingly irritated with spam on Connotea cluttering its RSS feeds. Emails to them unanswered. Does anyone still even work there? (via http://friendfeed.com/mattodd...)
Graham Steel and suelibrarian liked this
I think Ian's time is entirely taken up with other NPG projects at the moment...
- Cameron Neylon
My impression: Connotea is a broken, ugly mess and has been for as long as I've been aware of it, at least 3 years. I don't know why anyone would use it. CiteULike, on the other hand, gets better by the week and has responsive, friendly developers (plural).
- Neil Saunders
i'm still using it. didn't see spam. Only 1 problem for me - too slow. I'd like to switch to other manager but library is so huge. Anyone know how to export bookmarks from Connotea to Mendeley or Citeulike?
- Alexey
bibtex seems to be the best bet for moving in most cases. I'd probably go bibtex into citeulike and then move that across to Zotero or Mendeley as you need/like
- Cameron Neylon
In any case, we support BibTex, RIS (which everybody seems to treat differently, though), EndNote XML, and permanent sync from both CiteULike and Zotero (unfortunately not from Connotea yet).
- Victor / Mendeley Team
from iPhone
Alexey - if your library is "huge", you simply will not be able to export from Connotea. Bulk import/export was the first thing I tested when comparing Connotea/CiteULike about 3 years ago and it only takes ~ 100 items to break Connotea completely.
- Neil Saunders
Just tested this and it only exports first 1000 items to BibTex library (in a browser window, at least). Oh.
- Matthew Todd
oh piffle, didn't know that.
- Cameron Neylon
connotea has an API that can be used to export your bookmarks. I used it to move from connotea to delicious ( not citeulike or another digital library, because I don't write enough papers )
- Pierre Lindenbaum
Pierre, you should collaborate a bit more with your cool projects... you know I'd love to see your bioinfo hand in Bioclipse, where we lack in-depth expertise... :)
- Egon Willighagen
@Matthew... we have ourselves to blame a bit... or at least, the informaticians among us... Connotea is GPL v2 or later... nothing stops us from improving it... http://www.connotea.org/code
- Egon Willighagen
I attempted a local Connotea install, a long time ago. It has more Perl module dependencies than anything I've ever seen. I guess web development was a different game when the project was started, but still. Improvement = complete rewrite in modern web framework.
- Neil Saunders
Neil +1
- Pierre Lindenbaum
Mmmm... no Debian/Ubuntu packages :(
- Egon Willighagen
Researchers sped up an older mouse's healing time by joining it with a younger mouse (non-cellular mechanism) - http://harvardmagazine.com/2010...
Matt Mastracci, Mike Chelen, Tracy and Alexey liked this
she is very good scientist, parabiotic mice models started to apply since she was a postdoc in Irv Weissman lab.
- Alexey
(crossed arms, but smiling...hmm...)
- Mark A Jensen
I met her while I was at Harvard and concur with your assessment, Alexey :)
- Benjamin Tseng
Look at how induced pluripotent stem cells and new advances in stem cell R&D may drive personalized medicine - http://harvardmagazine.com/2010...
Alexey and imabonehead liked this
...as well as the ability to frown and cross arms at same time.
- Mark A Jensen
@Mark its the sign of any true scientist :)
- Benjamin Tseng
oh well-- I guess I'll just keep smiling and hacking...
- Mark A Jensen
sounds like propaganda to lobby iPS funding as a big thing, btw all medicine always was and it is personalized. It's how we were studied in med school 10 years ago - every patient should be treated individually, not by standard protocol, every clinical case could be unique. Treatment should be personalized based upon diagnostic findings. That's law of medicine went through all its history and especially in 19th century
- Alexey
another issue - who is going to pay for such expensive personalized diagnostics in case of it turns out to be the reality? I don't think your insurance will do that. New cell-based technologies should be also cost-effective and absolutely not ridiculously expensive
- Alexey
@Alexey, fair points, but I think the more tangible benefits/advances that drew me to this article were: (1) the advance in stem cell science to the point where cell transplant therapies could actually be a reality via iPS/reprogrammability [which could save cost by replacing something like insulin shots for the rest of your life for Type I diabetes with a one-time procedure] and (2) the potential to generate libraries of cell lines with particular difficult-to-study disease phenotypes (obesity, ALS, etc)
- Benjamin Tseng
@Alexey, on the "personalized medicine" front -- I don't think anyone (even personalized medicine proponents) would argue that doctors don't treat their patients like individuals -- the term is usually used (maybe it should be replaced?) to denote therapies selected/tailored to fit a patient's genetic background, something which doctors haven't been equipped (and won't be until the near future) to do yet.
- Benjamin Tseng
@Benjamin, not necessarily based on genetic background, but on clinical situation in general. Let's say - antibacterial therapy usually (not always) tailored in terms of bacteria sensitivity, derived from the patient - this approach used in the clinic more than 30 years and this is classical example of personalized medicine. Unfortunately today term "personalized medicine" mostly...
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- Alexey
Validating That Twitter Engagement Has Dropped Off. This solidified my feeling that only real relationships matter. http://blog.steffanantonas.com/focusin...
sofarsoShawn, maxilprof, Jaap Willem and 14 other people liked this
*Real* relationships meaning ... ?
- Carl Cabading
Meaning...with people you actually know, who are aware of you, what you care about, etc and who trust and listen to you. Everything else is a vanity metric.
- Steffan Antonas
If you climb out of the tech bubble long enough to look around, you'd discover you're absolutely wrong.
- Karoli
@Karoli - Did you read my post, or are you just making a statement based on my 140 character tweet? I'm interested to hear your thoughts. I'm willing to listen humbly if you're willing to make a data driven argument that holds water instead of just saying "you live in a tech bubble, and you're wrong". I'm looking at Hitwise Data, blog posts by people who have hundreds of thousands of followers, click through data etc. How about telling me why you think I'm off base. I'm all ears. ;-)
- Steffan Antonas
I read your post. I also realize I'm rapidly gaining a 'cranky lady geek' reputation here, but to say that only REAL LIFE relationships matter is simply ignoring reality. When you begin such an analysis by looking at the SUL as a measure of engagement, you've already hit the metric. No one but entertainers and geeks give a rolling rip about that SUL. Certainly real folks don't. I have...
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- Karoli
Tech blogging ,particularly when viewed thru the lens that is Robert Scoble, focuses on the metric of the next cool thing. Those of us who actually remain, discover community. For 16 years, community on the web has been my business. Political twitterers get it; art twitterers get it; mommy twitterers get it. When it is not viewed through the metric lens, what you discover is that REAL RELATIONSHIPS form, grow and thrive on Twitter. [/end rant]
- Karoli
or to put it in even shorter terms, leave the metrics; look at the conversation. Metrics are gamed.
- Karoli
So you unfollowed all those people who were following you? I'm sure you kept them as followers though. Kind of a huge douchebag move in my book. Yes I read your post and your weak logic for doing so. You're getting what you want to oh well, right?
- Self Deprecate Humor
I didn't unfollow anyone. What are you talking about? I follow those who engage. I'm not interested in following spammers and marketers or link farms.
- Karoli
Not you :P You're awesome
- Self Deprecate Humor
My concern is having all those followers that he followed back and then one day running a script that kind of kicked them all in the balls.
- Self Deprecate Humor
ah, okay gotcha. There are lots of people who do that. I follow the ones who I think are interesting even if they don't follow me, but again, unfollowing is a sign of following metrics...something I think creates false impressions.
- Karoli
Just to add my two cents, the reason you're off base is that people don't stop being "real" when they go online. They're still "real" people and if they engage in "real" interaction, they develop "real" relationships. As one who met a "twitter friend" in "real" life, I can tell you that the transition was seamless, both of us felt completely at ease because we "really" did know each...
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- Mark Welkie
Karoli: I unfollowed everyone because my inbound column in Seesmic had turned totally useless and so had my DMs thanks to spam. Now I've refollowed 16,000 people -- all manually -- and Twitter is 100x more useful today. I'd do it again in a second!
- Robert Scoble
Robert, your inbound stream is unmanageable no matter what. You're right -- the automatic follow of everyone who followed you was a mistake. I follow manually, usually as a result of a conversation. It seems to work.
- Karoli
I can see how one would get overwhelmed by an enormous following, quantity is not quality. The relationships will be superficial. But as one who's spent the last 20 years building relationships by virtue of the written word alone, I will join the growing chorus of dissent. :) Before I was online, I was a pen pal. I wrote to over 50 people, in almost as many countries--by hand,...
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- Deborah
This is a great discussion...Steffan, are you seeing why I answered the way I did now? All the obsession over the SUL is silly, because the SUL, like the new retweet, is a gameable metric. True community is not measured in clicks and follows.
- Karoli
I like how LinkedIn managed the scorekeeping that arose on their site. They capped the visible connections at 500. I think that twitter used the follower count and associated gaming to grow their network. I would love to see twitter cap the publicly visible followers at 500. It would change the community for the better.
- Jim Posner
Love that term-- "Vanity Metric"
- Kirsten Mitchell
from iPhone
Is there a short summary of what you're saying?
- Patricia
Yeah, approach ppl like numbers, you get no relationship.
- Deborah
Karoli was batting a 1000 on this thread. :)
- Micah Wittman
Hmm so my relationships on Twitter aren't real. Thanks for the enlightenment.
- Mona Nomura
great post Steffan! Agree!
- Alexey
@Mark Welkie - Right on. That's exactly what I'm talking about. I COMPLETELY agree with you, in fact, you've said better what I couldn't above in the third or fourth comment from the top - People don't stop becoming "real" when they're online. Totally the opposite. The beauty of Twitter is that you can create relationships with real people you've never met or would never have had a...
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- Steffan Antonas
@Karoli - Yes. Definitely a good discussion, but I do want to clear a few things up.... #1 I linked to my comment above to illustrate that EVEN the people on the SUL (in this case Anil Dash) do not get inundated with @'s etc - my point was NOT to glorify the SUL in any way. Just the opposite. I have many problems with the SUL and what it does to the ecosystem. The real point is that the...
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- Steffan Antonas
@Mona - That's not what I'm saying at all. If you're talking to people, engaging and having conversations on Twitter - that's real. You mistook the word "real" for "offline". Perhaps my fault, but I live online, so I don't separate "offline from online" when it comes to relationships. It's all real.
- Steffan Antonas
@Deborah - Thank you for that excellent summary. You said in one line what I was trying to say in a 3000 word blog post! See above - "Yeah, approach ppl like numbers, you get no relationship. - Deborah"
- Steffan Antonas
@Karoli - Btw, did you read the actual blog post, or just the comment I linked to. The post itself was what I was talking about when I asked "did you read it", not the comment. I think that's where the confusion about the SUL came from. ;-)
- Steffan Antonas
Steffan, thanks, glad I could encapsulate. I also think there has been a bit of misfired communicating in this thread. I went back and read your whole linked post and see we're on the same page. Your response to Mark makes that even more clear to me. Still, I've met ppl who consider all online interaction as "not real." And because many are using Twitter just to amass followers to whom...
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- Deborah
I read your blogpost and I agree with you 100%. You've echoed my own thoughts and feelings about my Twitter experience. Karoli made some great points as well. I think there was some miscommunication going on there because you are both saying similar things. IIRC, the great follower race began in late November or early December of 2008. Long before the SUL. Having followers just for the...
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- Mark Davidson
from BuddyFeed
YouTube - BBC Horizon - How Many People Can Live on Planet Earth? documentary must watch - http://www.youtube.com/watch...
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the graph of population growth with years look like oil peak graph, so if Earth now on the top of peak oil bell-shaped graph, you know what going to happen next
- Alexey
The End of Suburbia - 52 minute documentary on peak oil - http://bestdocumentaries.blogspot.com/2009...
i screamed all last 3 years - guys, move to the cities, emerge with communities, sell a car and get a bike!!!
- Alexey
Yes and once again - Yes!
- Denis Stankov
The five hottest biology papers of 2009 - http://www.the-scientist.com/blog...
iPS - 2 out of 5
- Alexey
The five hottest biology papers of 2009 - http://www.the-scientist.com/blog...
none released in 2009
- Alexey
Вертолетная прогулка над Дубаем - http://sergeydolya.livejournal.com/98888...
Dubai
- Alexey
Вертолетная прогулка над Дубаем - http://sergeydolya.livejournal.com/98888...
Dubai
- Alexey
A co-worker mentioned to me yesterday that a colleague of his is thinking about starting an online journal club type website for scientists. The idea seems to be discussions about papers, data sets, and other web-publishable materials, from any source, in a central location. It would also have discussions about scientific culture, which made me...
Abhishek Tiwari, Anders Norgaard, suelibrarian and 15 other people liked this
It would be a place where people (students, junior faculty, etc) could learn the ropes of academia and science without the pain and misery that traditionally is required. The differences I can see from existing services is the focus on journal club-style discussions and maybe a low barrier to entry
- Shirley Wu
from twhirl
But obviously, whatever he ends up pursuing should learn from the trials and tribulations of the many related services out there (including services like FF, which is also discussion-oriented)
- Shirley Wu
from twhirl
It's easy to immediately discount any proposal that sounds like yet another facebook for scientists, but there are still some interesting and potentially good ideas out there. Unfortunately, people who aren't as familiar with the existence of these tools always think of facebook as the ideal and as a brand new idea if applied to the scientist community. Hopefully I convinced my co-worker otherwise, while still encouraging the more innovative aspects of the concept. <end rant>
- Shirley Wu
from twhirl
Thanks for doing that.
- Mr. Gunn
AcaWiki is built around a very similar concept, and John Wilbanks makes an argument for bringing journal clubs online (cf. http://ff.im/airoV ).
- Daniel Mietchen
Shirley, Besides AcaWiki (great place to have these discussions, but I'm biased! http://acawiki.org/ ) your colleague also might be interested in GradTurkey, a journal-club discussion wiki originally aimed at grad students: http://gradturkey.fastcoder.net/
- Jodi Schneider
can discussion on AcaWiki be linkable and embeddable for public like you can do on FF? If not, so why don't do journal club on FF? Can't get it
- Alexey
I tried a site like this a few years ago. ResearchFire, or something like that? Never heard of it again.
- Neil Saunders
my comments on the topic in 08/07 http://pimm.wordpress.com/2007...
- Attila Csordas
Knol has many journal features built-in. Here is an example of a successful research journal on H1N1: http://knol.google.com/k...
- Bill Strathearn
John Wilbanks mentioned doing journal clubs online in his talk here recently: http://bit.ly/3jxnxr
- Walter Jessen
this topic came up during a discussion today with Mike Eisen of PLoS, re: why commenting hasn't really taken off - his thought is that people are more likely to comment if there's a central place to do it rather than individually at each journal website for each paper (how many of us access papers directly through journal websites except through PubMed anyway?). The whole time I was...
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- Shirley Wu
from twhirl
can somebody point to the platform for journal club online better then blog post? It's combine everything - presentation (ppt embedded from SlideShare or Gdocs, video embedded from YouTube/Vimeo...) presenter's opinion, discussion section under the post, embedded comments from FF, ranking of the presentation and number of views. Importantly you don't need to register or get account for commenting, it's public and linkable, moderatable . Whole world can participate. What can be better?
- Alexey
@Neil Saunders Were you thinking of JournalFire? We recently updated the site and are looking for feedback. I posted about it yesterday: http://friendfeed.com/the-lif...
- John Delacruz
Доктор Хата
Victor Tatarskii and Alexey liked this
думаю к 5-ой серии сорвется
- Victor Tatarskii
стопудово сорвется и еще Кади пристрастит
- Denis Stankov
дык он вроде все серии на колёсах был
- Alexey
Alexey: ты про Хауса или про Чапаева?
- Denis Stankov
а кто такой чапаеф?
- Alexey
викодина видимо уже не будет...
- Denis Stankov
DEA не дремлет!
- Victor Tatarskii
School halts baboon anthrax study - http://www.the-scientist.com/blog...
Especially I like last sentence "Deng did not reply to email and phone requests for comment."
- Alexey
mTOR Regulation and Therapeutic Rejuvenation of Aging Hematopoietic Stem Cells - Science Signaling - http://stke.sciencemag.org/cgi...
Khader Shameer liked this
2nd study showed extended life span of mice treated by Rapamycin
- Alexey
from Bookmarklet
Should the definition of micropenis vary according to ethnicity? - http://www.ncbirofl.com/2009...
everybody knew that
- Alexey
Science Translational Medicine cover - http://stm.sciencemag.org/content...
ONLINE COVER Animation of human lungs breathing in a 37° chamber. Lungs removed from donors for transplantation are often damaged but can be treated in the controlled environment of this transparent dome to improve their health. Gene therapy with interleukin-10 increases the chances that the lungs can be successfully transplanted into a recipient. See Cypel et al. in this issue. [Credit: Chris Bickel, AAAS]
- Alexey
from Bookmarklet
Hemostatic "Shaving Cream" Wins Award - http://www.medgadget.com/archive...
why it took so long for this great idea?
- Alexey
Фантастический Airbus А380 - http://sergeydolya.livejournal.com/84655...
would you fly in the plane like this?
- Alexey
AcaWiki: Increasing the Impact of Research Using Web 2.0 - http://acawiki.org/Home
Dan Hagon, OpenSci Info, Claudia Koltzenburg and 10 other people liked this
"AcaWiki is like "Wikipedia for academic research" designed to increase the impact of scholars, students, and bloggers by enabling them to share summaries and discuss academic papers online. AcaWiki turns research hidden in academic journals into something more dynamic and accessible."
- Daniel Mietchen
from Bookmarklet
Good idea, but unlikely to take off, IMHO.
- Björn Brembs
To my understanding it all rests on the willingness of people to write summaries of articles far more substantial than the already available abstracts.
- Jean-Claude Bradley
Alexey - I can see situation where people who don't have blogs would post on AcaWiki - but I don't know if there is a critical mass of people willing to do that
- Jean-Claude Bradley
I think there would need to be some sort of reward. I suggested perhaps for literature reviews (plenty of thesis chapters out there that never get published) that providing a doi and submission to the new Rapid Research Notes database might be interesting in that regard.
- Cameron Neylon
Interesting. DOIs cost money, but a fund for assigning DOIs would be good to have.
- Jodi Schneider
There is also http://sref.org/ as an alternative to DOI, and RRN may be able to handle both.
- Daniel Mietchen
@Jodi, they do, but not that much. If it's worth the CV fodder then I don't think a small payment for a doi is a big problem (if its around e.g. the $10 mark)
- Cameron Neylon
@UofILibrary Mendeley syncs with Zotero - anything you add there is automatically added to Mendeley, so you can actually use both!
Jean-Claude Bradley, Björn Brembs and Richard Akerman liked this
All in good time :-)
- Victor / Mendeley Team
In the meantime, Alexey, you could export RIS. It's not ongoing sync, but it works OK as a one time transfer. I believe you can get RIS for any selected tag or range from connotea, you don't have to get the whole thing.
- Mr. Gunn
Kiss my cytomegalovirus! - http://www.ncbirofl.com/2009...
awesome!
- Alexey
New drug target for cancer :The Scientist [11th November 2009] - http://www.the-scientist.com/blog...
Scientists have developed a new drug that blocks a transcription factor -- previously thought to be un-blockable -- that has been causally linked to leukemia and several other cancers of the lungs, ovaries, pancreas, and gastrointestinal tract, they report in Nature this week. The Notch transcription factor regulates cell-cell communication in the Notch signaling pathway, a system governing cell growth and development. Mutations in the transcription factor can result in uncontrolled cell growth, often causing cells to turn cancerous. But transcription factors are notoriously hard for medicinal chemists to target because they work by forming complexes with multiple proteins, leaving no open binding sites for small molecules to fit into.
- Alexey
from Bookmarklet
Family versus science :The Scientist [11th November 2009] - http://www.the-scientist.com/blog...
CAP, together with the Berkeley Center on Health, Economic & Family Security at the University of California, Berkeley, School of Law surveyed some 25,000 University of California postdocs and graduate students for the report. They found that married women with children were 35% less likely to get a tenure-track position than married men with children and 33% less likely to do so than single women without children.
- Alexey
from Bookmarklet
To Heal Diabetic Foot Ulcers, A New Drug Harnesses Stem Cells Inside Us All - http://www.medicalnewstoday.com/article...
"It appears that DSC127 directs MSCs to the injury site, mobilizing them to help repair wounded or burned skin, accelerate healing and reduce scar formation," said Edward J. Quilty, Chairman & CEO of Derma Sciences Inc. Based in Princeton, New Jersey, Derma Sciences develops, manufactures, and markets innovative wound care products. "DSC127," Quilty observed, "thus works as a catalyst for a stem cell treatment that is free of both the ethical controversies surrounding the medical use of fertilized embryos as well as potentially painful surgical interventions." Currently in a 75-patient Phase II diabetic foot ulcer clinical trial being conducted at some of the nation's top institutions, the drug is being considered for additional indications including venous leg ulcers, arterial ulcers, pressure ulcers, thermal and chemical wounds, and scar prevention. Pre-clinical animal studies have demonstrated the efficacy of the compound in accelerating healing and reducing scar formation. If...
more...
- Alexey
from Bookmarklet
Gene Therapy Halts Brain Disease in Two Boys -- Kaiser 2009 (1105): 1 -- ScienceNOW - http://sciencenow.sciencemag.org/cgi...
Gene fix. The blood cell with red dots has been engineered to make ADL, a protein that had been missing in this patient until he received gene therapy 2 years earlier.
- Alexey
from Bookmarklet
Engineered Rabbit Penises Raise Human Hopes | Wired Science | Wired.com - http://www.wired.com/wiredsc...
it is finally erected!!!
- Alexey
from Bookmarklet
Gene Therapy Halts Brain Disease in Two Boys -- Kaiser 2009 (1105): 1 -- ScienceNOW - http://sciencenow.sciencemag.org/cgi...
Gene fix. The blood cell with red dots has been engineered to make ADL, a protein that had been missing in this patient until he received gene therapy 2 years earlier.
- Alexey
from Bookmarklet
Google Wave vs Twitter at conferences - http://blog.freshnetworks.com/2009...
My bets are on Google Wave...
- Björn Brembs
Their description of the process sounds very like what conference attendees have been doing for some time, using FriendFeed. Shiny new technology sometimes generates amnesia, I think :-)
- Neil Saunders
+1 Neil I wish we could do less of the "OMG this new technology will change everything!!1!" and "meh, Your favorite technology sucks" both. Wave is cool because of the protocol, not because of the client.
- Mr. Gunn
In fact, it's uncool because of the client (which is just horrible)
- Deepak Singh
FF will be the best platform to cover conferences in real-time, Wave is still in development, lots of bugs, not public linkable, Twitter is the last one - suck at it. IMHO
- Alexey
Twitter can be amazing at conferences. I once remember following an entire talk standing in line at a Starbucks on a mobile phone entirely on Tweets. Friendfeed is great for discussion, twitter for soundbites/snippets and just keeping in touch.
- Deepak Singh
Smart use of hashtags works OK for conferences, and you can capture stuff that would otherwise go uncaptured because you don't have time to type more than 140 chars, but I agree, FF is much better if you have a laptop and wifi that works and all that.
- Mr. Gunn
how can you link or embed discussion on Twitter about let's say 1 talk? You easily do it on FF - you can see all of subsequent replies in one place, you can link to it
- Alexey
I do all FF things at work only through mobile, you don't need laptop to do all things on FF - everything you need is mobile device in your pocket
- Alexey
well, hashtags work OK for linking discussions and while ff mobile is easier, it's not as easy as banging out a quick sms to 40404.
- Mr. Gunn
Alexey, if you want in depth discussions then FF is the way to do. To grab a variety of snippets, exchange DM's on the fly, ask someone to ask specific questions in another room Twitter works really well. It's also better to find people with mutual interests, since the userbase is so much larger in general. Agree that when I used Twitter extensively at conferences FF did not exist, so behavior will be different now
- Deepak Singh
@Deepak - agree, "on the fly" Twitter could be better. Now we have enough tools to cover conferences in the real-time, only the problem is how to find folks who up to it? If I'll able to find 5-10 creative folks in 1k-10k attendee conference who up to FF/tweet/wave about it in real-time I'd be happy. The questions of tools of choice will be secondary. More likely these folks use all of them.
- Alexey
Alexey ... well said!!!
- Deepak Singh
from IM
I think setting up friendfeed with a twitter rss feed of the conf hashtag could give the best of both worlds. You can follow the conf in realtime but have the ensuing breakout discussions.
- Justin H. Johnson
from iPhone
Yes, Justin, and in fact, most people pipe their individual tweets in here as well.
- Mr. Gunn
Do somebody using Yep for manage your pdf library? How is it?
- Alexey
from Bookmarklet
I use it and have a lot of fun!
- Denis Stankov
I believe David Crotty's used it some in the past, not my fav,
- Mr. Gunn
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