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Carl Boettiger › Likes

Cameron Neylon
Faculty of 1000 strikes a blow against the Ingelfinger Rule - http://embargowatch.wordpress.com/2011...
Maybe we need a run of "Give the finger to Ingelfinger" t-shirts? - Cameron Neylon from Android
With a list of journals to name and shame on the back? - Cameron Neylon
agreed, awesome :) - Heather Piwowar
It has always bugged me that JAMIA follows the Ingelfinger rule. You have Informatics in title! Be about maximizing use of information! - Heather Piwowar
@Graham: I get 403 errors... - Björn Brembs
hahahahaha, these are great - Meg VMeg
Love it, looking forward to seeing these on Camden Market. Actually, it's not just an issue with posters/abstracts, as some of the journals seem to have very similar policies regarding pre-publication release of data and pdb structures. Policies regarding data doi's are not clear yet, but Cell (Elsevier) recently told us if data released in this way represents a significant contribution to the importance of a related article, then access to it should be embargoed until the article is published. - Scott Edmunds
re: zazzle, I won't use a commercial site that *requires* me to sign in just to see their products. - Bill Hooker
And the flickr picture is Ingelfinger giving the viewer the finger. The hand should be the other way around, surely? - Bill Hooker
Ross Mounce
yay! I've made it 2 the shortlist 4 a Panton Fellowship. Now i've got to make a 3min video on #OpenData | Time to unleash my creative skillz
Andrés G. Saravia
Hello, I'm starting a blog about my research as a Physics PhD student. It's brand new and lacks a lot of things but I will keep making it better in the spirit of open science.. Any comments and/or suggestions would be very appreciated. http://notebook.andresgsaravia.com.mx
Congratulations! And major props for you taking leap to open science, love it! - Steve Koch from Android
I added the notebook to the wikipedia article http://en.wikipedia.org/wiki... - Steve Koch
However, I note that the list is quite out of date, and it seems impossible to make / keep up to date. Wikipedia editors (e.g. Jean-Claude): what to do? - Steve Koch
If people start using J-C's ONS logos (http://onsclaims.wikispaces.com/), surely we could auto-generate a list. Initially it would be small enough that we could hand-curate (plus we'd all want to go look at every new site using the logo). - Bill Hooker
Thanks Steve I really appreciate it. And Bill I like the ONS logos and the idea behind them, I didn't know them but I have now one on my site :) - Andrés G. Saravia
I sent Andy and Anthony a note to add the in their new notebooks. Thanks for reminding us and great idea! - Steve Koch from Android
And btw Andrés, I love the set up of your notebook. The logo fits in great too - Steve Koch from Android
Congratulations, Andrés - you are certainly off for a good start. One thing I am missing in such blog-based notebooks is the version history. Anyone know of an example that actually has it public? - Daniel Mietchen
That's a really good point, Daniel. I literally forgot about that issue when Anthony switched from OWW to Wordpress. You wordpress guys know the answer? Versioning is very important for ONS! - Steve Koch
Its not straightforward in Wordpress to do versioning. I think KnowledgeBlogs achieves this by doing something complex like having a page for each version and a post for the most recent or something along those lines? there are a bunch of cludges basically but its not a native aspect of WP and that is a problem... - Cameron Neylon
Wouldn't it be possible to put the Wordpress installation into a GitHub repository and have each post, comment, edit or moderation trigger an auto-commit? - Daniel Mietchen
Sounds like a good idea to me, Daniel. But I don't have the experience to know. Anyone expert w/github to comment? - Steve Koch from Android
I guess that could work in principle but I'd have no idea about how to go about setting it up on a live server. It also doesn't really solve the central problem of how to make those versions accessible to the casual web viewer. Actually it also occurs to me that the WP content is in a database anyway so its probably not really visible to git in any useful form. - Cameron Neylon
Wordpress post-revision display is a simple solution: http://wordpress.org/extend... (OKF recommends I believe). I think Cameron is correct, you'd have to git-manage cached pages instead (or if making edits in an external editor, you could commit those to git & share them on github where a non-git user could easily review the history, but not an elegant solution). Re: ONS logos, nice discussion here: http://andymaloney.wordpress.com/2011... - Carl Boettiger
Steve Koch
Dear Open Science Friends -- I am going up for tenure this semester at the University of New Mexico, Dept. Physics. External letters are one of the most important components of my dossier. I am thinking that a co-signed letter from friends I've met in the Open Science community would be highly valued by those people evaluating my tenure case.
I am hoping that some of you would be willing to draft and co-sign a letter of support to be sent to my tenure committe--if so, I would be deeply grateful. Based on e-interactions with me, and in-person at ScienceOnline2010/2011 and ScienceCommons 2010 (Seattle), I think maybe some of you would have positive things to say about my research (I consider our lab's work in open notebook science, open data, etc. to be research) and service (promoting open science being external service). - Steve Koch
The committee wants to see specifically: "..evaluation of the quality, importance, and impact of his research and scholarship, and, if possible, a comparison with other physicists at similar stages in their academic careers." and "...Any comments you wish to make based on your knowledge of his teaching, interaction with students, mentorship, and service will also be appreciated." - Steve Koch
The standard method in our department is to mail letter requests to specific individuals, and to request hard copy signed letters. I've been thinking about this, and while I could ask one of you individually, it seems to me more appropriate, more powerful, and more fun to seek a co-signed letter. This has the risk of the various evaluation committees ignoring the letter, though. One... more... - Steve Koch
If anyone has better ideas, or knows of earlier examples of this from other universities, please post on here, or email me at stevekochscience@gmail.com - Steve Koch
I am really grateful for the years of support I've received from many of you open science supporters in my early career. I know I've been super-lucky to even land the tenure-track job and have always known that. I know that tenure would be a huge gift that is not something I deserve or am entitled to. Instead, I look at it as part of the way things work now, and being awarded tenure... more... - Steve Koch
So what am I asking? Without better ideas for how to do this: I am asking for people in the "open science" community who feel they are familiar with some of my lab's open science or my teaching of open science to state a willingness to be a co-signer of a tenure support letter. Then I am asking that group of people to nominate one person to provide the official letterhead and sign (with... more... - Steve Koch
They are looking at October 1 for deadline. Thank you thank you all! And like I said suggestions for a better process are welcomed! - Steve Koch
Do biologists qualify? If so, count me in. - Pawel Szczesny
@Pawel, absolutely! And Thank you! Everyone counts--all fields of academia (people that come to mind immediately are biology, neuroscience, physics, chemistry, library science), industry, and even those who may not currently have a paid position, but are active open science supporters. - Steve Koch
Count me in, natch. Regarding process: I think you are right to want individual letters from "high status" folks, to stay in the comfort zone of your committee. I suggest that the individual letters be different from the co-signed letter, which is a great idea and could be mentioned in the individual letters as "an instance of the wide web of collaborative opportunity opened up by Dr... more... - Bill Hooker
I'm in. - John Dupuis
Do you have any ppt or whatever of your scio10 or scio11 presentations handy? Was there a recording? I'd be happy to do up a short letter and certainly to cosign a joint letter. - John Dupuis
I'm in. I've served on tenure case and appointments-and-promotions committees, so I suspect a group-signed letter won't have as much weight as individual letters from as high up the academic feeding chain as you can go. Send me out-of-band email at gezelter@nd.edu if you want to discuss. - Dan Gezelter
I tend to agree with Dan. I'm more than happy to sign a community letter, though. - Egon Willighagen
I've never met you personally, so I don't think I should sign any individual letter, but I'd co-sign a letter of course! Just lt us know how you plan on doing that and I'll be there. - Björn Brembs
I'd be happy to help, in any way. I'm so sorry to be a biologist, but at least of a physicist descent (my father), so maybe...? :) - Marcin
I'll happily sign, not high up the feeding chain though I'm afraid :D - science3point0
OK, here's a start: http://piratepad.net/DpuxZJT... I haven't written tenure case letters before so it may need considerable chopping about, but at least we can get started. - Bill Hooker
Great start, Bill! I've co-signed too. - Heather Piwowar
Bill -- That is amazing! Thank you so much! That is wonderfully written and I appreciate it deeply. I've only been in a few departments in my young career, but I can tell you that UNM's physics department is full of faculty that care deeply about education and doing research for the benefit of society. So, I am confident that many of those voting on tenure will be very impressed by the... more... - Steve Koch
@Marcin I love interdisciplinary! Actually our science is focused on biology and have had students in the lab from biology, biomedical sciences, mechanical engineering, biomedical engineering, physics, and optical engineering. Moreover, I don't worry about the departments or academia / industry--with open science, we almost automatically ignore those credentials--while hard-earned,... more... - Steve Koch
@Dan Thank you for the experienced perspective! I've sent you an email with further thoughts / questions. I do accept the reality that I need those high-on-the-chain letters. And will seek those for sure. My gut is still telling me that at least for my department, a co-signed letter will add a lot of value, especially a letter such as Bill has drafted. I think for sure after the dust... more... - Steve Koch
@ John -- thank you for offering to co-sign! This is the only video I'm aware of (I think you were there & also my APOLOGIES for inadvertent slam on library journals!). That was the "data discoverability" session in 2011 and it was a ton of fun for me. Here is the link http://friendfeed.com/kochlab... and here are my notes from the session (with links) http://openwetware.org/wiki... - Steve Koch
Here's slides from 2010 Open Notebook Science presentation http://www.slideshare.net/skoch3... - Steve Koch
Here are my notes (with links) for the ScienceOnline2011 Data Discoverability session: and here are my notes from the session (with links) http://openwetware.org/wiki... - Steve Koch
@others who've piped in--thank you! I am excited to have this support - Steve Koch
Steve - I'm happy to co-sign but I do agree with Dan that individual letters are generally preferred. But if your tenure committee is saying that this is the way to go, definitely follow their direction. - Jean-Claude Bradley
I'm happy to sign as well. Best of luck, Steve. - Mr. Gunn
Now that people are back from science online, *bump* - Bill Hooker
Where do I sign.... - Cameron Neylon
added my name - Jonathan Eisen
mine too! - Scott Edmunds
Thank you everyone! Jonathan Eisen has graciously signed and mailed in a snail mail copy of the open letter to my committee. I don't expect to hear anything about it (positive/negative/neutral) until December, maybe January. I will of course update you with any news. Thank you again, everyone: so much support made me feel great! - Steve Koch
science3point0
FigShare teams up with Digital Science, but remains open and independent: http://www.digital-science.com/welcomi...
Digital Science’s relationship with FigShare represents the first of its kind in the company’s history: a community-based, open science project that will retain its autonomy whilst receiving support from the division. - science3point0
Daniel Mietchen
Who on Twitter primarily tweets what could be (or indeed are) lab notebook entries, like @fanosearch ? Thanks for any pointers.
@leeworden on twitter is a mirror of the lab notebook entries posted on leeworden.net - Lee Worden
Added. Thanks, Lee! - Daniel Mietchen
I want to try something along these lines but haven't got that far yet... - Cameron Neylon
peter murray-rust
Cameron Neylon
Wears the passion? Yes it does rather… - http://cameronneylon.net/blog...
Quite some months ago an article in Cancer Therapy and Biology by Scott Kern of Johns Hopkins kicked up an almighty online stink. The article entitled "Where's the passion" bemoaned the lack of hard core dedication amongst the younger researchers that the author saw around him. This article got a lot of people very ... - Cameron Neylon
Peter Binfield
Very very pleased to see us launch our API - for accessing all PLoS journals content - http://api.plos.org/ Go build something!
Checking out the examples now, interesting to see use of Javascript http://api.plos.org/examples/ - Mike Chelen
Cool, Pete - and thanks for leading the crowd once more. - Daniel Mietchen
Well, not quite (some others beat us to it, including Springer, Elsevier, Mendeley) but we have been wanting to do this for ages. Plus ours is on the full text and fully open. - Peter Binfield
I meant the "full text and fully open" part. - Daniel Mietchen
The Elsiver API one seems discontinued? (http://www.programmableweb.com/api...) Looks like Scopus has an API. others? - Carl Boettiger
Lindenbaum tools for NCBI Pubmed? http://friendfeed.com/yokofak... - joergkurtwegner
Speaking of PubMed, one of its major limitations is that it does not provide full-text search. PLoS and Mendeley do. So I think it would be useful to have a little app (e.g. a browser plugin) that takes a PubMed search, passes it on to the PLoS/ Mendeley search engines and displays the results in the context of the original PubMed search. Anyone interested in that (e.g. as a warm-up for http://ff.im/FIwlT )? - Daniel Mietchen
That's a neat idea, Daniel. - Mr. Gunn
Couple of updates for any of you entering the competition. Nephoscale are offering 10 free cloud servers for entrants using PLoS APIs see: http://blogs.plos.org/plos... And today we upgraded search to also include "search within figure caption" so now you can do cool things with our figures too. - Peter Binfield
Ross Mounce
RT @Puffles2010: *Puffles thinks data sets for all publicly-funded research shd generally be made freely available - & that we shd have a "national databank"
Rutger Vos
ANNOUNCEMENT: COMPUTATIONAL PHYLOINFORMATICS TRAINING August 1-11 2011, Kyoto (Application Deadline: May 31, 2011) http://academy.nescent.org/wiki...
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Only ten days left to register! - Rutger Vos
Victor / Mendeley Team
Mendeley’s research catalog is now wikified! Come help us organize the world’s research. - http://www.mendeley.com/blog...
I like what @blJOg said about the "Pandora-style" approach to discovering literature, especially since Mendeley's always been described as taking a last.fm approach. - Mr. Gunn
Very cool. I gave it a whirl by creating a wiki page for a tag "dna unzipping." http://www.mendeley.com/tags... I'm a little wary to do any more, though, since I don't know how to track pages I've edited, watch for changes, etc. - Steve Koch
Also, I agree with the comment from Andrew that it's difficult to get to a tag page. I guess the problem is that I don't really know how to get out of "my library" to the "mendeley library." When I click on my own tags, I just see my own papers that I've tagged with that tag. - Steve Koch
Heather Piwowar
Interesting discussion questions for the #DataCitation workshop at Harvard tomorrow: http://projects.iq.harvard.edu/datacit...
Very related to #beyondimpact citation discussions: #DataCitation discussion Qs for workshop at Harvard tomorrow: http://bit.ly/kIx9SX - Heather Piwowar
#beyondimpact see esp questions about aggregators: "If attribution is given to each source, can this be done by reference? Is it sufficient to cite an aggregator if the aggregator cites all sources?..." - Heather Piwowar
#beyondimpact also questions about tools: "Current indexing services and tracking tools often do not support support queries or analysis of the data citation currently included in articles (even if these include DOI's), and many strip out identifiers to non-traditional works. What is necessary to extend tools designed for citing and tracking use of other works for data citation?..." - Heather Piwowar
#beyondimpact also about incentives: "Data citation and replicable research are more often stated in policy than followed in practice. What incentives and interventions would be most useful to align practice with policy, and encourage appropriate data citation?" - Heather Piwowar
#beyondimpact And this one warms my heart: "What research is required to understand the impact, incentives, requirements, etc. related to data citation?" - Heather Piwowar
Jean-Claude Bradley
Collaboration using Open Notebook Science in Academia book chapter - http://usefulchem.blogspot.com/2011...
Collaboration using Open Notebook Science in Academia book chapter
Heather Piwowar
Has anyone thought of citation-shortening, like url-shortening but as work-around for max # cites rules in journals? ugly but necessary? ...
... esp for citing large amounts of data reuse. See here for early version of idea http://bit.ly/kdkHUC . Mostly thinking of shortening not of each citation but rather as a pointer to a registry entry that expands into all of the actual citations -- for instances when need to cite many datasets for example - Heather Piwowar
... trick of course to get citation databases to index the expended versions and link, but in their best interest. - Heather Piwowar
... thought inspired by @cboettig comment on recent blog post: http://bit.ly/iflU3N - Heather Piwowar
Citation shortening is often done by citing review papers. - Martin Fenner
True! But that "method" doesn't work as well for citing datasets :) Other ideas for getting around the max#cites issues for mega data reuse? Meta-analyses often include citations in table or supp mat, but then not part of the citation databases, so less credit and links. - Heather Piwowar
How about we campaign to kill off the max # of cites rule, instead? Even those dinosaurs who insist on a print version can print selected references with a note "full refs online". So there's no good reason for arbitrary restrictions on length, # figs, # cites, etc. (Pre-emptive: yes, restrictions can help authors focus and prevent rambling. So can editors, who are always telling me about all the value they add.) - Bill Hooker
Agreed, that would be great, but I think it will be hard. It requires many journals to buy in. At least some journals care a lot about the online and paper copies being the same. - Heather Piwowar
I don't have any good ideas, but I agree with Bill. Any limit to citation length should have very good reason in modern day. I don't think citing review articles is very often effective--it just compounds the citation context problem even further. - Steve Koch
Someone suggested this for FigShare saying, I've uploaded 20 datasets and I want to cite different groups of them in different papers, could we have a tool where you group different sets of databases and this generates a new handle (or DOI). It's a great idea, just not top priority on the dev list right now. - science3point0
cool! yup. ideally the mapping would be stored somewhere that citation databases could easily index what the new handle points to. Does that mean that DataCite should handle it, I wonder, so that the mapping is part of the metadata for the collapsed citation and easily accessible to citation databases? - Heather Piwowar
If look at how the ISA-tab communities metadata tools (http://isatab.sourceforge.net/) structures things into: investigation, study and assay - using these should provide some of that type of functionality as many individual (and combinations of) datasets can be grouped under a single investigation. I think they are currently working with Datacite, so future versions of their tools should hopefully allow doi's to be created for much larger citable units. - Scott Edmunds
[I should declare that we (BGI/GigaScience) are working to give our databases an ISA-tab compliant structure, although a lot of the EBI and a growing list of other databases use it too] - Scott Edmunds
Roderic Page
Martin Fenner
Direct links to figures and tables using component DOIs - http://blogs.plos.org/mfenner...
excellent timing, Martin, CTT is preparing to do exactly this from No. 11 onwards - thanks - Claudia Koltzenburg
Claudia, what is your preliminary experience with component DOIs? Are they difficult to implement for a journal? And will you offer them for tables and figures, or also for other content? - Martin Fenner
we are preparing to start on component DOIs so this is exactly what we are looking into at the moment, Martin, so far we were thinking of tables and figures only, and now there is another little golden pearl from Martin Fenner in our to-do bucket to relish :-) will keep you updated, - Claudia Koltzenburg
new question: can PMC deal with component doi in their DTD? (CTT has just passed PMC content review successfully) - should probably check PLoS xml @PMC - Claudia Koltzenburg
I don't know the details, but the example I use in my blog post uses this URL in PubMed Central: http://www.ncbi.nlm.nih.gov/pmc.... In other words, both PubMed Central ID and component DOI. - Martin Fenner
thanks, will find out more - Claudia Koltzenburg
DataCite Hannover branch (our doi registration agency) says CTT is the first they know to be explicitly interested in component doi, they are ready to register them. Now we need to find out more about how we can save extra xml export hours by combining the NLM schema that is focussed on text with the DataCite schema that was created for Data, (re NLM and component doi we will now talk to ZBMed in Cologne) ... and then there are figures, tables, films, audio - would OAI-ORE be of any help? - Claudia Koltzenburg
does anyone know if anyone else is finding out if component doi are difficult to implement for a journal? keen on others' experiences, esp. from fields relevant for PMC, actually keen to learn about some short track, too :-) - Claudia Koltzenburg
Kubke
Dr. No Money: The Broken Science Funding System: Scientific American - http://www.scientificamerican.com/article...
"That is the approach taken by the Howard Hughes Medical Institute, the largest private supporter of medical research in the U.S. It has selected some 330 researchers with a demonstrated track record of success, as well as 50 up-and-coming young scientists, and annually distributes about $500 million among them with a minimum of red tape. In 2009 three economists compared this system with the standard National Institutes of Health grant. The NIH grants last three years, end abruptly if they are not renewed and have very strict requirements—for instance, preventing scientists from shifting money from a project that is not working out to a more promising approach. Howard Hughes grants last for five years, are usually renewed, provide a grace period even if not continued and encourage reallocation of resources on the fly. The economists found that Howard Hughes grants led to higher-impact research, even when the researchers were compared with an equally elite sample of NIH applicants." - Kubke from Bookmarklet
Michael Barton
GitWrite - blogging for nerds - http://gitwrite.com/
looks like a potentially great platform for a lab notebook... - Carl Boettiger
Sounds an awful lot like http://pages.github.com/ GitHub Pages is an awesome platform for hosting documentation. For example, we use it to host http://gunicorn.org from this GitHub branch: http://github.com/benoitc... - Paul J. Davis
There's a great desktop/cloud notebook app to be written using git as a back end. Anybody got into the guts of this and seen what is different if anything under the hood? - Cameron Neylon from twhirl
I know that the Mercurial vs. Git debate seems to have been won by git in the Open Science community, but if you want a saner life you should look at http://hatta-wiki.org/ (Also see http://www.mzlinux.org/node... for a list of Mercurial/Git backed wiki engines.) True nerds should consider an Emacs Org mode backed blog or wiki http://orgmode.org/worg... which can also be combined with revision control. - Matt Leifer
Just thought about an Emacs org-mode + git solution, too. Especially as it can include executable code snippets via Babel: http://orgmode.org/worg... (at the bottom of this page you can find a description how this can be used for reproducible research). - Konrad Förstner
The server software used for display must be available for the content to be truly portable. Would be happy to see even if only basic features were available so far. - Mike Chelen
Hatta looks good, wonder how difficult it is to get set up? - Mike Chelen
Ended up using Github's Git-backed wikis https://github.com/blog.... Now if only there were a way to allow comments similar to blog posts... - Mike Chelen
Daniel Mietchen
"GitHub has evolved to solve the same general problem that scientific publishing does: making modular, validated units of knowledge easily usable by a global community, with mechanisms that efficiently allocate prestige to proven contributors. GitHub has the advantage of doing this with 21st century technology, the social web, while academic publishing is based on the printing press. This suggests an opportunity for the scientific community to evolve its publishing practices by assimilating mechanisms proven to work for GitHub." - Daniel Mietchen from Bookmarklet
But it isn't clear that the model similarities of version control repositories are enough to overcome the real model differences with any kind of scholarly publishing (that's not code), surely? - Chris Rusbridge
Another quote: " An article describing a genomic database is nowhere near as useful as an open API for accessing it. " @ Chris - yes, that is not clear. But "if we knew what we are doing, it wouldn't be called research, would it?" (or so the saying goes). - Daniel Mietchen
"GitHub did not succeed by being a social network of programmers. It succeeded by being a social network of code. We need a social network of science, meaning scientific bundles of knowledge must be structured and accessible by API, with the connections among those bundles and appropriate utility metrics being what connects and prioritizes scientists." - Daniel Mietchen
Ah, and that's the rub, then. Structure. No can haz structure it in research, except retrospectively. There's so much that remains uncomputable and efforts to increase the computability of the output are great, but only so far as they don't place barriers in the way out the output. Put another way, structured semantic publications would be great, but not everything is appropriate for publication therein, so perhaps what is needed is a less top-down approach. I do like the general metaphor. - Mr. Gunn
Why must those bundles be structured? Why can they not simply be "semanticized" -- tagged, marked up -- within a system that can impose structure based on semantic markup where appropriate and leave unstructured that which does not require it? E.g. if I have a story of some kind to tell, the system can take my objects Intro, M&M, Results and Discussion and structure something we all... more... - Bill Hooker
Dave Bacon
Michael Nielsen on Open Science at TEDxWaterloo http://www.youtube.com/watch... Just glad he didn't use scirate as a failed example :)
Michael Nielsen on Open Science at TEDxWaterloo http://youtu.be/DnWocYKqvhw Just glad he didn't use scirate as a failed example :)
Play
Cameron Neylon
Best practice in Science and Coding. Holding up a mirror. - http://cameronneylon.net/present...
The following is the text from which I spoke today at the .Astronomy conference...There’s a funny thing about the science and coding communities. Each seems to think that the other has all the answers. - Cameron Neylon
"The mythology doesn’t quite live up to the hype" - brilliant idea to look into this relation more specifically - would be useful for quite a number of ... well, both :-) - Claudia Koltzenburg
re complexity effects of mirrors, see Attila Csörgö's awesome scientific artwork, Image No. 4 here, http://docs.google.com/viewer... - Claudia Koltzenburg
"I’ve never been able to reproduce an experiment based only on a paper in my life" - so what does the hype about "papers" tell us? - Claudia Koltzenburg
Depending on how exact you want to reproduce, I've been lucky enough to do that several times. Maybe that varies from field to field? - Björn Brembs
I think it varies a lot...its probably also relevant that I flit from one field to another so often don't have assumed experience/knowledge. But the notion that this is a standard that everyone works to is what I wanted to challenge. - Cameron Neylon
well challenged, we should keep going on this and push the discussion further - Claudia Koltzenburg
Steve Koch
Andy Maloney defends his Ph.D. on Wednesday! Here is his chapter on Open Science experiences: User:Andy Maloney/Open Science - OpenWetWare - http://www.openwetware.org/wiki...
Andy Maloney defends his Ph.D. on Wednesday!  Here is his chapter on Open Science experiences: User:Andy Maloney/Open Science - OpenWetWare
It's a huge file (with embedded movies), but you can download his complete dissertation as a PDF from our server: http://kochlab.org/files... All of this information is on the wiki pages as well. - Steve Koch
Congratatulations, Andy! He passed his exam today, just minor revisions to dissertation required. http://www.openwetware.org/wiki... - Steve Koch
I searched the document for "movie" and checked all figures that came up that way. The first two (1.3 and 1.6) did not display for me, all the rest (1.7, 1.9, 2.7, 2.10, 2.11, 2.13, 2.14, 4.2) went fine. - Daniel Mietchen
I also read the "open science" chapter and wish every dissertation would contain such a chapter with reflections about the way in which the research was performed _and communicated_. - Daniel Mietchen
Cameron Neylon
A return to “bursty work” - http://cameronneylon.net/blog...
What seems like an age ago a group of us discussed a different way of doing scientific research. One partly inspired by the modular building blocks approach of some of the best open source software projects but also by a view that there were tremendous efficiency gains to be found in enabling specialisation of ... - Cameron Neylon
interested in seeing this story unfolding - you may have invented the genre of positive thrillers here, Cameron ;-) - Claudia Koltzenburg
Lots of niggling details to work out...like who has time to actually do the work :-) - Cameron Neylon
No, that's entirely separate. Trying to enter my timesheets... - Cameron Neylon
I remember the bursty work discussion. That was before Deepak was too cool to hang out with us in here. It was also when I was still a grad student and had time for that sort of work. Maybe that's your answer... - Mr. Gunn from Android
It looks like we are all quite "desperate" to make this damn idea work... - Pawel Szczesny
If anyone of you are interested over the last year I've been setting up a service that addresses some of these points. If you get a few moments, please take a look and tell me what you think: http://zombal.com - Zombal
Its a classic case of that 2x2 square model (urgent vs non-urgent, important vs non-important). To enable this model to work there has to be capacity in the system and therein lies the problem. Because we always operate beyond capacity there is little ability to switch to these kinds of projects. Also there is little prestige in being a cog in someone else's wheel. - Cameron Neylon
Pawel, it is an idea that should work, and works really well in other domains. Just frustrated that the systems we have in place in the life science/science world don't encourage that, despite the obvious advantages - Deepak Singh
Deepak, I agree. And I've been trying for quite a while to make it work in life sciences without much of a success yet (obviously) and (obviously) I'm as frustrated as anybody else we're not there yet... - Pawel Szczesny
Nic Weber
Cameron Neylon
Of interest to #altmetrics folks? Track on Recommendation, Data Sharing, and Research practice at iKNOW conference http://i-know.tugraz.at/i-scien...
via Peter Kraker - Cameron Neylon
Jonathan Eisen
The story behind the story of my new #PLoSOne paper on "Stalking the fourth domain of life" #metagenomics #fb - http://phylogenomics.blogspot.com/2011...
The story behind the story of my new #PLoSOne paper on "Stalking the fourth domain of life" #metagenomics #fb
I enjoyed reading that. I probably would never have picked up the paper itself and read it through, which would have been my loss as this is some neat science. For my money, a blog post is much, much better than a press release! - Bill Hooker
Also -- a link to the backstory in the paper comments wouldn't go amiss. - Bill Hooker
Paper over my head, but blog post great. Also, Carl Zimmer's post about it is wonderful. Awesome. - Bora Zivkovic
Fascinating. Love the blog post. Also, I was able to follow the abstract / intro / conclusions in the paper pretty well, seems very well written and thoughtful. @Bill I posted a link to the blog in the comments for you (and me, and everyone). - Steve Koch
Bill - added a link to the backstory in the paper comments ... - Jonathan Eisen
Ricardo Vidal
Quite happy to see I already follow Google's R style guide. :-) http://google-styleguide.googlecode.com/svn...
Heather Piwowar
RT @jasonHoyt: World's real-time citation rate? Last month was 272 cites/hr inserted w/ Mendeley Word/OO plugin http://www.mendeley.com/
Jonathan Eisen
Ecological Society has been publishig data papers for many years: http://esapubs.org/archive...
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