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Jason Tsai › Likes
The five hottest biology papers of 2009 :The Scientist [17th December 2009] - http://www.the-scientist.com/blog...
Jason Tsai and Yann Abraham liked this
For the five coldest, pls see my cv....
- Mark A Jensen
LOL @ Mark
- Alejandro Montenegro
I present to you... the Rings! - http://www.flickr.com/photos...
Semiha, Live4Emma (L4S), Jason Tsai and 2 other people liked this
Erin McGuire - http://webspace.ringling.edu/~emcgui...
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jadé0307, Parth Awasthi, Jason Tsai and 69 other people liked this
Sequencing Genomes: From Individuals to Populations - http://bfgp.oxfordjournals.org/cgi...
Jason Tsai liked this
Visual CV attempt - http://www.flickr.com/photos...
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Peter Murray, Deepak Singh, Mike Chelen and 15 other people liked this
Feedback request. I try to make a visual overview of my experience so far and my future plans. Any comments regarding both, visual side and scientific/career side really appreciated.
- Pawel Szczesny
One quick suggestion: increase the font size and color differences. It might emphasize your primary interests a bit more.
- tim
from Alert Thingy
Thanks Timothy. That's a good suggestion. I work on another version that would incorporate some more details on the past projects, but so far it's even less readable than this one.
- Pawel Szczesny
I really like the concept of this. I take it the colors correspond to particular positions you held? Have you tried using a color gradient for the categories (photography, science, programming, ...) and different fonts to distinguish each job/educational position?
- Chris Lasher
Thanks Chris, that's a great suggestion! Having a "now" line makes current color code a little redundant.
- Pawel Szczesny
Good idea. How would you show projects that are still on? Maybe you can change the text direction?
- Marcin
Most people with color deficient vision (like mine) will not be able to tell your red from your green (I can't). Also it seems a little odd that there is only one thing in the photography category (a hobby?) and so the columns do not really line up. Maybe a third color for non-work-related? And seconding Chris' idea to use fonts to distinguish where you learned/worked on each item in the list.
- Bill Hooker
@Bill Did you notice Pawel plots the words according to two axes: skillset along the X-axis, and time of gaining that experience along the Y-axis? I missed this at first and was wondering about the Photo category, too, but then I realized how "scientific animations" and "molecular visualizations" spanned both Science and Photography, and hence, they're in between them on the X-axis. That's neat, because you can see that Pawel's interest in visual things started off in night photography...
- Chris Lasher
...and when combined with his exposure to science led him to do, say, visualization of biological networks. Really cool concept. Also, good call about reds and greens.
- Chris Lasher
Marcin, things still going are around the "now" line (dashed line in the middle). I don't think exact start/end does matter, it's more about how things circulate in time. Bill, Chris explained already what is the idea behind three "columns" and placing things. In the first approximation phrases were connected (and it was easier to get the idea about various inspirations), but I removed them for the clarity. Colors will be changed.
- Pawel Szczesny
Thank you all for comments. Updated version with more explanations and feedback request is here: http://freelancingscience.com/2008...
- Pawel Szczesny
Can you describe the method and source data used? It is informative and looks nice :)
- Mike Chelen
Mike, it was a manual work done in Inkscape. I work on something similar done in Processing, but it's still at a draft stage.
- Pawel Szczesny
That would cool to see, definitely more challenges though. Thanks
- Mike Chelen
it's a great idea, it looks great, and it's a great way to have a quick overview of your competences! congrats!
- Adrien Joly
Global discovery of adaptive mutations. - http://www.citeulike.org/user...
Pedro Beltrao and Jason Tsai liked this
StatsRUs - http://pj.freefaculty.org/R...
Jason Tsai, Deepak Singh, Mr. Gunn and 2 other people liked this
If you need a tip sheet for R, here it is. This is not a substitute for R documentation, just a list of things I'm using to remember what I read in the email list.
- Neil Saunders
SciBar, SciFoo, Sci woot - http://shirleywho.wordpress.com/2009...
Bora Zivkovic, Peter Miller, Graham Steel and 17 other people liked this
extremely jealous :)
- Frank
Very nice summary. And now I see what I missed at SciFoo - other than the Pixar session I went to completely different sessions.
- Martin Fenner
Sounds like you went through hell, Shirley. I'm so very sorry for you.
- Iddo Friedberg
Releasing Scientific Software, Some Website Basics - http://boscoh.com/science...
Dan Gezelter, Jason Tsai, Steve Koch and Neil Saunders liked this
I like your website, but wonder why you didn't choose an existing repository such as sourceforge, Google code, github? Not a criticism, just curious.
- Neil Saunders
You can't emphasize enough how important annotated, working examples are.
- Dan Gezelter
@Neil. I've released another piece of software under sourceforge: http://hollow.sourceforge.net/. The problem with google-code is that you can't redesign the front-page. Sourcecode let's you do your front-page. However, I've never had any contributors for my projects so I don't need all the clutter that is part of the standard github/sourceforge/google-code pages. I wanted to go for a...
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- Bosco Ho
Rajarshi Guha: Detexify LaTeX handwritten symbol recognition - http://detexify.kirelabs.org/classif...
Pierre Lindenbaum, Allyson Lister, Jason Tsai and 2 other people liked this
Cool!
- Egon Willighagen
very nice
- Duncan Hull
Some Modest Advice for Graduate Students by Prof. Stearns - http://www.yale.edu/eeb...
Jason Tsai, Mitchell J Stanton-Cook, Chris Lasher and Neil Saunders liked this
"When you first arrive, read and think widely and exhaustively for a year." -- and he makes clear that he means, don't take any classes or do any experiments! In what grad school will that not get you kicked out?
- Bill Hooker
Apart from that, though, it's good advice -- "if someone hands you a problem, you won't feel that it is yours, you won't have that possessiveness that makes you want to work on it". Water it down just enough to not get kicked out and it's sound.
- Bill Hooker
Coming from outside the US, I've always found the requirement to take classes odd, compared with UK/Australia where a postgrad degree is straight into the lab, all research, 3-4 years. How do US people feel? Is it beneficial to do classes too? Are there places where you don't have to?
- Neil Saunders
Neil, I viewed it as a kinda catch-up, because many of the people entering the program didn't come straight from college. Some had done some industry work, some had done some travel/research fellowships abroad, etc.
- Mr. Gunn
At my school, coursework was valued for exposing students to a wide swath of microbiology and molecular biology subfields at the primary literature level (rather than textbook). These courses were helpful in getting used to critical reading of the literature, and the writing assignments often included an R01-style grant proposal based on your ideas.
- Brian Haugen
@bill no shit! I was on my first expedition within one week and had my first data by the end of my first semester! My advisor was a hit-the-ground-running guy. I love the advice though. I think by grad school time you should know how to learn on your own though. Technical, like he says, are fine. The only course I took in grad school were statistics courses. 3 of them. Everything else was discussion group credits and research credits
- Kevin Z
from twhirl
"You can expect a stab of terror at this point. Don't worry - it goes on like this for awhile, then it gradually gets worse." oh, joy, something to look forward to.
- Christina Pikas
Crucial Differences Between Non-Embryonic and Embryonic Stem Cells - via MrGunn - http://thebulletin.us/article...
Morton Fox, Sally Church, Jason Tsai and Mr. Gunn liked this
Some "facts" are inaccurate, but a good synopsis of current thinking. For example, there are clinical trials going on using ES cells.
- Jim Hardy
from Bookmarklet
"all frozen human embryos should be given a chance to be born"?!?! Current thinking perhaps in certain ideological camps.
- Heather
By "current thinking" I mean what a lot of people think about the topic. Certainly not my views on the topic, but the "general public" would likely agree with this writers sentiment. I got into a conversation with a religious nutter across the aisle on the 4 hr flight back from #sbcPA about why ES research is so important.
- Jim Hardy
I was sitting next to a woman a few weeks back who mentioned as we were chatting that her son had autism. I had to ask. She knew all the talking points. Wanting to keep the conversation polite, I mentioned a few things re: mmr rates and asked "didn't the guy who found the link have to retract his findings"? I'd like to believe I planted a seed, but I am not sure I did. If only I could...
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- Mr. Gunn
Haha, that'd be more likely, Mr. Gunn. It's disgusting how one celebrity can brainwash an entire nation.
- Brian Krueger - LabSpaces
(panting here, with sweating palms as I climb upon my soapbox) Mr Gunn and Brian, as a mother whose son was suspected of being autistic (instead deals with constant therapies under a nos diagnosis related to delay), I can assure you that the desire to find a reason has nothing to do with common, uncommon, or scientific sense. I am as disgusted as you are by Pretty Smiling Blond Women...
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- Mickey Schafer
@Jim - much relieved! @Mickey - the major difference I think is that, although there is a daunting supply of crap as well as useful research findings, you and your friend know how to think critically. You won't take someone's word, you will ask for evidence. Most people, I'm afraid, will defer. Out of lack of confidence, out of relative disinterest, or perhaps other reasons. Education can teach people to think critically, even if it can't teach all facts needed for later life.
- Heather
I agree, Heather, but more frequently, I find the medical community recommending that parents "make their own decisions based on the research" (this is what my son's ENT said -- a man I trusted b/c my father trained him -- to which I replied with not a little sarcasm how parents who don't have doctorates in linguistics or come from patent-holding MD/PhD parentage possibly make such...
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- Mickey Schafer
Boston Magazine: The League of Extraordinary Biologists - http://www.bostonmagazine.com/scripts...
Benjamin Tseng, Jason Tsai and Mickey Schafer liked this
Meh, more Boston hype...
- Jim Hardy
from Bookmarklet
"Hype", maybe, but exactly the kind of thing I commented on in a different discussion -- that science, as an enterprise, needs more narrative -- the public responds to narrative, and since their taxes are tied to funding, having super-hero writing about any group of scientists helps them to feel better about where their $$ go -- also, private investors like this kind of thing, too. That...
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- Mickey Schafer
"Collectively, the trio, along with their idiosyncratic bosses, have put Boston at the epicenter of a movement that proponents believe will be no less transformative than the Renaissance" Perhaps only mildly sensationalized.
- Jim Hardy
jealous, me? No, really, in the stem cell field it's how they are perceived. And as a developmental biologist, I've followed Melton's work for a while. But I am still totally jealous. HHMI professors at 35? I'm feeling highly demotivated now. Fine if it makes taxpayers happy, though.
- Heather
lol, but quietly, Heather -- I get to work with the HHMI funded undergrads here, students with only the vaguest notion of how lucky they are. I simply guide their writing, sometimes early publication.
- Mickey Schafer
Finishing annotation of S.macrospora - comparative assembly worked out great.
Jason Tsai, Neil Saunders and Jan Aerts liked this
Sounds cool. Any interesting ncRNAs?
- Paul Gardner
not there yet...
- Jason Stajich
Unskilled and unaware of it - http://www.mailund.dk/index...
Jason Tsai, Marcos de Carvalho, Sung W. Lim and 6 other people liked this
OK, so dumb people think they are smarter than they really are, and smart people tend to be self-critical. Nice to see an intuition as old as mankind finally put to an empirical test.
- Iddo Friedberg
Ah, this pretty much encapsulates my entire past couple weeks. I guess it would be entirely too snarky to email this to someone?
- Mr. Gunn
On of my long-time favorite articles. I especially love last two sentences: "Although we feel we have done a competent job in making a strong case for this analysis, studying it empirically, and drawing out relevant implications, our thesis leaves us with one haunting worry that we cannot vanquish. That worry is that this article may contain faulty logic, methodological errors, or poor...
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- Lars Juhl Jensen
Neil Tyson rebukes Richard Dawkins - http://www.youtube.com/watch...
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Jason Tsai, Mr. Gunn, Allyson Lister and 3 other people liked this
Spot on. Perfect. Outstanding.
- Paulo Nuin
Paulo, are you referring to Neil Tyson's rebuke or to Dawkins's response at the end?
- Ruchira S. Datta
Tyson's rebuke.
- Paulo Nuin
now let's have an intelligent, reasoned response and show people how intelligent debate is really done!
- Mr. Gunn
Show off :-)
- Paulo Nuin
In general I don't think I agree with Dawkins' militant stance. If it is true that the human mind is easy prey to persuasive power of any cause (ex. religion, nationalism), than militant atheism can also be one of these powerful causes. People might end up doing "whatever it takes" to educate the "idiot masses". I think the emphasis should be on education and critical thinking more than religion. Educating the next generations to be protected against the power of a cause.
- Pedro Beltrao
The pleasure and importance of printed journals : Nature - http://www.nature.com/nature...
Bora Zivkovic, Jason Tsai, Mary Canady and 17 other people liked this
Someone needs to upgrade from dial-up...... And get off their ridiculously high horse.
- Wladimir Labeikovsky
from Bookmarklet
and learn about print on demand.
- Pedro Beltrao
Liking the comments rather than the letter, obviously :-) I guess they're entitled to their (ridiculous, wrong-headed, irrelevant) opinion.
- Neil Saunders
The only thing I can identify with is this act of discovering while browsing. There is no very good equivalent online for this (yet)
- Pedro Beltrao
The quality comment is what kills me. As if somehow cellulose and ink enhance the quality of the peer review...
- Wladimir Labeikovsky
All his points are killing me: You want to browse during breakfast? Has the guy ever heard of a "browser"? Been reading my news et al. during breakfast for the last 10 years. Laptops FTW! And yes, Wladimir: how does cellulose and ink make a journal any better, I wonder? I think we should get together and write a pointed reply to Nature!
- Björn Brembs
Wow, Bjorn, feel free to include my name on the letter, but I wonder if it's worth the bother. It's not like we'd even have any common ground to discuss.
- Mr. Gunn
@Mr. Gunn: Worth smorth. Consider the fun! :-)
- Björn Brembs
It would be fun!
- Mr. Gunn
Only problem may be that the letter which is the most fun writing won't be the one getting published, lol :-)
- Björn Brembs
I've had a letter published in the print edition. I know to what degree those things are edited before they hit the page.
- Mr. Gunn
'Until Nature comes up with a new business model, to read this story in full you will need to login or make a payment'
- Andrew Spong
@Mr. Gunn: So you'd think "upgrade from dial-up" and "ridiculously high horse" would be edited out? :-) That cracked me up :-)
- Björn Brembs
Here's my first draft: http://etherpad.com/FZ2N9FKECI
- Björn Brembs
As for random browsing, wikis have it by default, and it's the outcome of many a search on a journal's site or on other parts of the web.
- Daniel Mietchen
Despite the fact that printed journals contribute only a small fraction of the total amount of paper I think it is a question of mind set and awareness. Why get hundreds of printed pages of a journal if you only skim through a small part of it and read only a tiny part at all? That's quite a waste of resources (paper, ink, energy for production and transportation). Yes, paper...
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- Konrad Förstner
One more on random browsing: http://search.twitter.com/search... .
- Daniel Mietchen
Yes, Konrad. See also http://ff.im/4GRMM.
- Daniel Mietchen
After the fall of Genset in 2006, they started to put their whole library in the garbage. I've tried to save a part of the journals (see this picture http://www.flickr.com/photos... ). I sent some e-mails to the local libraries, to the centers of research, etc... Nobody asked for those journals and at the end, all those books ended into the bin.
- Pierre Lindenbaum
@Pierre - Really a shame, maybe try next time bookcrossing.com or freecycle.org at least for the books. I had a similar experience when I wanted to donate some books in quite good shape to the local library. They didn't take them for whatever reason.
- Konrad Förstner
That's pretty good, Björn, but I wouldn't even concede the point about discovery. I think discovery through re-sharing of bookmarks (connotea/citeulike/Mendeley(soon)) and through article use stats (Mendeley, PLoS) works better than randomly paging through a magazine.
- Mr. Gunn
@Mr. Gunn, I don't know about that. We pick topics and people tend to be somewhat close to what interest us. I can't understand half of what is in a regular issue of Nature but I guess that if I ever browsed it in print I would spend more time on articles that I would never even look at the abstract. I am not even saying that one way is better than the other .. just that my online browsing habits are much more focused than would be if I had to check paper versions.
- Pedro Beltrao
Yeah, I'm definitely more focused online, but the serendipity of print limits you to that one article, whereas recommendation online can come from the whole body of work. Maybe we need a good way to browse recommendations?
- Mr. Gunn
Is there an analogy about paging through a set of recommendations from trusted people rather than through someone (the editors) with whom you have no direct connection?
- Cameron Neylon
I page through F1000 listings, FF bookmarks (citeUlike and connotea) from others, and my broad search terms. Would that count? My subjective impression is that this leads to a broader sample of the literature than if I were just browsing the hip journals. But it certainly also feels less leisurely and comfy :-)
- Björn Brembs
Great conversation. I am a strong believer that social bookmarking and networking tools can do a better job of nudging serendipity along than flipping through a paper journal. Use of these tools increases the chances of coming across relevant discoveries in adjacent fields. (shameless plug: http://2collab.com/ is designed with this goal in mind.) That said, my former position at Lulu.com left me a firm believer that print-on-demand is the way to go whenever print is prefered.
- Michael Habib
"the proportion of reading by U.S. science faculty from browsing decreased in recent years, replaced by other means of learning about articles that are read. While the proportion of readings decreased over the years, however, that number of readings found by browsing remains about the same: 88 readings in 1977 and 95 in 2005. Readings from searches increased from 17 to 78 readings between these two years." - Tab. 1 in http://www.dlib.org/dlib... .
- Daniel Mietchen
"the quality of these prestigious journals could gradually decline to the standard of many of today's web-only journals." What a flippiant remark, as above how does the medium of information transfer effect the quality of the content. What a dinausaur, lets start a charitiable fund to buy them an iphone - although will will have to advertise this via a telegram
- Frank
And indeed given some effort they might actually rise to the standard of several of today's web-only journals, one can at least hope...
- Cameron Neylon
I'll play devil's advocate here. My first reaction was rather like those above, but there's room for all, no? I liked getting American Scientist in print, though have now opted for online. But there are places laptops aren't very practical. Breakfast isn't one. I don't want my serendipity forced on me, either, cf Pedro. Comment about quality might have to do with the lower cost barrier for a new journal to enter web-only vs print, but didn't like idea that quality for established journals would decline!
- Heather
From a practical standpoint I find that when I'm reading something in print, my mindset is different and I have a longer attention span and can actually get through a long article without realizing there's something else I need to look at or do online. I think there is still a place for printed journals, but more for reviews or 'popular' science such as GEN or the Scientist. If it's a primary research paper you really need to read for your work or research, I think the media doesn't matter.
- Mary Canady
Does anyone have an idea about the best way to cluster a bunch of sequences based on pairwise global similarities? Any tools that can do that or suggestions?
Brad Chapman, Jason Stajich and Jason Tsai liked this
What sort of global similarities do you mean?
- Michael Barton
I guess you need to pick a similarity/distance measure that makes sense for what you are interested in and then pick an appropriate clustering algorithm. These both will depend on what you want to do in the end with the clusters.
- Pedro Beltrao
+1 CD-HIT, you can also try BLASTclust.
- Khader Shameer
Thanks people! i think what i need are pairwise identities derived from comparing the whole sequence (globally) against each other and not parts of it(local). I think BLASTclust incorporates local alignments so might not be ideal. Seems like CD-hit is good start.
- george
You could try multiple sequence alignment, phylogenetic tree estimation, then cut the tree for the number of clusters you want.
- Michael Barton
Wikipedia has a nice reference list http://en.wikipedia.org/wiki...
- Pawel Szczesny
I have written a program called FLOCK: Full Length Overlap Clustering of Kindred, to flocculate sequences into global homology clusters. So naturally I think that's the best way ;-) . I haven't gotten around to releasing it yet though (mainly I need to port it to use HMMER instead of SAM). So far we are using it within our group and for our collaborators.
- Ruchira S. Datta
Michael, most multiple sequence alignment methods are not robust to the sequences not being alignable. They will align them anyway, incorrectly.
- Ruchira S. Datta
I should also mention CLANS: http://bioinfoserver.rsbs.anu.edu.au/program... - hard to beat if you actually want to _see_ what you're doing :)
- Pawel Szczesny
@Ruchira please is it possible to share FLOCK? and some documentation? It sounds like something i would want to use as well for the current clustering work. thanks
- george
Managing and Analyzing Next-Generation Sequence Data - http://www.citeulike.org/user...
Jan Aerts and Jason Tsai liked this
Computer Scientist Barbara Liskov on good and bad research (acm.org) - http://www.cs.man.ac.uk/~hulld...
Khader Shameer, Richard Akerman and Jason Tsai liked this
It's much better to go for the thing that's exciting. But the question of how you know what's worth working on and what's not separates someone who's going to be really good at research and someone who's not. There's no prescription. It comes from your own intuition and judgment.
- Duncan Hull
Alternative Splicing of PTC7 in Saccharomyces cerevisiae Determines Protein Localization - http://www.citeulike.org/user...
Jason Tsai liked this
Synonymous genes explore different evolutionary landscapes. - http://www.citeulike.org/user...
Jason Tsai liked this
Lox: The last genome for electrophoretic Sanger? - http://omicsomics.blogspot.com/2009...
Jason Tsai and Allyson Lister liked this
Sanger sequencing is not dead yet, but how many edge cases would benefit from de novo sequencing the 'old fashioned' way when next-gen technologies fail to deliver?
- Daniel Swan
On the challenges of conference blogging : Genetic Future - http://scienceblogs.com/genetic...
Mr. Gunn, Berci Mesko, MD, Jason Tsai and 19 other people liked this
My comment: "Honestly.....this should not be an issue. The requirement that "To attend CSHL meetings, reporters agree to obtain permission from a speaker before writing up any results." borders on censorship and any decent reporter should say a loud a clear NO to such a request. Giving a talk at a conference is a public presentation, if you want to keep your data secret, then don't give a talk. If any conference organizer asks this of me, I'll either refuse to attend or do my blogging/twittering anyway. I expect any serious science-blogger to do the same. These are rules we must refuse to abide by.....honestly."
- Nils Reinton
from Bookmarklet
Liking for Nils' comments in the thread. "If your "unfettered presentation of unpublished work" cannot withstand the scrutiny of anyone but selected attendees, you shouldn't present it at a scientific conference. Such presentations belong in cults, sects or secret societies. Regardless of the venue however, no reporter (or blogger, or twitterer) should ever sign anything resembling a stamp of approval as a prerequisite to publish."
- Bill Hooker
I think the issue is really different to this. It's simply that people think they are speaking to a room of people they can see, and when they realize they aren't they get upset. There are situations where robust and honest debate is improved by agreeing that the details of what happens within a room are confidential. What is important is that there is a discussion of the "rules" and...
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- Cameron Neylon
This could go either way, but I'm definitely on Nils' side. Others that are less open probably fall on the other side
- Brian Krueger - LabSpaces
I agree with Nils but I think being polite and asking (and respecting other people's requests) is a productive way of spreading that message. If you want people to be open, be open about how you are making them open.
- Cameron Neylon
I think Cam's point could be addressed by conference organizers making sure that every presenter was aware that if they didn't want to be blogged and tweeted they must say so at the outset. That way there's no need to ask permission and individual speakers' wishes can be accomodated.
- Bill Hooker
Even better, part of the registration for speakers should be to indicate if they would prefer NOT to allow blogging, tweeting, etc during their talk. Then it can be indicated in the conference program and stragglers to any particular talk don't have to be in the dark. It might also lead to and interesting study of whether there is a correlation between "willingness to be...
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- Shirley Wu
+1 shwu, that is a much better idea
- Bill Hooker
+1 shwu, I agree and prefer that presenters get the choice on this topic, not the organizer.
- joergkurtwegner
Agree with Shirley that such information upfront would solve this (should be non-existing) problem. In the comment thread to the post there is one comment suggesting that these issues are specific to biology. Is this true ? Here's the quote: "This particular attitude of trying to enforce semi-close/semi-open (depending on your point of view) conferences seems to be something particular...
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- Nils Reinton
As I said to someone the other day, I want a t-shirt with a big CC-BY on the front of it (and on the back "this opinion can be freely shared and re-used) ;-)
- Cameron Neylon
Actually I remember what it was - Brian Kelly was videoing me giving a talk a few nights back and asked me to explicitly say on the video that re-use and posting of material was ok.
- Cameron Neylon
Cam, I love the t-shirt idea!
- Bill Hooker
Agree completely with Shirley ... and I want that T-Shirt
- Deepak Singh
Ditto on the shirt.
- Brian Krueger - LabSpaces
Ooh I can't wait to go to a scientific talk to see a sign at the door that reads "No blogging allowed"
- Wladimir Labeikovsky
Cam's comments remind me of http://researchremix.wordpress.com/2008... from Heather Piwowar, April 2008. I made a couple of suggestions shortly thereafter about t-shirts based on this. I shall now contact my e-fashion guru as to creating some designs and will crowd-source early on..
- Graham Steel
Did someone mention a t-shirt? This is my area. I'm onto it. Cameron: which of the different CC license images is it that you wanted on front?
- Karen James
...choose from: http://creativecommons.org/about...
- Karen James
Blimey. "t-shirt gal" has arrived already. Thanks Karen, sorry, "t-shirt-gal"
- Graham Steel
Andrew Maynard weighs in: http://2020science.org/2009...
- Karen James
shouldn't cc themselves be selling the t-shirts? (they do have a shop of their own, y'know!)
- Joe Dunckley
Well, this whole experience has certainly taught me a lot about the interface between blogging and reporting; I'll be approaching conference blogging with considerably more caution next time. I do generally agree with Nils that open conferences are the ideal, although I am more sympathetic than he is about the pragmatic decision of conference organisers to place restrictions. Long term, though, I think something like Shirley's "opt out" model is the only viable solution.
- Daniel MacArthur
But will they allow me to use pen and paper? If yes, can I take my notes home? If yes, can I show it to a colleague? If yes, how many colleagues can read it? Seriously, I always thought that the main objective of a conference was to do science communication, not stop it.
- Marcos de Carvalho
There's a lot of discussion around this issue. It seems clear enough to me and I think Cameron and Shirley summed it up well. The onus is on conference organisers to (a) be aware of social media, (b) have a clear policy for their meeting, (c) make sure all attendees are aware of the policy. In the CSHL case, it just seems like there were rules for accredited media, but no-one had even thought about the unaccredited - i.e. everyone else.
- Neil Saunders
On the t-shirt issue the thing I had in mind was first and second in the "icon" category next to each other (see http://creativecommons.org/about...). The reason I've never gone on and done anything about it was precisely because it seemed like it ought to be a CC thing to release (and make money on) and I kept failing to suggest it to someone there when we had our heads on. But...
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- Cameron Neylon
Speaking as a conference organizer (albeit not for scientific meetings), I think the (a), (b), and (c) specified by Neil above are about as much as anyone can expect. Even if a speaker were to say (in advance) that they didn't want to be blogged or have their message broken up in disparate tweets, there's no way for conference organizers to enforce such a request. You can ask that...
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- Jill O'Neill
Quote from latest comment in the thread: "Second, lets face the power of amorality: Impeach tweeting/blogging/news coverage to avoid scoopers? First, have you already see a news feed precise enough to scoop someone? Second, considering the number of ruthless sharks in science, any scientist would be crazy to present interesting data still scoopable in any meeting being large or small". - well said
- Nils Reinton
In regards to "any scientist would be crazy to present interesting data still scoopable in any meeting being large or small" -- if the data were very interesting and highly tweeted and blogged, it would increase the level of shame a ruthless shark would endure upon trying to scoop. That is, tweeting and blogging so the whole world knows should (in my mind) reduce probability of scooping.
- Steve Koch
I always struggle when "scooping" enters any debate. I just don't believe in it.
- Neil Saunders
@Neil: what do you make of the stories so many people tell? Here's one I was told: A presented preliminary results from a knockout mouse model at a conference, B went home from that conference and repeated the work using siRNA and published first, claiming priority in an area in which he had not previously had an interest. Yes, A was still free to publish the mouse work, but you know...
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- Bill Hooker
@Bill I agree, and it has often ruined students along with the PI. Now I think about it from your angle. "A" presents preliminary results. The audience is excited -- they tweet & blog. "A" talks with more people afterwards who tweet and blog some more. "A" and A's students respond electronically by commenting on blogs and providing links to their Open Notebook Science. Is "B" really going to be able to rush home and publish "first?"
- Steve Koch
>>And I've heard plenty of stories where the "scooper" effectively prevented the "scoopee" from publishing, since you know how much emphasis is placed on novelty.<< journal policy seems to be the weakest link here. does anyone have info on whether (and how) the "scooping problem" manifests itself in physics and other fields enlightened enough to possess a preprint infrastructure?
- Wladimir Labeikovsky
Wladimir: good point. Andre Brown of Biocurious says that biologists look at arXiv and say, "how can you afford to make preprints public, you'll get scooped" and physicists look at biology and say "how can you live without a preprint server to get your preprints out there into the community without the publishing delay?" It's a totally different mindset, and I can't figure out how to get biologists to switch.
- Bill Hooker
See slide 11 here: http://www.arl.org/sparc... (warning, pdf!)
- Bill Hooker
Biologists will switch when they ask themselves "is there really such a thing as scooping?", instead of blindly accepting the establishment line that there is.
- Neil Saunders
Bill: That's great! I've had both conversations at least half a dozen times with both physicists and biologists, usually while discussing why the arXiv took off in physics, and not in biology. (Physicist: "It's because physics is more competitive than biology". Biologist: "It's because biology is more competitive than physics.") It's very difficult to keep a straight face.
- Michael Nielsen
As a biophysicist, I don't have any insight to add :) I think I see what Neil means now (maybe?), and it's consistent with what Bill and I were saying. Once the majority of the grant review panel (or tenure review panel) doesn't believe in scooping, then scooping will go away. In order for people not to believe in scooping, they need to believe in preprints (already done for physics), open notebooks, blogs, conference presentations with public slideshare, tweets, etc. So it's going to take a while.
- Steve Koch
Aw c'mon Neil, what about my story of A and B and the conference? Or here's another, told by none other than PZ Myers: https://www.blogger.com/comment... (5th comment). How is that not scooping (and theft, to boot)?
- Bill Hooker
Well, it's widely known what happened, so why doesn't that take the sting of of being scooped?
- Mr. Gunn
Consistent hashing - http://michaelnielsen.org/blog...
Abhishek Tiwari, Jason Tsai and Deepak Singh liked this
The mathematical symbols in this post come up a bit funny in my browser, for some reason. Not a problem I have in other posts. If anyone has any clues as to why, I'd love to hear!!
- Michael Nielsen
I noticed that they are GIF; is there an option to generate e.g. PNG? Another idea - may be that you need to point to a TrueType font path in whatever config file controls the latex rendering.
- Neil Saunders
Thanks for the suggestions, Neil. Earlier posts also rendered as gifs with no problems. I can't think of what config file could have changed, but I'll do as you suggest and poke around a bit. There's nothing that I can think of related to LaTeX which has changed since mid-February, and things were still working then...
- Michael Nielsen
Time to change to MathML?
- Matt Leifer
How well does it work? The few experiments I know of with MathML make it sound like a nightmare. Jacques Distler was promoting it on his blog for a while, but made it sound incredibly finicky...
- Michael Nielsen
I haven't worked with MathML for years, but I too remember it being finicky and hard to author. I would have thought tools would have improved by now, though.
- D0r0th34
On Ruby: Good Programmers and How to Become One - http://on-ruby.blogspot.com/2009...
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Gene expression: Structure versus codon bias - http://www.nature.com/doifind...
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Thesis Theme for WordPress - http://diythemes.com/thesis...
Jason Tsai, Deepak Singh, Marko Saric and Abhishek Tiwari liked this
I really like the way this looks. Might have to switch on my own blog!
- Mr. Gunn
That is very nice and clean.
- Bill Hooker
Thesis is great. I use it on my blog and love it. Check out http://www.howtomakemyblog.com to see what can be done with Thesis.
- Marko Saric
I am very tempted to use it as I contemplate a new design
- Deepak Singh
RT @girlscientist: See, not just me and @noahwilliamgray grappling with the morality of twittering from CSHL: http://blogs.sciencemag.org/science...
Jason Tsai, Wladimir Labeikovsky, Alexey and 10 other people liked this
Better late than never. All meeting organisers need to wake up to social networking, decide on their policy and make it explicit, before the meeting. There's also a difference between broadcasting the details of a presentation and a tweet such as "person X is about to talk on topic Y".
- Neil Saunders
Not sure what the best policy is - it seems like requiring bloggers and twitterers to register beforehand and get presenter approval is going to result in far fewer people covering the conference - but I suppose that might not be considered a bad thing by some, if that coverage means blog and twitter posts.
- Shirley Wu
Wow! That just boggles the mind. I never thought the line between scientist and journalist was that thin.
- Peter Murray
“They weren’t held to the same standards as the media” - that's just a failure to recognise that on the web, we are all "the media".
- Neil Saunders
Seems fair enough. It's just common courtesy to get approval before discussing/disseminating someone else's unpublished results. Although, I think it's kind of dumb. If you paid the entrance fee, you get to hear the talk, the results are no longer secret, and the biggest competitors are probably in attendance anyway, so really, what's the big deal.
- Brian Krueger - LabSpaces
I think people come to conferences exactly to have this kind of interaction they're trying to squelch. It's going to be hard to draw the line here, too. I think the only people who should have to ask for permission are the people who have a reason to sensationalize or spin the material, which are mostly journalists and not bloggers. Even in the case where a blogger does hype or...
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- Mr. Gunn
They should take a page from tech conferences. There are accredited journalists, many of whom blog and twitter. They can even have a dedicated bloggers section for full time bloggers, but you can blog and tweet about talks unless the speaker says otherwise
- Deepak Singh
Similar thread here: http://ff.im/3xNjm
- Brian Krueger - LabSpaces
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