Scope, Completeness, and Accuracy of Drug Information in Wikipedia -- Clauson et al. 42 (12): 1814 -- The Annals of Pharmacotherapy - http://www.theannals.com/cgi...
"OBJECTIVE: To compare the scope, completeness, and accuracy of drug information in Wikipedia with that of a free, online, traditionally edited database (Medscape Drug Reference [MDR])."
- Michael Nielsen
Growth graph for the longest published synthetic DNA: http://bit.ly/5oaEE Doubles roughly once every two years, with some weaving around. Includes references.
- Michael Nielsen
"“… the National Archives’ technology branch is so antiquated that it cannot process some of the most common software programs. Specifically, the study states, the archives “is still unable to accept Microsoft Word documents and PowerPoint slides.” I would like to think this is because those formats are proprietary and saving them actually has all kinds of sticky legal and versioning issues… But it does beg the question, if they are not ingesting Powerpoint and Word files, what are they ingesting?"
- Michael Nielsen
Does anyone have any experience with SocialVibe? "With the SocialVibe widget, bloggers can donate real money to their charities without the need to dip into their own pockets. Instead, the money is generated from brand advertisers that the bloggers self-select as the sponsor (e.g. Showtime, Sprint, Colgate, Kraft Foods, etc.). To be more specific, once bloggers install the SocialVibe sidebar widget on their Wordpress blog, money will be earned for charities every time readers engage with the widget (e.g. rating a Showtime video clip). Bloggers can switch their cause and sponsor as often as they like, and receive regular updates from their charity about goal progress and impact."
- Michael Nielsen
Here's an example of the new identity service used to track authors on the arXiv. Has both a html and RSS version, so you track the feeds of individual authors. Coverage is incomplete - for my account it's about 2/3 - but authors can claim their papers.
- Michael Nielsen
I really like the idea of aggregating the RSS streams of all your favourite authors.
- Michael Nielsen
Bah, as if I can find all of my passwords for my papers from grad student days. Doh! (edit: hm, should have put this on the other thread)
- Dave Bacon
I think I've still got all mine (yay hard disk space). Fishing them out and entering them would take a while, though. But for some papers I never received any.
- Michael Nielsen
Surely there is some way of claiming ownership of papers for which you no longer have the passwords. Perhaps by contacting someone at the arXiv?
- Matt Leifer
BTW, something really needs to be done about "lazy" arXiv authors who get other people to do all their uploads. I know several people like this and they are never going to bother with claiming their papers.
- Matt Leifer
Sarah - Hadn't seen it (probably because it doesn't cover quant-ph). But it looks really interesting. Have you used it?
- Michael Nielsen
arXiv sorter is astro-ph and cond-mat only, so is unlikely to appeal to us (current and former) quant-ph types.
- Matt Leifer
Matt - If it becomes widely used, people will claim their papers, simply to avoid being invisible (same reason many people upload to the arXiv at all). Usual chicken-and-egg situation.
- Michael Nielsen
Useful for the like of me, too, especially with an RSS feed. It's darn hard to get papers-by-author out of arXiv now.
- D0r0th34
Yes, it makes widgets that list papers by author a lot easier to write. On the downside it means that I have a couple of widgets to rewrite.
- Matt Leifer
Interesting: "Arxivsorter uses the network of co-authorship [on the preprint arXiv] to estimate a proximity between people. It then ranks a list of publications using a friends-of-friends algorithm. "
- Michael Nielsen
"It is a long-term goal of arXiv to accurately identify and disambiguate all authors of all articles in arXiv. Such identification would provide accurate results for queries such as "show me all the other papers by the particular John Smith that wrote this paper", something that can be done only approximately with text-based searches. It would also permit construction of an author-article graph which is useful for relevance assessment and bibliometric analysis."
- Michael Nielsen
I seem to recall you could only get a noisy list of your papers from arXiv. Does this help any?
- Seb Paquet
Looks like it helps a lot. My next delicious link shows an example... should come through to FF shortly.
- Michael Nielsen
Main immediate problem seems to be that it's incomplete. 38 papers listed; I think I have 50-60 at the arXiv. Claiming them looks like it might be quite tedious, and potentially involve a lot of emailing coauthors. You need to establish you actually are an author, which means you need some of the identifying data initially sent by the arxiv when uploading the papers. For some of my papers I don't have that; my coauthors do.
- Michael Nielsen
Seems that it's mostly older papers missing. For people who started using arXiv after 1998, looks like the listing might be fairly complete.
- Michael Nielsen
Great discussion of climate change from Gavin Schmidt (more in-depth than standard media fare) - http://edge.org/3rd_cul...
Very interesting discussion of climate change, from Gavin Schmidt.
- Michael Nielsen
Having just read this in great detail (and reread parts of it), let me very highly recommend this article. It has some comments in it that are very interesting from an open science perspective, but that's almost incidental compared to the meat of the article.
- Michael Nielsen
Issued 2009-07-01: "GM management has noticed the continuing high trading volume in GM's common stock at prices in excess of $1. GM management continues to remind investors of its strong belief that there will be no value for the common stockholders in the bankruptcy liquidation process, even under the most optimistic of scenarios. Stockholders of a company in chapter 11 generally receive value only if all claims of the company's secured and unsecured creditors are fully satisfied. In this case, GM management strongly believes all such claims will not be fully satisfied, leading to its conclusion that GM common stock will have no value. "
- Michael Nielsen
"the Smyth Report [on the development of the US atomic bomb] stressed that scientific information should be released to the public not because its creation had been funded by taxpayers, but because it would enable them to make informed decisions about how the science should be used. "
- Michael Nielsen
I've only fooled around with it on test files, but am considering using it for a large project. Anybody have any major gotchas to report? Or does it work well?
- Michael Nielsen
I really like it. I use it almost exclusively for word processing, although I haven't used it for a large project yet. Detailed formatting can be a bit wonky and largish files can be slow to load. The sharing and collaborative features also work very well.
- John Dupuis
Thanks, John. How large can the files get before you start to notice the speed?
- Michael Nielsen
Search the web? Oh right, I see what you mean :) I like it a lot, my colleagues at work hate it. One of their issues is lack of features - especially citation/bibliography - as compared with their word processors. Their other issues are too numerous and depressing to mention :)
- Neil Saunders
Install Gears so you can have offline access too.
- Paulo Nuin
Neil: heh. (And thanks for the comments, they're very helpful!) The spectrum of opinions on Docs online seems to range from utter hatred to thinking Docs is the greatest invention in the history of humanity. Tough work slogging through that.
- Michael Nielsen
Paulo - Thanks for the suggestion. I'll hold off a bit, and try it out online first, to see what I think, and then install Gears if it works well. I must admit I'd be happier having local control over my data.
- Michael Nielsen
I am using for grant writing and people are liking it. Of course it lacks a lot of features but it can be a good start for collaborative work.
- Paulo Nuin
Michael, I've only seen it be slow on large spreadsheets -- maybe several hundred rows. As for lack of feature, yeah, it's pretty minimalistic that way. However, they did just add a bare-bones footnote feature which I haven't had a chance to play with yet.
- John Dupuis
Very nice to get an initial draft of a multi-person paper or grant going - in the end it needs to go out to Word to get formating etc correct. If only they could include bib mgmt via Google
- Rajarshi Guha
On the feature issue: I'm happy enough (for now) with a pretty minimal feature set. My testing shows it's got most of what I need, although the lack of bibliography management will be a bit of a pain. I'll give it a real go.
- Michael Nielsen
Thankyou, everyone, for the feedback. I put this up 28 minutes (!) ago, figuring I'd go to bed, and with luck a few people would comment by morning. Little did I know :-) So thankyou all - I'm going to head off to bed in a few minutes, but if anyone has more comments, I'll read and reply in the morning. Cheers!
- Michael Nielsen
Agree with Rajarshi. It works really well for collaborative drafts. As you approach the final version, you need to go to a local copy to clean it up and format. The problem I have is that my peers (at work) can't get past the unfamiliarity, need to sign up, login, learn something new etc. etc. to see the collaborative benefits.
- Neil Saunders
Like said above, very useful to collaborate with, my wife and I organized our wedding basically using google docs. Only downside is when you need proper formatting for printing. If you are happy with rough formatting, that's fine, but precision printing (like address labels) is very hard, much better to export to word or excel.
- Nick Boucart
agree with what everyone else has said. Just to add it seems to scale well to large numbers of authors in a way that wikis do not - at least with simultaneous editing. In my experience tech phobic people prefer it to wikis but formatting has to be done elsewhere. Bibliography is a major weakness
- Cameron Neylon
via fftogo
I've only used it for small things where I want my doc in the cloud.
- Richard Akerman
Thanks for all the extra comments, especially the comments on how it compares to wikis, and the limitations with formatting.
- Michael Nielsen
Kambiz - That's a really interesting idea, which I may play with. How well do you find it works with large documents?
- Michael Nielsen
Spreadsheets are nice but not for massive datasets - the formatting issue for the text docs is annoying and puzzling as to why it hasn't been solved - also strange that GoogleDocs don't tend to show up on Google searches
- Jean-Claude Bradley
using Gdocs last 2 years, can't live without it today, amazing tool, but Presentations part still bad tho
- Alexey
I've only used the forms part to develop a survey. The forms feature is extremely limited. No edit after submission, no complex field types, no skinning, editing the form rearranges fields etc. But it does have nice features for doing stuff with the data once collected, so it's a tradeoff.
- Todd Hoff
I have been using it to draft papers, and bibliography works fine if you use BibTeX and have different documents for the .tex and the .bib files. Problem for some collaborators (and for chasing bugs introduced by them): TeX syntax highlighting is not available, and compiling has to be done offline.
- Daniel Mietchen
I have a comment on the presentation module -- I first used it about a year ago for a fairly important presentation that I was collaborating on with someone from the other side of the continent. The collaborative parts worked very well, but the presentation module itself was barely adequate for even a simple presentation. They have improved it quite a bit since then including being able to export to PowerPoint format.
- John Dupuis
I have used to collaborate on draft documents. It works much better than emailing around a copy of a document to different authors. The problem is usually more getting other people to use it. The spreadsheets are not useful enough for what I need. The presentations app is nice but so far I use it mostly to hold backup copies of presentations in case all else fails.
- Pedro Beltrao
John - Does the presentation module support basic animations? I'd be pretty tempted to try a collaborative presentation, which I've never done before.
- Michael Nielsen
Thanks for the pointer, Graham. I've got about a thousand unread blogposts in Google Reader, and I guess yours is in that batch...
- Michael Nielsen
I have used Google Docs and Google Spreadsheets for a large collaboration on a book, with five authors. The book was done in LaTeX with BibTeX, so compiling the files had to be done on a local machine. However, the ease of simultaneous editing by many people was very useful. Also very useful for us was the addition of the "upload-and-share--PDF" feature to Google Docs, which happened near the end of our project. I used this feature to upload the compiled document to share with all coauthors.
- Dimitrios Diamantaras
Google Docs is a better notepad than Yahoo Notepad, plus is helpful in data spreadsheets that go everywhere.
- Mike Reynolds
Dimitrios - it's very helpful to know it can be used for a very large project like that.
- Michael Nielsen
More: we also used Google Spreadsheets to do a collaborative proofreading exercise, for which Spreadsheets was fine. I can suggest zoho.com as an alternative, with even more features, such as a graphical front-end for equations, which then runs LaTeX on the server that makes a beautiful equation graphic. It is a graphic, though, and its alignment with text presents problems. I have not checked out bib management on Google Docs or Zoho, as I don't need it.
- Dimitrios Diamantaras
They did just implement something called "incremental reveal" but AFAIK nothing beyond that.
- John Dupuis
Yet one more note: we also used a wiki in the early stages of the project, and kept using it for activity updates. However, had we started on Google Docs from the beginning, there would have been little reason to use a wiki.
- Dimitrios Diamantaras
Oh yes, if you post a PDF file with more than 100 pages, Google Docs will only display the first 100. However, if you share it, those you share it with will be able to download the whole file.
- Dimitrios Diamantaras
Very irritating. I use it mainly because I have no better option. Printing is a poorly-integrated joke, I can't get the stupid thing to write in one font, and Google Gears never quite works right with it.
- i80and
I see Google Docs as a gateway drug to wikis. I felt the word processor starting to slow down around 10k words. My main beef with it is that while my kids use it routinely, several of my colleagues apparently can't figure it out. But I've used it successfully with several clueful collaborators. The Table of Contents feature rulez.
- Seb Paquet
For small informal text docs it seems to work reasonably well. There's a limit on the length / size of individual documents, which can be a pain if you're writing something big. 'help' tells you the details. Also, if you export to WORD you get a bunch of embedded styles that are tricky to get rid of. Collaborative editing of spreadsheets whilst on the phone trying to agree budget details for proposals works effectively.
- hardisty
I rather like the non-fancy look of simple programs like this. If I can only write in arial with minimal formatting, I tend to focus on what I'm saying more than if I have formatted the text to look fancy. Once colleagues and I are happy with the words, then export to Word and prettify. Used it to write the main text of several grant apps in recent months, including Bjoern's. Insertion of pictures is the only annoying thing that came up - has to be of specific formats and small-ish.
- Matthew Todd
I've found it easier to move the docs to Word by exporting to RTF. Etherpad.com has to be mentioned in this thread; it's useful for people who want up-to-the-second sync between editors.
- Seb Paquet
I use GDocs quite a bit. As Pedro said it's great to do collaborative work but usually that hard part is getting the collaborators on board with the idea. The spreadsheets are OK, but anything a little more complex and it becomes a bit of an ordeal to work with. Specially with very large and complex spreadsheets that pan over multiple sheets. Although I love the graphs :-)
- Ricardo Vidal
Spreadsheet features are useful when pulling XML or CSV data from other websites, and for making the results easily accessible online in multiple formats. Performance suffers relative to standalone programs, although FF 3.5 and Chrome help a bit.
- Mike Chelen
I use Docs as my lab notebook. Of course, I also back up all my docs to my hard drive with a nightly script. As I've said before, use the cloud, love the cloud, just don't trust the cloud.
- Chris Miller
I like Google Docs mainly because of the integration with Gmail. I use it for reading Microsoft Word .doc email attachments. Reading in Google docs is just one click away and is much simpler than downloading the attachment. As a Mac user with no Microsoft products installed it is a godsend, as I no longer have to send annoying emails to people reminding them to send .rtf, .pdf or plain...
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- Matt Leifer
Same here, Matt, though I write collaborative TeX documents in Google Docs, too.
- Daniel Mietchen
Tim O'Reilly: "I'm effectively selecting, noticing and then trying to use the platform that I have built to amplify the wisdom and the knowledge of the people in my community. "
- Michael Nielsen
Interesting comment from Andy McGregor about UK funding for new technologies in higher eduction, thought it might be of interest to many here. Here's an excerpt: "I work for an agency in the UK called JISC (http://www.jisc.ac.uk) that is set up to support education and research in higher education by promoting innovation in new technologies. We fund a lot of innovation projects in the area of scholarly communication, and it struck me reading the post how much of the work we are funding relates to the points you make in your article We have funded 40 rapid innovation projects these are short agile projects that have just started and are designed to experiment and try out solutions to user problems, similar to start ups you mention in your post. A couple which sprang to mind as I read your post and are worth mentioning are a way to manage and publish data sets which uses a notecard metaphor: http://www.jisc.ac.uk/whatwed... and a way to use bayesian filtering...
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- Michael Nielsen
via Bookmarklet
JISC is one of the most innovative funders in this space in the UK (or indeed internationally). I dislike the way and the mode in which they fund (very short notice calls, far too little money) but nonetheless they have imagination an actually act on it in a way that other UK research councils rarely do. I have the usual sour grapes from not getting things which I thought were important funded obviously but even so the idea of the Rapid Innovation call was very cool.
- Cameron Neylon
tends to be limited to around £50k which isn't enough to employ a new person. Which means in turn that if you don't have local staff on rolling contracts that you can bring up then you can't play. Have been a couple of exceptions recently, but that was no good because they gave the money to something else. It can be a very difficult game to break into from the outside of the existing community.
- Cameron Neylon
I wonder if you could talk with JISC about using the 50k to start spinoffs? YCombinator (Reddit, Backtype,Scribd and loads of other companies) typically starts companies with about 15k US, for 5-10% equity. The result is fantastically talented and motivated developers, with real ownership over the project (and thus determination to make it work). Of course, the money doesn't last long, but it's long enough to see if there's a there there, so to speak, and to attract further money.
- Michael Nielsen
Perhaps, although startups isn't really their remit. They are more focused on infrastructure for higher education so projects often have to use pieces of previously funded services. Thinking more and more that the only way to get those kind of things started is to get right out of the academic sector.
- Cameron Neylon
Extremely interesting article, Michael. Three thoughts: 1) You mention poor execution - this is important. There can be a communication breakdown between programmers and scientists - scientists are generally not tech-savvy and don't understand the tools being provided for them, and may be unwilling to spend time designing tools when they should be doing something else. There needs to be...
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- Matthew Todd
"If a person inside an industry needs to frequently explain why it’s not dead, they’re almost certainly wrong."
- Jodi Schneider
Mattew - on point 1, absolutely. On point 2, it's a really interesting question. I think you can break it up into two parts. There's the immediate economic question: in our society, with our current legal and governmental setup, what's going to happen to the news? That's a purely factual question, devoid of values, and it's the question my essay addresses. But there's a normative...
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- Michael Nielsen
It certainly looks little different in life sciences, where dynamics of the change is mainly directed by funding bodies (and their requirements to publish in Nature instead of PLoS One), not technological advancement. For that reason I'm also not sure how examples from media industry can be applied to science - if NYT editors were NIH grant reviewers, TechCrunch at some point would stop getting grants, right? So, any news whether and how science funding industry is about to be disrupted? :)
- Pawel Szczesny
Great essay! One comment: I don't think there is a general feeling that companies fail _because_ they are evil. There may be a feeling that companies _are evil while they fail_. Most people can see that OpenAccess is globally much better for science and society. But the local business decisions of Toll Access companies are at odds with the global good. That alone is bad. And TA companies then try to delay their decline with dishonest PR campaigns like PRISM that is even worse. Right?
- Anders Norgaard
Agree it's a great essay. You didn't mention anything about publications semantically linked to the primary data, workflows, evidence they are based on. This seems to be an area attracting lots of interest in several disciplines.
- hardisty
"Regardless of the final outcome, the biggest lesson for ML [Machine Learning] from the Netflix contest has been the formidable performance edge of ensemble methods."
- Michael Nielsen
"One of the things that particularly makes me feel incompetent is my lack of knowledge of scientific literature, and (to a greater extent?) my lack of enthusiasm for reading it. I don't know why, and I give myself grief for this, but I often find reading scientific papers just plain boring. The funny thing is, I really appreciate science, by which I mean the technique of elucidating one's knowledge of the world through rigorous, reproducible means, and keeping a skeptical mindset, especially when it comes to one's own work. Likewise, I will never cease to find biology or computational technology among the most satisfactory pursuits for the very limited time and energy I have here on this good Earth. Yes, science, itself, is awesome, but the excitement of it gets stripped away in a lot of formal education environments, and for me, in the way scientists present it in their formal literature."
- Michael Nielsen
"The Stack Overflow Knowledge Exchange Platform Designed by Jeff Atwood and Joel Spolsky, Stack Overflow has rapidly become the best place for programmers to get answers to technical questions. Now there's a way to get the same kind of site for your audience. Bird calls? Stamp collecting? It's up to you The idea of a knowledge exchange, running the same software as Stack Overflow, can be applied to just about any subject matter. With StackExchange™, you can run a site with all the same features that made Stack Overflow successful. Customizable look and feel StackExchange allows you to override style sheets, choose color schemes, and provide your own logo. You can use a stackexchange.com URL (for example, philately.stackexchange.com) or your own top-level domain. You can also insert arbitrary HTML into the parts of the page where stackoverflow.com would display advertising."
- Michael Nielsen
I've only just come across the Stack Overflow podcast recently.. this has been mentioned a few times since then. I like the way they are opening up not just the platform but the data too...
- Daniel Swan
Wow. So shall we try SO for scientists?
- Michael Kuhn
But SO works because it's a site for IT geeks. I don't think it would work for science. What would you ask here ? A bibliographic reference ? Some help with a protocol ?...
- Pierre
I would ask the same kind of questions we are asking and answering now in the life scientists room.
- Michael Kuhn
@michael But most of the time, we don't ask any question here :-)
- Pierre
@Pierre -- we have had a few cases though, and people have got really good useful answers. My own example: http://friendfeed.com/billhoo.... Perhaps it's just a matter of FF'ers slowly developing the habit of bringing questions here?
- Bill Hooker
It would work for chemistry if there were a quick, intuitive way to share a) data b) pictures and c) video along with posts on SO. If there's any kind of barrier to that, people won't bother. Sharing code is so easy in comparison. I guess also that a chemical lab is quite a social place - lots of people around you you can ask first. Don't programmers often work in physical isolation, where their collaborators are online?
- Matthew Todd
I think it is hard to predict if scientist in general would accept it as a tool - if the critical mass of a certain scientific community accepts it it might become a useful resource for them. Another direction: It could be useful for teaching - students ask certain questions that are answered by others.
- Konrad Förstner
@Pierre - thanks for the hint - but I guess there are many different ways of approaching the online teaching aspect like there are many ways of dealing with programming related topics. Maybe I haven't found the SO like functionality in Scitable but what make SO so attractive to me is its simplicity and pure focus on "I have a question - who has the best answer?".
- Konrad Förstner
"For seven months, The New York Times managed to keep out of the news the fact that one of its reporters, David Rohde, had been kidnapped by the Taliban. But that was pretty straightforward compared with keeping it off Wikipedia. Times executives believed that publicity would raise Mr. Rohde’s value to his captors as a bargaining chip and reduce his chance of survival. Persuading another publication or a broadcaster not to report the kidnapping usually meant just a phone call from one editor to another, said Bill Keller, executive editor of The Times. But Wikipedia, which operates under the philosophy that anyone can be an editor, and that all information should be public, is a vastly different world. "
- Michael Nielsen