Allyson Lister › Likes

Steve Koch
Erika Check Hayden's Nature News article about Rosie Redfield's Open Science replication of arsenic work
peter murray-rust
Cameron Neylon
In which my heart goes out to Postdoc B -
Nicely reflect the inability of funding and hiring agencies to fairly judge the quality of post-docs... - Egon Willighagen
as a complete outsider, I'm still horrified that someone is expected to have *3* postdocs that last as much as 12 years before they get to settle down into a long term job in a stable location (if they are lucky). I'm also horrified that you could go through all of these post docs and then not be able to find a faculty position. - Christina Pikas
Dunno where you heard those stories, but, ummm... my first post-doc was 1 year (center closed down), then 1.2 years (due to personal needs, I needed to leave NL to change scene), then 2 years (grants unsuccessful), then 3 months (to fill a gap), and now on a 1 year contract... - Egon Willighagen
Mine were 4 years, 2.5 years, 4 years. - Bill Hooker
Mine were 1y (would have been extended but left early), 1.2y (pump-prime funding, 'follow-up' grant unsuccessful), 3y (happy to keep me on, but as employee), 3y (fellowship). - Noel O'Boyle
Mr. Gunn
Part of the Digital Economy Act, allowing the music industry to force ISPs to block websites, is DEAD! #dingdong -
nice to see some good news for a change - Mr. Gunn from Bookmarklet
peter murray-rust
What’s wrong with scholarly publishing? It’s only for academics. -
Cameron Neylon
RT @Czernie: Interested to know. What are considered some key/ seminal/ critical readings on open scholarship and digital scholarship?
Hard to pick just one from Paul David (, but maybe this: - Bill Hooker
digital scholarship? like digital humanities? gosh, too bad RepoRat left here, she could rattle a bunch off. - Christina Pikas
David Bradley
Backup all your GMail and Google+ data -
Google has a tremendous number of free services they offer which many of your probably take advantage of. But have you ever considered what you might lose if all of a sudden you lost access to your account? Just like all import data on your hard drive, your critical data in “the cloud” should also have backup consideration. Google lets you "liberate" all your data so that you can download and store with feet firmly on the ground rather than head in the clouds... - David Bradley
Rajarshi Guha
Test Your Vocabulary - Blog -
I'm estimated at roughly 12k English words... though I read a lot, in any language, I such at exact meanings of words... still I enjoy Pratchett very much :) - Egon Willighagen
30,000 - average for a native speaker of my age. I thought I'd do better than average :( - Andrew Lang
I wouldn't take this too seriously, but it was fun to do. (39,300) - Bill Hooker
"Our children will never know the link between the two"
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Björn Brembs
Why I will never pursue cheating again - A Computer Scientist in a Business School - http://behind-the-enemy-lines....
Why I will never pursue cheating again - A Computer Scientist in a Business School
"After spending a tremendous amount of time fighting and pursuing all the cheating cases, I decided that it makes no sense to fight it. The incentive structures simply do not reward such efforts. The Nash equilibrium is to let the students cheat and "perform well"; in exchange, I get back great evaluations." - Björn Brembs from Bookmarklet
Weird -- I cannot get to the link. - Mickey Schafer
Thank the FSM for content scrapers: - John Dupuis
Maybe the problem is in the creating of assignments for which it is so easy to cheat? - Todd Hoff
This is exactly what I find, too: "One interesting observation: Almost all cheating happened within groups with cultural ties. Koreans copy from Koreans. Indians from Indians. Greeks from Greeks. Jews from Jews. Chinese from Chinese. Not just in international students (we do not have that many in the undergrad program), but within US-born students. A result of socializing in similar... more... - Mickey Schafer
Todd -- that is a lovely idea, and certainly we can work on making assignments more difficult to cheat on, but it is also impractical. First, if a student is going to learn to write a science paper, then s/he has to write a science paper. Learning about the process doesn't work; the student must write. Second, there's good evidence that writing about something increases understanding --... more... - Mickey Schafer
And the extra prep still cannot resolve the problem that Turnitin cannot address: that in the sciences, technical jargon has no synonyms, quoting is discouraged/avoided, grammatical paraphrasing is so limited as to be worthless, meaning that students cannot merely be taught not to plagiarize: they have to be taught how to deal with information like a practicing scientist deals with... more... - Mickey Schafer
@John -- thanks for the working link! - Mickey Schafer
I cached a copy as well: - Chris Miller
Yes, I was quite surprised when I went back to it the next day and it wasn't there... does anyone know why he took it down? - Allyson Lister
Very strange indeed - and such a useful post. One can only assume the university asked him to? Mickey raises the exact points I was thinking about when reading the post. There is definitely room for improvement in terms of making plagiarism more difficult, but it's impossible to avoid it completely. - Björn Brembs
Follow up about the issue, here: And yes, he was pressured to take down the post. - John Dupuis
I'm astonished that anyone is surprised the post disappeared. My first thought on reading it was, he'll get fired for this. It's probably too public now for him to lose his job, but I expect him to face more punishment/reprisal of the invidious sort that he described in the post. Make no mistake, universities are businesses now, the students are customers, and they are buying imprimatur, NOT education. - Bill Hooker
I predict that he'll ultimately restore the post but modified so it'll be harder to identify individual students. Not that I thought it was that easy to do that before, but I think that'll be the thing they'll make him do. - John Dupuis
That's the (bogus) hook on which they are hanging the legal threat, certainly. I doubt the post will go back up, because no one actually cares about violations of student privacy (even if they did happen in that post, which they didn't). The university admin cares about the blot on its public copybook, the open airing of one of its dirty little DADT secrets. It's no surprise to anyone... more... - Bill Hooker
Thank you Chris Miller for the link to your cache of the original posting. As the reaction was coming out I was sharing it with members of the Fac Sen Council here at NYU, as well as others. Almost all found it a compelling read. Speaking for myself I hope it might engender a wider and constructive discussion here. I am chagrined at the takedown of the post. - carolh
I am likewise distressed by the higher ed post linked by John. We've had a special task force at UF looking at cheating in general; I was in one of the focus groups. My impression was that cheating was well-known, actively despised, but the solutions come up against the most precious resource: time. Research profs, particularly those at the beginning of their careers, were overwhelmed... more... - Mickey Schafer
Cameron Neylon
Minor side issue or should've been flagged by review? @dgmacarthur on stats sleight of hand that got past Nature revs
seems vali stats are important here. Should've been flagged in review. Maybe it was? Then ignored? - Rajarshi Guha
What? There is a paper *with*statistics in Nature? - Björn Brembs from iPhone
@dgmacarthur had some comments on twitter. It looks like a failure from my perspective. Actually I'm not entirely convinced the paper really fits with Nature's criteria actually, at least as I understood them, but that's another issue. Q is whether it is an example of something flashy, but wrong getting through, or just a minor technical side issue that isn't really that important? - Cameron Neylon
(Insert my usual comment about how this is responsibility of authors not reviewers) - Noel O'Boyle
But in a journal like Nature which trades on the high quality of its peer review process I'd expect something like this to be called. Especially when it looks like its what got the paper into Nature... - Cameron Neylon
Does Nature trade on this? I thought it was on high-impact papers (and nice pictures). - Noel O'Boyle
peter murray-rust
The ethics of “stealing” scientific articles and civil disobedience -
Not everyone downloads full repositories, but it is clear that the publishing is serious at suing your ass over their IP... who's/what's next... - Egon Willighagen
maybe the FF room that helps people find papers...? :( Popular, but I have always wondered how legal it is... - Allyson Lister
@Allyson - probably illegal anywhere. Copyright depends on the domain (US != UK != FR etc) and may be civil or criminal. Danages may depend on showing what harm has been created. This is reinforced by contract law which relates to individual publisher-academia contracts. They could contain almost any restrictions (I suppose they could also allow sharing of files but I bet they don't) - peter murray-rust
I have said repeatedly since we started the Refs Wanted room that it is my belief that small-scale p2p access sharing falls under Fair Use, being merely a (sometimes) more efficient version of inter-library loan. - Bill Hooker
@Bill - while I sympathize I doubt the law will. Fair use is not a UK term (and it is manly operable in the US only). Moreover I am not sure that everyone has right to an ILL. My guess is that it only works for staff in Universities affiliated to the scheme. - peter murray-rust
@PMR, it doesn't matter what either of us thinks anyway, all that counts is the outcome of the court case if there is one -- and in most places you can have all the justice you can afford, which means that the publishers will probably win. Which is why I always thought Swartz' "guerilla OA" was foolish, and this latest thing of his is probably equally hare-brained. In the case of FF... more... - Bill Hooker
I think we should try and mount some sort of campaign, similarly to the UK libel-law campaign. Swartz, in my eyes is a hero and needs support. Billion-dollar corporations on one side, tax-payer funded research on the other. Shouldn't this be a slam dunk? Who does one turn to in such a situation? - Björn Brembs
@Bill thanks for the info on Guerilla OA (which I do not approve of). From what I read (and this is only over half a day) the latest incident seems to be done deliberately in the opn. If it was clandestine, I don't approve - if it was deliberate civil disobedience (and yes, I have read peter Suber on this) then I have empathy. If it was for the purpose of corpus analysis I am slightly... more... - peter murray-rust
Björn, I don't think evolution (fight and tweak non-gold-OA journals) will solve the problem here; I think this needs revolution (stop publishing on non-gold-OA journals). - Egon Willighagen
I definitely think we should try and start a revolution and I'm campaigning towards it with what little means I have. I'm just not sure it's all that realistic that we'll succeed :-) Which of course doesn't stop me from pushing for revolution anyway :-) - Björn Brembs
The campaign for Aaron is already mounting: Be sure to sign the petition! - Björn Brembs
The details of this particular incident remain murky for now, but what seems increasingly clear to me is that Egon is right: if we as scientists do not stop publishing in non-gold-OA journals then we are part of the problem and it will never end. Only when it is clear that billion-dollar profits can no longer be made from scholarly publishing will the forces behind this sort of affair lose interest and wander off to befoul some other domain of human enterprise. - Bill Hooker
I agree with Bill and Egon that this would definitely help. Much more effective and realistic, IMHO, would be a campaign to get everyone to start making their own, personal PDF copies which everyone has for their own use, available to the public. Fairly easy to do and relatively risk free if enough people are doing it. Filesharing for papers is way overdue... - Björn Brembs
Regarding the JSTOR dump on the Pirate Bay,do people condone that and if so, why? It seems that JSTOR did spend time, money and effort on digitizing the material - so it seems that hiding the results of digitization behind a paywall is reasonable. Sure, the originals themselves are PD - and anybody could digitize them and make them freely available; or charge for them like JSTOR. Or have I missed something? - Rajarshi Guha
Two good blog posts on the original incident: - Bill Hooker
While I agree there's no point in using JSTOR papers for these actions, most commenters I've read so far see the wider point of the broken scholarly publishing system. - Björn Brembs
Keynote: Janet Thornton - The Evolution of Enzyme Mechanisms and Functional Diversity
10 year Keynote for ECCB - Shannon McWeeney
Special call-out to Elixir session today at 2:30 Hall F2 - Shannon McWeeney
Trying to understand life from molecules to systems - Venkata P. Satagopam
She's a "data junkie" -- everything depends on having your data properly organized and being able to extract information from it. - Barb Bryant
Most of our information is still at the parts level, with emerging data on interactions, reactions and pathways - Barb Bryant
at EBI - data doubling every 5 months 12 petabytes of storage currently - Shannon McWeeney
EBI contains presently 12 petabytes of data - Venkata P. Satagopam
We need to look not only at proteins but also at the small molecules, the metabolites. - Barb Bryant
Plants have way more metabolites than we do. - Barb Bryant
Cheminformatics is older but smaller than bioinformatics; largely confined to industry. The tools are not freely available, with notable exceptions. - Barb Bryant
Differences between the proteome and the metabolome, e.g. no evolution and hierarchical structure of metabolites. - Roland Krause
"Way back in the 90s" they were trying to define the reactome - the reactions necessary for life. - Barb Bryant
From the proteome and the metabolome to the reactome: How many reactions are necessary for life? - Roland Krause
Enzymes are important part of biological molecular reasons - Venkata P. Satagopam
Enzymes are called by name and EC number. - Roland Krause
Handling the reactions computationally is a challenge - Venkata P. Satagopam
The classification of enzymes are four-part: classes, subclasses, sub-subclass, serial number (typically the substrate) - Roland Krause
Capture only the chemical level, no biological dependence such as co-factors - Roland Krause
There is no one to one relationship between EC numbers and protein families - Venkata P. Satagopam
The reactome contains 4154 reactions - Venkata P. Satagopam
They wanted to build tools that would handle the actual chemistry. - Barb Bryant
There has been a lot of work in the past 10 years in tools to handle the chemistry. Includes Kanehisa 2004, Gasteiger 2008, Aris-De-Sousa 2008, Schomburg 2010. Unfortunately, most of the software isn't freely available, and only tackles part of the problem. - Barb Bryant
There is a huge literature on comparing small molecules to each other. So that's well covered. - Barb Bryant
They also needed to map the atoms from each side of the equation to each other: atom-atom mapping. This works by matching the largest common moiety first, and iterating. The Mesa (?) database of about 300 reactions is a gold standard to check the quality of the mapping. - Barb Bryant
You need to be able to compare reactions to each other - reaction similarity. - Barb Bryant
To describe the changes in the bonds that take place, you use the Dugundji-Ugi model -- you make a matrix showing the bonds for reactants and products; subtracting the matrices gives you the reaction matrix. - Barb Bryant
EC-BLAST created by Syed Asad Rahman; it allows you to compare reactions by bond similarity, reaction centre similarity or substrate structure similarity. - Barb Bryant
Chemicals have several fingerprints bond change, structure, stereo fingerprint - Venkata P. Satagopam
(See KillerApp talk I think Tues 11:45am) - Barb Bryant
CDK (Chemistry development kit) free software, - Venkata P. Satagopam
They looked into redefining the enzyme classification system. - Barb Bryant
Ligases in principle simple, most are 6.1s are amino-acyl-tRNA synthases - Venkata P. Satagopam
The EC-BLAST-server (URL above) is in closed beta. - Roland Krause
Compared two reactions using Tanimoto coefficient - Venkata P. Satagopam
"This heatmap might look good to you, to me it looks fantastic!" Similarity between substrates is now close the EC classification. Differences might be based on the EC classification. - Roland Krause
FunTree - Understanding enzyme families and evolution Poster #Z06 - Venkata P. Satagopam
Why are some structures capable of so many different enzymatic functions? Which are the residues that led to change of function? - Roland Krause
Examples from the Phosphatidylinositol-Phosphodiesterase-Superfamily, a multi-domain protein family. - Roland Krause
They looked at the multi-domain architecture of the phosphatidylinositol-phosphodiesterase superfamily. Adding new domains doesn't add enzyme function to members of this family. - Barb Bryant
One need to understand the evolution to better understand the EC classification - Venkata P. Satagopam
The tree constructed from structure has three main groups. Branches of the tree are distinguished by differences in substrate, product, presence of a metal co-factor, or mechanism. - Barb Bryant
Matrix showing how frequently there are evolutionary changes within and between classes. Evolution tends to create new enzymes within the same class, having the same mechanism but changing the substrate or product. - Barb Bryant
Most of the enzyme evol happening in the last sub class level - Venkata P. Satagopam
Question from the floor: is this an opportunity to abandon the EC classification method and move on to a better one? Answer: no. The EC structure is very sensible. Also, it is powerful because everybody uses it. Also, in the first class we examined, it matches pretty well to the similarity measure we developed. - Barb Bryant
# Best keynote so far - Roland Krause
Question: sometimes you have a huge protein to carry out a single small reaction. Have you noticed any clues to why this happens? A: we have some thoughts related to protein function. First, most proteins are multi-functional. They interact with other proteins and do other sorts of things. Secondly, some of the substrates are quite large. We have a sort of domino theory of enzyme... more... - Barb Bryant
Cameron Neylon
Towards Executable Journals -
There is also Sweave of course... - Egon Willighagen
There are some small simple steps that chemistry publishers can use immediately to add "automatic executable functions" to catch errors in papers. For example simply running a melting point search using this free open tool would have caught a huge melting point error in a 2008 paper on this compound... more... - Jean-Claude Bradley
Have you started using Chem4Word yet? - Egon Willighagen
Egon - actually our institution no longer supports Microsoft Office for students as of the fall term :) - Jean-Claude Bradley
Oh, cool! - Egon Willighagen
Daniel Mietchen
Mashups Reveal World's Top Scientific Cities - Technology Review -
Mashups Reveal World's Top Scientific Cities - Technology Review
Mashups Reveal World's Top Scientific Cities - Technology Review
"Combining citation data with Google Maps reveals the cities where science prospers, and those where it doesn't." - Daniel Mietchen from Bookmarklet
"Bornmann and Leydesdorff's maps raise a number of questions. Not least of these is the performance of Cambridge, MA, home to two of the world's top institutions in MIT and Harvard, which could reasonably be expected to feature strongly in the data. Yet, Cambridge, MA, does not appear at all." - Andrew Lang
I wonder if there's any correlation between population size and performance on this metric? There's a synergy that results from having multiple research groups within drinking-together distance, and this favors larger cities for obvious reasons. - Bill Hooker
Online physics map is here:; chemistry and psychology are figure2.html and figure3.html, respectively - Bill Hooker
@ Andrew, they corrected that in the comments and at arxiv: . - Daniel Mietchen
@Daniel, thanks, I thought that would have been amazing. :) - Andrew Lang
@Bill I was looking at that 'population size' issues and was surprised at not seeing too many differences between Australia and New Zealand (which show as very different performance levels by other metrics) - I was also looking at the Nature graphic ( and surprised to see cities like College Park (state university campus)... more... - Kubke
normalization is a question: by population, by GDP and/or other measurement of funding, etc. - Ramy Karam Aziz
The focus on Egypt reveals two small cities but nothing form Cairo or Alexandria? This is not possible - Ramy Karam Aziz
Simon Cockell
Really impressed with Tagxedo - shaped word clouds. Here is a word cloud of my PhD thesis in the shape of a Drosophila: -
Really impressed with Tagxedo - shaped word clouds. Here is a word cloud of my PhD thesis in the shape of a Drosophila:
Posted via email from Simon's posterous - Simon Cockell from Posterous
Simon Cockell
Watched #sts134 live on (, and on Google Earth. That thing moves quick :) -
Watched #sts134 live on (, and on Google Earth. That thing moves quick :)
Posted via email from Simon's posterous - Simon Cockell from Posterous
Daniel Mietchen
My "written evidence" on peer review has reached the UK Parliament’s Science and Technology Committee
They didn't link to my blog post, though, and put a "©Parliamentary copyright" on the text (instead of CC0, the default license of my blog). - Daniel Mietchen
Apparently, they got 93 responses of this kind (source: playing with the URL; full list at ). For an 80-page critique of the peer review process, see . - Daniel Mietchen
Cool! - Björn Brembs
See also - was surprised to see that it hadn't existed before. - Daniel Mietchen
Not sure how it is in the uk, but in new Zealand govt documents fall under 'crown copyright' which i understand is a special (and unavoidable) beast- check if uk parliament copyright gives allowances similar to public domain - Kubke from iPhone
Last week, they had the first hearings (or "oral evidence", in their terms): - interesting debate, e.g. "If [peer review] disappeared tomorrow, what would the consequences be?" my main problem with that discussion is that little attention is being paid to the different ways in which peer review could be performed. - Daniel Mietchen
"Q59 Stephen Metcalfe: Has social media, by which I mean blogs, etcetera, had an impact on this process at all? Are they helpful, or is it just a proliferation of unchecked views? Professor Pethica: There will be a change of view depending upon the age of the person to whom you are asking that question. With the research students it is quite common. As one gets somewhat older, the utilisation is probably less. Chair: It is the same in this building. " (in parliament, that is) - Daniel Mietchen
Comment on the "oral evidence": - Daniel Mietchen
Jonathan Eisen
Strange things at #PLoS; a public call to get rid of the constraints of describing author contributions -
Steve Koch
@plos @plosone Is it really forbidden to have a numbered reference such as "24. personal communication from Steve Koch?" The PLoS ONE production staff didn't complain, but on re-reading style guidlines, it says not to. I'd prefer to leave it in, since it gives credit to someone. Thanks for any advice!
I must admit that whenever I see these types of reference it does wind me up a bit. Clearly it's great to give attribution but I kind of think that references should pass some practical means of verifiability. - Dan Hagon from Android
I'm with Dan, pers. comms should not be listed as references. Instead of "blah blah blah (ref. 12)", just use "blah blah blah (Steve Koch, pers. comm.)" in the text. If you wanna get fancy, make the name a mailto: link with subject: about that pers comm in [citation]. - Bill Hooker
Interesting. Sorry, Andy! Gonna have to change that reference to blah blah blah (Steve koch pers. comm) style - Steve Koch
Wait... how about a compromise? We could keep the numbered reference and link to the handle of our poster on Nature Precedings? In the updated version of the poster, we describe the advice from Erik Schaffer at the conference. - Steve Koch
The issue with numbering it is that makes the assertion look like a peer-reviewed statement. It also screws up citation graph analysis, but I don't expect you to care about that. - Mr. Gunn
Hmmm. That's sort of out the window, because we are already linking to open notebook science notebook pages, and other html links that are not peer-reviewed. I guess in my experience (or field), I've never assumed that numbered references meant the assertion was backed up by peer review or even a publication.. For example, numbered references often link to footnote explanations, as I... more... - Steve Koch
Curious to hear what you and the others above think about the idea of linking to our poster on Nature Precedings. It's from the conference where the suggestion was made to us, and I note this on the poster PDF. In my opinion now, without hearing from the others above, that's a superior method of attribution, versus just "blah blah (steve koch, pers. comm.)" - Steve Koch
I said that wrong. Numbering implies that it's not a personal communication. Of course links to wikis and such are entirely fine. - Mr. Gunn
I agree with Dan and Bill too. I want to expand the reasons a little bit. The criterion for me is not just whether it's peer reviewed or not, but its uniqueness. Let's say you have the following: We argue the earth is not the center of the universe (Steve Koch, personal communication) ..then later in the text... these results agree with data about the use of FriendFeed in science (Steve Koch, personal communication). ---->1/2 - Ramy Karam Aziz
2/2 --> If you use (24) for both it's assumed that these are the same "personal communication" which is not the case. If you use (24) for the first then (55) for the second, then you have two different numbers referring to the same thing. If you start saying personal communication 1 and personal communication 2 then it's total nonsense. Another reason is that nobody can access these personal communications in the same way the authors accessed them. - Ramy Karam Aziz
Will be even funnier if Steve Koch is also the author. You can certain reference your past paper as (Koch et al.); but can you reference your self-communication? - Ramy Karam Aziz
A reference should be something tangible and revisit-able -- a blog entry, a wiki page, a peer-reviewed paper. Pers comms are ephemeral; they shouldn't be used to support anything significant or crucial to the paper and I think it's rather a pointless workaround to cite the last time a particular pers comm was used. Think of the reader: all you want them to know is that the idea came from Erik; why should they go read the poster to find that out? - Bill Hooker
@Bill, the same reason the reader looks at any reference? To get further information or double check. Considering how most peer reviewed publications are closed access and have permanent errors, I can see much utility to citing NP poster, including: (1) it's "permanent" I.e. a handle instead of just URL. (2) it allows for versioning so I can correct things. (3) it allows for commenting.... more... - Steve Koch from Android
That's my point though -- what further information is there in the poster, that's not in the paper? What is there to double check about "we got this idea from Erik, so we're giving him props"? (Don't get me wrong, it's awesome that you are giving him props, that's not the issue here.) I feel like I must be missing something. (1) doesn't matter unless there's more in the poster than in... more... - Bill Hooker
The more I think about it, the more it seems like what you want here is a sentence in the acknowledgements section, not a pers comm in the paper itself. Again -- I feel I'm missing something. - Bill Hooker
This is a very interesting conversation particularly since I teach my students that "personal communication" is an entirely valid form of reference. I've had many students pass data by experts in an email or F2F conversation -- as a result, the student gains the opinion of someone way more deeply experienced. But I read this in papers frequently, too -- researchers get results, and... more... - Mickey Schafer
@Bill, I think the idea that a reference MUST be something revisitable is too constricting. It negates the value and contribution that informal communication makes to research. There's also a terrific history of such "informal" conversations being prime motivators in getting new science done and current work improved. Have a reference that refers to a publication doesn't guarantee the... more... - Mickey Schafer
Egon Willighagen
Supplementary files, publishing, and standards #2 -
Supplementary files, publishing, and standards #2
nice example Egon :) - Jean-Claude Bradley
You mention Excel - we tried to avoid using it for our archives but couldn't find an open format for saving a Google Spreadsheets while retaining formulas and web service calls - do you know of any? - Jean-Claude Bradley
No, that would make an interesting experiment... I guess the OpenDocument Format (OpenOffice) should capture some of it, if not all, but that depends not just on the format, but also on Google to implement the writer completely... - Egon Willighagen
More importantly... the MS Office Open XML format (.xslx, .docx, etc) ) is not that bad. It's not binary, it's XML-based, wrapped in a zip file. Anyone can make implementations, etc. The documentation is not perfect, and the format still allows for unspecified binary blobs, etc, but for your purposes might be 'Open' enough. - Egon Willighagen
Good suggestion Egon - we'll take a look at that for our next archive - Jean-Claude Bradley
Daniel Mietchen
The information about the licensing of an article should be as easily available as that about doi or other article properties, but it isn't. Why? See also .
I completely agree. But the DOI is unfortunately difficult to find in PubMed. - Martin Fenner
PubMed is one of the few things that will regularly have me tearing my hair out for a variety of reasons - Sally Church
I had difficulties finding this thread, as FF search is broken once again, so adding in a few keywords for Google & delicious: #copyright #license #PubMed #search . - Daniel Mietchen
Just curious, what would seeing a CC-BY license on an article indexed in PubMed mean to you? [i.e., how would you use the article, if you could use it with attribution?] I'd like to get a sense of what problem this would solve for you. - Rachel Walden
Ruchira S. Datta
Thanks so much for the coverage today!
I happily join in this shoulder clapping reverence to your group's important contribution to the success of this meeting. What else could ISCB do to support your efforts? - Burkhard Rost
How about some form of travel award, or registration discount? It might be conditioned on some minimum microblogging metric (carefully designed to avoid perverse incentives). - Ruchira S. Datta
Barb Bryant
PLoS Session on How to Write a Good Paper
Phil Bourne and Steven Brenner are presenting for the first hour, 10:45-11:40. - Barb Bryant
Having published good papers consistently counts for at least 50% of career advancement. - Barb Bryant
(Phil only published 2 papers in a 10-year period while he was leading the PDB. That was a big mistake for traditional career path, but he wouldn't have done it any different way. It was an issue when he came up for tenure.) - Barb Bryant
Other things that matter in an academic career: Teching/mentoring, gratns, community service, good talks and networking. - Barb Bryant
Steven: For a young scientist, papers matter even more. - Barb Bryant
Steven: When I'm looking at a postdoc or junior faculty applicant, I look at where they trained, who their advisor was. I look at what papers they were first author on. Then, is there any paper that is a real standout and important. Then, how many papers, and what is their nature. - Barb Bryant
Andrej: what your rmentor says about you makes a lot of difference too. - Barb Bryant
Alan Turing - signal processing. At AT&T he gave a talk that was never published; we attempted to reiterate this in a recent PLoS CB paper: 2007 3(10)e213. - Barb Bryant
Phil: Work only on important problems. Work with important people. You have to figure out for yourself what is important. - Barb Bryant
Do this when you're young. - Barb Bryant
You need more than brains: you need courage. The system is not well geared for (especially) young people to take risks. Risky papers are often rejected. We're beginning to see evidence of how the review system fails. The review system supports incremental work better than risky, outstanding work. - Barb Bryant
Take PLoS ONE. PLoS ONE was intended to be a place to put work that may not be enormously innovative, but it is sound. But what has happened is that it got a number of risky papers, some of which have turned out to be important, and highly cited. So this journal that is supposed to be at the lower end of things, has a relative high impact factor. - Barb Bryant
Steven: Examples. Original paper where we wrote about the SCOP database. Very highly cited. Rejected by reviewers; my advisor battled the journal to get it published. My arguably most important paper, identifying targets of nonsense-mediated decay, was rejected by three journals. Most-cited paper in field of alternative splicing or nonsense-mediated decay. Don't be discouraged! If it's important, it will eventually be recognized. - Barb Bryant
Phil: The PDB paper has been cited 10,000 times. Noone has ever read it... - Barb Bryant
Luck favors the prepared mind. - Barb Bryant
Time management is critical. The amount of time in the lab doesn't necessarily translate to productivity. You don't get taught how to manage your time well. Read books on time management. - Barb Bryant
Work from your heart. If your heart is not in it, you won't succeed. You need the passion to go the extra nine yards to do a great piece of work. - Barb Bryant
So all of that was prerequisite to writing a paper. Now, how do you do it? - Barb Bryant
Start writing the paper on Day 1. - Barb Bryant
Draft paper helps focus the work, makes sure that you write it up; is easily shared with colleagues for feedback that can help you with the work itself. - Barb Bryant
Steven: another reason to have it written up early in draft form -- I ignore "in preparation" on a resume. If they say "in preparation, draft available", that makes an impact if I can see the draft. - Barb Bryant
Steven: another reason to write the introduction early: "A month in the laboratory can save you an afternoon in the library." Being forced to write the introduction might help you find previous work that will change what you do. - Barb Bryant
Phil: If you hate writing, get over it. If you do not write well, take classes. Now. - Barb Bryant
? I wonder if they have suggestions for people who just don't have good command of English -- what about working with a writer, etc.? - Barb Bryant
Try to see your paper as the reviewer will see it. Try to look at it "from a distance." - Barb Bryant
It might be motivating to you to realize that the paper is going to be your (scientific) legacy, long after you're gone. - Barb Bryant
Some ingredients of a good paper: novlety, good coverage of the literature, good data, strong statistical support, clarity of presentation, thought-provoking discussion. - Barb Bryant
Look at the scope statements of the journal you're thinking of submitting to. - Barb Bryant
Don't rely on your PI to tell you the novelty of the work - figure it out for yourself. - Barb Bryant
In discussion, guide people to build on the work. - Barb Bryant
DON'T try and prove that you are smart. - Barb Bryant
Avoid the kitchen sink syndrome = putting too much that is not relevant into the paper. - Barb Bryant
Maintain a good bibliographic database (EndNote, RefWorks, etc.). Consult a citation index (ISI, Google Scholar); consider using that to annotate your database entries. Use a tool like Mendeley to store annotations. - Barb Bryant
(Mendeley is a way of annotating PDFs; you can share annotations.) Explore social bookmarking to find out what others have been saying about papers. - Barb Bryant
Q: how important is the citation index of a paper? A: not important. What matters is how good and relevant the paper is. - Barb Bryant
In 2000, Phil wrote a paper on alternative views of looking at protein space. For 5 years, noone cited it. But then it became a hot topic and citations started to pick up. - Barb Bryant
Steven: There is a tendency to have a winner-take-all approach. Everyone will cite one paper, even if there is a more relevant paper. It's important to go out and find out which papers really are most relevant. - Barb Bryant
Steven: Have your whole lab get together and pick one program to store your data. Even if it's not the best program, being able to share the tool is really valuable. Phil: we lack good project management tools that map to the scientific endeavor to allow us to share and maintain output from the lab. Come talk to me about developing a company around this... - Barb Bryant
Phil: Have colleagues critique your paper. - Barb Bryant
Become a reviewer early. Shadow more senior people in reviewing. Look at the other reviews of the paper. - Barb Bryant
Approach program committees of conferences. - Barb Bryant
Hold journal clubs. Identify good and bad papers in journal club and elsewhere and study tehm. A good paper will likely tell a story and be enjoyable to read and follow. It's pitched at the right level for the intended audience. - Barb Bryant
Acknowledge the people who submitted the review. - Barb Bryant
Q: will the program committees and journals accept volunteer reviewers, or do you have to be asked? Steven: There are two ways this can work. First, a PI can invite a student of theirs to help review it. Second, if I can't review it myself, I can recommend someone in my lab to do the reviewer completely themselves. The editor then can choose whether to use this student/postdoc reviewer. - Barb Bryant
Choose the journal wisely. Do you read that journal? Do you cite it? Is it a top-notch editorial board? Does it have highly accessed papers? What is the rejection rate? What is the average time to publication? (Find out by talking to people who have published in that journal.) Is it indexed in PubMed? - Barb Bryant
And, most importantly, does the scope match your work?? - Barb Bryant
Use the presubmission inquiry if the journal has one; it helps in determining scope. - Barb Bryant
Mark: what emphasis to place on how highly cited the journal is? Phil: I don't care anymore at my point in my career. This is my personal opinion. The review process is quite broken. But others judge job candidates by this. What do you think? - Barb Bryant
Mark: shouldn't think about impact factors. - Barb Bryant
Phil: Other communities do not have a review process, but a moderation. Then it is how much it is accessed by the community is the judgment of its worth. - Barb Bryant
Steven: You need to think about who will be evaluating you in your career. Traditionalists will care about which journal. If you are looking for a job right out of post-doc, won't have time to have gotten citations on the paper, so which journal matters more. It helps to have letters of reference that describe the importance of the work. - Barb Bryant
It helps to understand the editorial process. - Barb Bryant
Know that the best scientists get rejected and/or have to make major revisions. - Barb Bryant
Post-review phase. Again, "get over it". Buckle down and do the work. Don't be defensive. Address every aspect of the reviewers' concern. It's fine to disagree with a reviewer, but have the conversation, don't shy away from it. Make it clear how your revision addresses the reviewers' points. - Barb Bryant
Examples of a good paper and bad paper... No time to do this... - Barb Bryant
Steven: Bear in mind that the reason we do science is to create new knowledge and contribute that to the body of scientific knowledge. You do that through your papers. So papers must be an effective conduit. - Barb Bryant
Steven: Ability to communicate is key. Most of us are not great writers. You need to figure out what works for you. Team writing can be very effective. Example: one student had to talk it through first. - Barb Bryant
Share it with colleagues before sending it out for review. - Barb Bryant
Make sure you make it easy for the reviewers. Example: when you make a revision, make it clear what you changed. - Barb Bryant
Figures. When people flip through a paper, they usually look at the figures first. You should invest major effort in getting the figures perfect. You might revise a figure 100 times. I have people in my lab take a course in the visual presentation of information. - Barb Bryant
Steven (still): it's important to make sure that you are right. If you have 10 papers and one has a major flaw, that can be devastating. - Barb Bryant
Surya Saha - just finished PhD and starting post-doc. Has these questions from first-time authors - Barb Bryant
(We are going into the second half of the workshop, with a panel of 7 people) - Barb Bryant
Surya: what happens inside the editorial process of a journal? - Barb Bryant
Nils Gehlenberg - student. Pros and cons for new authors of supporting alternative publishing and evaluation models. - Barb Bryant
Article metrics. At yesterday's future of scientific publishing - I can influence citing in blogs and social networking sites. Should I go out and market my papers? - Barb Bryant
What about publishing that are not papers - like data, or software tools? Will that look good on my resume? - Barb Bryant
Mark Gerstein (experienced author): Scientific publishing in the future. - Barb Bryant
We are seeing a distinction between databases and journals getting blurred. People are approaching reading like databases -- you query for an article. Also, people read database entries, e.g., to find out about gene function. - Barb Bryant
It's hard to fit everything into conventional journal articles or biological databases. Why are people citing SCOP so much (for example)? Are they *reading* it? Or is it associated with a piece of code or database that they're using? The latter, often. - Barb Bryant
People cite a paper not because they read it but because they saw an easy-to-read summary or someone cited it in a lecture that they saw. - Barb Bryant
Mark's view: We can update scientific publishing; make it more multi-tiered, more compatible with the digital world. I advocate a structured digital paper. It's not a single narrative, but a set of streams of information - some computer-readable and structured; one or more stream for the human reader. - Barb Bryant
You do this not as separate from the paper publishing, but as part of publishing the paper. - Barb Bryant
Structured abstract. Structured digital table. (Are examples) - Barb Bryant
Chris Sander speaks next. - Barb Bryant
We have a project: the Factoid Project. - Barb Bryant
Factoid Project: require authors to submit basic facts they've derived to a database. - Barb Bryant
Scientific publishing needs to be revolutionalized. - Barb Bryant
We need to take away power from reviewers and editors. - Barb Bryant
We should engage in marketing our papers (though prefer a different term) - Barb Bryant
We should change how papers are evaluated by potential employers and tenure committees and so on. - Barb Bryant
Talks about figures with (A), (B), (C), and having to find the letter in the caption. Figure captions are hard to read and understand. In Time Magazine, you won’t see those. Appeal: make figures an integrated information panel. Let’s put together a small working group; write up an opinion piece, send it to journals and ask for a change. I’ll help. - Barb Bryant
Chris proposes another working group about assessing a paper’s impact and the author’s contribution. - Barb Bryant
Chris: Doesn't like PLoS Computational Biology because of the goal of increasing the rejection rate to improve impact factor. Optimize scientific contribution not rejection rate. - Barb Bryant
Chris: How your papers get advertised. You can promote your own work. Don't just rely on the editors. Don't just rely on the reviewers. Don't rely on the paper coming out and someone maybe reading it and citing it. Coming here and doing posters. - Barb Bryant
Gary Benson: Professor at BU; editor at NAR. Edits web server issue, an annual special issue. - Barb Bryant
I like papers, says Gary. I like looking at figures. I like when people put a lot of effort into organizing their thoughts. I like it when people use examples in their papers. - Barb Bryant if you're interested to submit a paper. - Barb Bryant
In Comp Bio, people make predictions about something. It's easy to make predictions; it's not easy to validate them. At NAR, we have a strict policy that you have to show considerable evidence of validation, with data that was not used to develop the model you're presenting. - Barb Bryant
Pitfalls for journal submission. - Barb Bryant
Prior publication: Arxiv is an archive; that is not considered (by NAR) a citable publication, so it's OK - would not exclude your article for that reason. On the other hand, we saw a paper previously appearing in PLoS Currents -- and we do consider that a prior publication because cited in PubMed. - Barb Bryant
Conference submissions are prior publications in some cases. Conference proceedings can have fairly large papers, and are usually citable. - Barb Bryant
Open access: this is a journal's way to compete with online repositories. It's a way to make your paper free to everyone. All publishing should be like that - but it costs money. Authors have to pay usually, for open access. - Barb Bryant
The review process at NAR: Senior editor evaluates for meeting scope. Pass it on; next editor again considers scope. If that passes, then get reviewers. Authors are asked to suggest reviewers. If you propose reviewers, pick people who are not your friends but are knowledgeable in the area. - Barb Bryant
We pick 2 reviewers. You appreciate as an editor getting suggestions for reviewers. I usually respond positively to volunteer reviewers. - Barb Bryant
Reviews usually take 2 weeks at our journal. Some are good, some are not. You want more than a paragraph! Then the editors try to make a judgment based on those reviews. If there is disagreement the editors will seek a third review, and this can take additional time. The editor usually informs the author of this delay. - Barb Bryant
We try to have a 30-day turnaround time. Then if the reviews are positive, you get a chance to modify your paper, and our goal is 60 days. - Barb Bryant
Be non-confrontational in your letter responding to the reviewers that accompanies your revised manuscript. This is a dialogue between you and the reviewers, monitored by the editor. - Barb Bryant
End of Gary's introduction - Barb Bryant
Andrej Sali speaks next. - Barb Bryant
Presubmission inquiry - the editor is looking both at scope and at quality. It's important to put effort into this. - Barb Bryant
Suggested reviewer lists: I found through experience that it is difficult for authors to predict which reviewers will be fair or supportive, or negative. You may think someone is your friend, but they are not always your friend. Don't put too much attention onto who you think is your friend. - Barb Bryant
Phil will put his slides on the PLoS CB website; Andrej thinks that’s great, and he’ll be requiring people in his group to go through them. - Barb Bryant
Try to satisfy reviewers. Why not? Obviously, you want to do what you think is right scientifically, so do not compromise that. - Barb Bryant
Collect common wisdom within your lab about writing. In my (Andrej's) group: definitely start with written document on Day 1. Outline the manuscript before you start the project. Keep it up to date as the process goes on. Keep in mind the key idea - why should people read it? Summarize that in the title. No more than 2-3 sentences on the main message. - Barb Bryant
On to Alfonso Valencia, editor of Bioinformatics. - Barb Bryant
What to publish: your work. Where to publish: Bioinformatics, obviously. :-). When to publish: not before my holidays. - Barb Bryant
There is both opportunity and risk. Consider the music industry: the web has had a huge impact; musicians aren't sure how they are going to survive. Newspapers too - huge changes. - Barb Bryant
The web affects not only science reporting but science production. - Barb Bryant
People who have already built a solid scientific reputation can afford to try out and champion new modes of publishing. Young scientists have to be much more careful so as not to harm their career. - Barb Bryant
Not all papers are equal. Application notes are different than scientific papers are different than discovery notes. - Barb Bryant
It's more important to be able to build on a paper than to reproduce the paper. A good paper enables more research. - Barb Bryant
Publications are an essential instrument not only for knowledge distribution but also as a tool for organizational decision-making: evaluation of institutions, grants, fellowships, positions. - Barb Bryant
Before replacing impact factors, think: with what? - Barb Bryant
You don't have to do all that the referees/editors ask for, even if it means your paper gets rejected. Use your own scientific judgment. - Barb Bryant
Build on others' work. Quote them fairly and with respect. - Barb Bryant
Discuss your results in meetings and with colleagues before publishing. In bioinformatics, the risk of being scooped is minimal. The benefit of sharing and getting feedback is enormous. - Barb Bryant
bb, thanks for the comprehensive coverage! - Ruchira S. Datta
You're welcome! :-) - Barb Bryant from email
Thanks! - Mr. Gunn
A big thank you for the coverage bb - Yann Abraham
yes, just great, bb! - Claudia Koltzenburg
Daniel Mietchen
Today was a strategic day, it seems -
Today was a strategic day, it seems
In particular, I came across the Wellcome Trust's Strategic Plan 2010-20 and ICSU's Strategic Plan 2012-2017. Furthermore, as a follow-up to our previous conversations, Janet Haven from the Open Society Institute's Information Initiative sent me some supplementary questions in relation to their strategy (in which open science may or may not play a role, but it is now kind of short-listed as a potential major strategic element), on which I will briefly reflect here before passing on the ball to you. Finally, a major scientific society asked me for input about the likely advantages and drawbacks of allowing, as per default, all content of the scientific sessions of their conferences to be broadcast live in any medium, and whether it would be sensible to make this a standard requirement whenever they sign the contract with the organizers of an upcoming conference. - Daniel Mietchen
Still waiting for input on why scientific societies should allow broadcasting from their conferences. perhaps the most comprehensive coverage of related issues is at and but they do not really dissect the options from the perspective of a scientific society. - Daniel Mietchen
Some good questions here. When we wrote the articles mentioned above, we did it in conjunction with the ISCB, so we were thinking about scientific societies and how we could help them make their policies. In fact, we divided our suggestions into three lists in the first article above: guidelines for policy creation for organisers/societies; guidelines for policy creation wrt bloggers, and wrt the presenters. - Allyson Lister
However, what we deliberately didn't do was try to suggest what the policy should be for a given society or organising committee - just things to consider when making the policy, and tips for advertising that policy. IMHO if the conference is not meant to be private (i.e. invitation only), and is intended to disseminate information to a wide audience, then it behooves the society/organisers to have an open conference. - Allyson Lister
I would suggest that the societies recommend to conference organisers (if the conference is an open one anyway) that the conference follows the "Guidelines for Organizers" section, and implement a policy which encourages live blogging. You could even record audio or video, if there is that ability. ISCB and the conference organisers were very, very helpful to bloggers. They advertised the FF room and Twitter tags ahead of time, gave out power sockets, and asked us if there was anything they could do to help - Allyson Lister
Simply having signs up in the lecture halls and having notices up on the conference website stating explicitly what is and is not allowed would be very beneficial for all concerned. Choosing whether or not to give the presenters the freedom to modify those default rules (to be either more or less restrictive) on a talk-by-talk basis would also be useful information. - Allyson Lister
Thanks for chiming in, Allyson, and I agree with all your comments. However, as pointed out above, the guidelines for organizers are mainly on how to communicate a decision, not how to reach it. So I guess I will have to phrase out your "Conferences that highlight published material would be more likely to encourage live blogging, while those covering unpublished results would be less likely to favor such efforts." - Daniel Mietchen
Yes, I think that's right. Filling out that part would be best. Some reasons for being open would include: 1) Internet-based communication is central to today's science, and societies should embrace it rather than try to legislate against it... - Allyson Lister
2) "With the advent of live blogging, all conference attendees can become reporters who collect, prepare, and distribute information or related commentary about current events. When presenters are using their talks as a method of publicizing their data, such reporting complements their intentions. Live blogging allows scientists and journalists to have a shared purpose, and as such they should abide by a shared conference reporting policy." - Allyson Lister
3) "In the end, live blogging does not change what information is broadcast from a conference, merely how fast it is propagated." 4) "Organizers and scientists alike gain from embracing social networking applications, which now support an unprecedented timeliness and level of visibility for both social aspects of the conference and the knowledge presented there. Conferences where information is intended to be public should embrace this timeliness as an amplifier." - Allyson Lister
Bora: On organizing and/or participating in a Conference in the age of Twitter - - Daniel Mietchen
Good link, Daniel - thanks! - Allyson Lister
See also on the future of conferences as we know them, and on blogging archaeology. - Daniel Mietchen
I used to play Syogi many times and played computer syogi 東大将棋, Bonanza .this scene suggest that this picture check. - Ami Iida
Please play with Syogi free soft bonanza chess. 6-stage power of this software is amateur. - Ami Iida
I was actually surprised to find out at the end of an invitation-only conference that people (at least the ones I talked to) would have been fine with blogging (which I hadn't done). Apparently there are other reasons for invitation-only conferences than sharing unpublished results that one doesn't want widely circulated. - Ruchira S. Datta
Daniel, as Allyson has mentioned we tried to lay out the issues but didn't explicitly advocate an opinion taking one side. Here we were advocating clear guidelines--I think everyone benefits from knowing clearly as soon as possible what the guidelines are, whatever they may be. - Ruchira S. Datta
I think some people may be afraid of openness because it's not what they're used to or how things have always been done. So encouraging them to think things through explicitly may indirectly lead to more openness. - Ruchira S. Datta
@ Ami - I was trying to play Shogi while in Japan, but there were two problems: (1) As a foreign student, I had to live in a 留学生会館 where, naturally, basically nobody was familiar with the game, (2) none of the Japanese students I asked at university were interested in the game, and the few of my colleagues in the lab who visibly offered themselves some leisure invariably preferred... more... - Daniel Mietchen
@ Ruchira - I agree that some gentle guidance towards thinking those problems through is helpful. But it is not enough. For instance, at the conference that I am attending right now, they have a Twitter stream (cf. ) but despite 3400 attendees, there have been less than 200 tweets in six days so far (including those from the various pre-conferences and... more... - Daniel Mietchen
Have you ever played "Go"? I think Go is an attractive game than Syougi.(囲碁は本将棋よりも強烈に面白い) - Ami Iida
囲碁は二十年前にちょっと遊びました。でも将棋がもっと好きです。 - Daniel Mietchen
Garret McMahon
Omega-3 lesson: Not so much brain boost as fishy research | Comment is free | -
Omega-3 lesson: Not so much brain boost as fishy research | Comment is free |
Shirley Wu
Ms. Humble, science cookie chef extraordinaire -
Pierre Lindenbaum
Rt @affordanceinfo 33% of scientists are now using blogs for writing, reading or as a lab notebook #Idontbelieveit
That can't be right - any links to the full details of the study claiming a third of scientists are using blogs? - Jean-Claude Bradley
Astonishing figure, I agree. Not my experience. - Bora Zivkovic
Much too high number, IMHO. - Björn Brembs
It does say 'reading'. 33% of scientists reading blogs is plausible. - Pedro Beltrao from Android
From my interactions I find it hard to accept that 33% of scientists even read blogs - we would have to see how the population was selected - Jean-Claude Bradley
Maybe it's estimated by (total number of blogs written or read by scientists) / (total number of scientists) ..... :) - Steve Koch
If it is based on percentages of scientists who RESPONDED to an online survey it would be skewed. Those who ignored the online survey are not likely to read blogs - Jean-Claude Bradley
that % seems way too high to me too. When I tried to search for this online for a project I couldn't find that many. - Elizabeth Brown
The percentage might include those reading non-scientific blogs? E.g., "have you ever read a blog-post?" - Ruchira S. Datta
What everyone else said. I'd be astonished if the real figure is > 5%. - Bill Hooker
That number sounds about right Bill. Too bad there isn't a link to the details of the study. - Jean-Claude Bradley
Martin Fenner
Can you tweet from Cold Spring Harbor Laboratory meetings? « Embargo Watch -
While I would say it should be up to the researcher to state up front if he doesn't want people talking about his presentation, I can respect that some in their audience might not even have known what twitter was. It's certainly better than trying to ban twitter entirely. - Mr. Gunn
I find the bit at the bottom odd. How is saying you've submitted something, whether or not you name the journal, invoke the Ingelfinger rule? If you've said what you were going to say, then its out there already surely? Whether you've submitted it somewhere is immaterial. I've seen dozens of talks with references to papers "in press" or "submitted" to various journals. The latter always seems like trying a bit hard to me... - Cameron Neylon
Part of the issue that many scientists don't realise is that once they are presenting in a conference, the data is essentially in the semi public domain. Personally, I use common sense and don't tweet unpublished data, but some of the hysteria around Twitter is bemusing. - Sally Church
I think CSHL was just trying to make an issue of it, really, by asking everyone for permission, and probably expected a much higher rate of NOs than they got. That said, they do seem to be trying to be reasonable about it, and that's better than the previous "Ban it all" attitude they had. - Mr. Gunn
Agreed, I think CSHL have taken a very reasonable position that makes sense. There are some issues around the distinction between professional and non-professional reporting but if that's a way of squaring the circle for the moment it's a reasonable approach. - Cameron Neylon
I think that last year Twitter has taken the CSHL Biology of Genomes meeting by surprise, and this year's policy is a step forward. 2011 might again be different. I'm looking forward to the ASCO meeting in two weeks. Last year the number of Twitter users and tweets was very, very low considering that more than 30.000 people attended. - Martin Fenner
Martin Fenner
Announcing Science Online London 2010: We are delighted to announce that Nature Network, Mendeley, and the British Library will host Science Online London 2010 on 3-4 September (Fri/Sat) 2010. The event will take place at the British Library.
The conference organising committee comprises Victor Henning (Mendeley), Matt Brown and Lou Woodley (Nature Publishing Group), Sarah Kemmitt (British Library), Richard P. Grant (Faculty of 1000) and Martin Fenner (Hannover Medical School). - Martin Fenner
In the next few days you should find more info at the official webpage ( and Nature Network forum ( The registration page and Wiki for session suggestions will come a little bit later. Unfortunately we will have to charge £50 for registration, as the costs for hosting the event have more than doubled because of the extra day and the larger venue (we expect 250 people instead of 150 people the last two years). - Martin Fenner
You can suggest sessions for Science Online London here, in the Nature Network forum or by sending email to We will set up a session wiki in the coming weeks. Some people have already suggested sessions, we will also put them in the wiki. - Martin Fenner
@Martin, really looking forward to this year's event. This is maybe a bit off-topic for a session idea, but perhaps something on change management from an expert in the field would help with selling the idea of online science to others who just don't get it yet? ( I'm just thinking back to the session on legal aspects of blogging last year which I think was in a similar vein. - Dan Hagon
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