Michael Kuhn › Likes

Pawel Szczesny
It's already hanging in our department...
... so OAgeek made a statement out of my question? how dare she ;-) - Claudia Koltzenburg
Claudia, it's just another Claudia, right? I will change that to @Repositories :) - Pawel Szczesny
I think citing @OAgeek here makes more sense than @Repositories, but they usually cooperate closely ;-) non-claimer: both write from my IP ;-) - Claudia Koltzenburg
Not much changed here... - Cameron Neylon
Steve Koch
Hey Gilbert Lewis: Has life evolved a use for deuterium? Or does it just tolerate it? - http://stevekochresearch.blogspot.com/2010...
Lazy question: Anyone know where to purchase seeds for research? Tobacco and mustard seed are my only ideas ... - Steve Koch
extend expt to tobacco varietals -- http://www.thetobaccoseed.com/Tobacco...; herbs and vegetables -- http://www.stokeseeds.com/home...; another idea would be to work with seed researchers (e.g. http://www.ag.ohio-state.edu/~seedbi..., UNM's own botany dept) to pick the best candidates and sources. My google-fu is not the strongest but those links could get you started. - Bill Hooker
What I forgot to say: this is a really interesting line of thought and an elegant experimental way to start following it -- I really hope you will do this! When you switch the units (17mM!!) it becomes much more intuitive to look for biological effects and adaptations. - Bill Hooker
Thanks, Bill! Just to get a foothold, I ordered some Virginia seeds from that first link. I'll see if they sprout in water like they did back in 1933. I'm glad you liked the story, too! Maybe I will take the luxury this weekend of writing up an experimental plan, I've resisted so far, but it sounds like fun :) - Steve Koch
As an alternative to the Google search, did you try to feed http://www.biosemantics.org/jane... with some relevant key words? I just pasted in a part of your blog post and saw things like http://www.ncbi.nlm.nih.gov/sites... and http://www.ncbi.nlm.nih.gov/sites... and... more... - Daniel Mietchen
Thanks, Daniel, I hadn't thought of using JANE. Trying it out now.. - Steve Koch
Found an article that looks interesting: http://www.springerlink.com/content... "Effect of deuterium-depleted water on reproduction of rainbow trout" From the abstract / intro (all I've read so far), they say deuterium-depleted water increases survival of embryonic roe (I don't know if I'm using the terminology correctly). They also cite prior literature saying that prior... more... - Steve Koch
It turns out in his 1934 Science paper (which as of July 2011 is not indexed correctly on Web of Science), Gilbert Lewis specifically calls for experiments with deuterium-depleted water to see whether life forms have adapted a need for D in normal cellular operations. "It is not inconceivable that heavy hydrogen, which exists in small amounts in all natural water, may actually be... more... - Steve Koch
HL02: Jacques Colinge - The Central Human Proteome
Which are the commonly expressed in human? - Roland Krause
7 cell lines, 1D gels, 50 bands, Orbitrap MS-MS - Roland Krause
Membrane proteins underrepresented, no other biases for characteristics such as PI, MW found. Abundant proteins. - Roland Krause
Overlap of 45% with Su, PNAS 2002 transcriptome study. Similar processes enriched. - Roland Krause
Human protein atlas (Ponten, MSB, 2009), overlap of 40%, mass sensitivity limited. - Roland Krause
Protein found generally well conserved. More interesting, genes are exon-rich. - Roland Krause
Increased number of interactions. - Roland Krause
The central proteome is central in the interactome (by centrality measures). - Roland Krause
83% enzymes, 77% primary metabolism, significant enrichment in drug targets (176 from DrugBank) - Roland Krause
Specialized functions of the core proteome interwoven by connectors. - Roland Krause
10% of the core proteome are poorly annotated. - Roland Krause
Significant overlap with viral host factors. - Roland Krause
Data publicly available. - Roland Krause
Q: Map of the central proteome against housekeeping genes? - Roland Krause
A: No, not directly but other works defined abundant genes as such. - Roland Krause
Q: Kinases as cancer targets, relevance in the data set? A: 40 kinases in the data set. Overlap with cancer much bigger than only kinases. - Roland Krause
Q: Both expression levels and abundance levels. Correlation? A; Poor overlap between the two suggests expression levels are little correlated. [..] - Roland Krause
Q: Have you looked at recent sequencing studies for transcriptomics [not only Su et al] . A: Studies by Chris Burge report 10.000 genes, much too many to compare because copy number might be very low, comparison very difficult. Unclear functional relevance. - Roland Krause
Q: Centrality. Have you looked at the complexome? A: You recognize proteasome, spiicesosome. Q: How many is in complexes: A: Two thirds, there are not many complexes that work alone. - Roland Krause
Q: Are poorly annotated proteins underrepresented? A: Depends on the number of PubMed abstracts that make a protein underrepresented. - Roland Krause
marcovhv: In NYC you HAVE to ride your bike in the bike lane. At all times. Or you’ll face a $50 fine. This guy is pretty brave. I think if I was planning to crash into all the obstacles in the bike lane, I would at least wear long trousers, not shorts. Kudos to him for making the point. - http://bsag.tumblr.com/post...
In NYC you HAVE to ride your bike in the bike lane. At all times. Or you’ll face a $50 fine.
This guy is pretty brave. I think if I was planning to crash into all the obstacles in the bike lane, I would at least wear long trousers, not shorts. Kudos to him for making the point.
Deepak Singh
How Radiolab Is Transforming the Airwaves [longform.org] - http://www.nytimes.com/2011...
Björn Brembs
Pedro Beltrao will interview in Berlin on April 13! http://www.mdc-berlin.de/en... I hope we can meet...
Hi Bjorn - yes, I will be in Berlin from the 12th to the 14th. It would be great to meet up. Are you at he MDC ? - Pedro Beltrao
I'm on the other side of town, actually. The MDC is in such a remote place, people are usually surprised it's still a part of Berlin :-) I guess the 13th will be all busy for you, so what would be a good time to meet on any of the other days? I can drive up to the MDC. - Björn Brembs
Michael Barton
(4) Linux: What are some time-saving tips that every Linux user should know - http://quora.com/Linux...
switch to a mac? .... :) - Rajarshi Guha
Roderic Page
Linking the NCBI taxonomy to BBC Wildlife Finder - http://iphylo.blogspot.com/2011...
Cameron Neylon
A collaborative proposal on research metrics - http://cameronneylon.net/blog...
When we talk about open research practice, more efficient research communication, wider diversity of publication we always come up against the same problem. What's in it for the jobbing scientist? This is so prevalent that it has been reformulated at "Singh's Law" (by analogy with Godwin's law) that any discussion of research practice will inevitably end when someone brings up career advancement or tenure. The question is what do we actually do about this? n opportunity has arisen for some funding to support a project here. My proposal is to bring a relevant group of stakeholders together; funders, technologists, scientists, adminstrators, media, publishers, and aggregators, to identify needs and then to actually build some things. - Cameron Neylon
Wonder whether Andrew Treolar might have insight to contribute http://andrew.treloar.net/ - Kubke
AT certainly has experience of the problem and also seems to be collecting a lot of data... - Cameron Neylon
He was strong about making data sets a primary citable object at the data matters meeting where I met him, to make the 'use' of the data as trackable as any publication - Kubke
Yep, I think that's a key theme. Need to make sure have Dryad and Datacite involvement with this. - Cameron Neylon
He suggested giving the 'data' a DOI and tap onto the search/link/tracking that already exists for paper publications as something which could provide an initial viable solution - Kubke
Essentially this is what the DataCite project are doing. I think Dryad is connected with them as well. I worry about using dois for this because I would rather URLs [ducks in case geoff bilder arrives to pummel me (-; ] but the reality is that the scientific mindset seems to be doi = real so I think it's going to be the way we move forward in practice. - Cameron Neylon
The redirection mainly. Essentially it breaks a whole set of fun things that you can do with URLs. None of which to be fair are very commonly done. Also in principle they could be enabled through the doi redirect. Essentially its a minor quibble that it doesn't add anything technically and breaks some stuff. But the reasons for dois are fundamentally social not technical. - Cameron Neylon from twhirl
I'm a big DOI fan. Just yesterday I ran into a few duplicate papers in the Mendeley library. One reason is that there are several URLs associated with a paper: PubMed, Journal HTML page, Journal PDF, institutional repository URL,... Not to mention that many URLs break over time. - Martin Fenner
And DOIs would really help to automatically find science blog posts associated with a paper. The Journal of Neuroscience editorial about supplementary information in August has no DOI. Almost impossible to find all blog posts (there are many) that talk about this editorial. - Martin Fenner
All true but I guess my problem is that fundamentally dois are a special system so that generic web tools (and yes particularly semantic web tools) will break over them and the info won't get incorporated into the wider web. e.g. Martin's problem could be solved by an owl:sameAs which would mean that it would be transparent to other web systems. But with dois someone has to build... more... - Cameron Neylon
None of which changes the reality. DOIs are dominant and are here to stay as far as I can tell so I just need to get over it and move on... - Cameron Neylon
Just added a comment and we need to do more than offering incentives for "re-use". - joergkurtwegner
While I am a big fan of finer-grained measures of contribution (e.g. peer review), I am not convinced that the current proposal should be stretched to cover such measures. It seems to me that what is wanted here is a hard-nosed, outcome-focused project designed to answer hard questions about ROI. For that purpose, a close focus on re-use is probably optimal. - Bill Hooker
Nice proposal. It currently focuses strongly on funder needs. Useful, perhaps necessary, but it means delayed and indirect rewards to the jobbing scientist. Would it make sense to work in a more direct focus on "jobbing scientist needs" too, with possible hacks of automated reuse-metric CVs and reuse-metricful tenure packages? - Heather Piwowar
Joerg - I commented on your comment back at the proposal. Two things really. My view is that the "measuring re-use" idea covers things like review. A good review needs to be "cited" in some way and that re-use measured and rewarded. I'm not quite sure where you're going with the micropayments thing. A kind of micropayments has been tried by EPSRC in the UK where they pay £50 or... more... - Cameron Neylon
Heather, good point. Although the response I've got suggests that people are interested enough in the possibility of getting credit for a more diverse range of things that thats enough at the moment. But yes, the CV is a very good place to realise some benefits. Need to talk to someone inside VIVO I think to see if there is some low hanging fruit there. - Cameron Neylon
@Bill , @Cameron - I understand your views and the ROI question is important. As long as we agree that there is some measure, recognition, and reward scheme I agree. So, a re-use needs to be tracked otherwise, we need to prevent ab-use of re-use. - joergkurtwegner
So if I'm reading you right your core point is that we shouldn't assume that simply by measuring something that the rewards will flow from that. That it is important to consider explicit reward schemes, which might include payment or aggregated micropayment? - Cameron Neylon
Actually it strikes me that both Joerg and Heather are pointing in the same direction here. Keeping up the issue of direct benefits. - Cameron Neylon
Cameron, what is your timeline for the proposal and what sort of additional help would be useful at this point? The current draft doesn't have references: do you need any? Other help? - Heather Piwowar
References (both to literature and to other projects) would be a big help. Contacts with funders would be useful if anyone has them. And proof reading still valuable. I'm currently checking with the funder whether this is heading in the right direction and then I'll start pulling in contributors more. Timeline is really about a week though the quicker the better I suspect. - Cameron Neylon
Also anyone got a good contact on the inside of VIVO? I know that Mackenzie Smith is on their advisory board but don't have any good contacts on the inside. It would be an obvious source of data. - Cameron Neylon
Sounds good. I've added (REF) indications where it seems like references might be appropriate, to facilitate crowdsourcing. Cameron, please edit as needed based on the intended document length and number of refs expected by the funding body? - Heather Piwowar
Yep, still working on those last two questions... ;-) - Cameron Neylon
what came of this? - Claudia Koltzenburg
Got the money, running the workshop: http://beyond-impact.org - Cameron Neylon
Simon Cockell
Stack Exchange and the future of BioStar - http://blog.fuzzierlogic.com/archive...
Over the weekend I saw this tweet from Stack Overflow/Exchange founder Joel Spolsky. The content of the link he posted has served to crystallise some of my thinking of the last couple of weeks with relation to the Bioinformatics question and answer site BioStar. The link Spolsky posted in the tweet was to a failed [...] - Simon Cockell
Now with feedback from Jeff Atwood. Encouraging. - Simon Cockell from iPhone
Matthew Todd
ScienceDirect - Cell : Intercellular Nanotubes Mediate Bacterial Communication - http://www.sciencedirect.com/science...
Jeez "Electron microscopy revealed the existence of variously sized tubular extensions bridging neighboring cells, serving as a route for exchange of intracellular molecules. These nanotubes also formed in an interspecies manner, between B. subtilis and Staphylococcus aureus, and even between B. subtilis and the evolutionary distant bacterium Escherichia coli." - Matthew Todd from Bookmarklet
Wow. If this is not some kind of artefact, it's a big deal. Without having read the (paywalled) paper, only watched the (free) video, I have one immediate question: these structures are up to 1 micron in length and 40-120nm wide; why have they never been observed before? - Bill Hooker
Exactly. - Matthew Todd
This beats arsenicum by light years... also, why was this rejected by Nature and Science... (or is Cell that good?) - Egon Willighagen
Spoke with two biochemists recently who said it was their top journal, yes. - Matthew Todd from Android
That's why we call it "CNS disease" :-) - Cameron Neylon
Cameron Neylon
Latest incarnation of my Gatekeeper is dead/Discovery Deficit story published in Serials: http://dx.doi.org/10.1629/2421
Martin Fenner
Papers 2: the reference manager made with love - http://blogs.plos.org/mfenner...
Rajarshi Guha
Cheminformatics and Hotness (or lack thereof) - http://blog.rguha.net/?p=921
I've certainly learned (and am still learning) a lot of chemistry. - Andrew Lang
Björn Brembs
NeuroDojo: We haven’t seen this in a mammal! Rewrite the textbooks! - http://neurodojo.blogspot.com/2011...
NeuroDojo: We haven’t seen this in a mammal! Rewrite the textbooks!
Rich Apodaca
Daniel Mietchen
Top ten reasons why academics do not contribute to Wikipedia - Draft - http://en.wikiversity.org/wiki...
"1. Wiki edits do not count for tenure. 2. Wiki edits take away time from my research. 3. Wiki edits could actually damage my reputation. 4. I do not know what that would be good for. 5. I do not know how to do that. 6. I do not want others to modify what I wrote. 7. The quality of wiki articles in my field is rather low, and I value my time too highly to help fix that. 8. I do not want to spend my time correcting stuff that had been correct before but was vandalized in between. 9. I am not allowed to post my original research in there. 10. None of my peers does it. 11. None of my peers reads here. 12. I do not want others to see the kind of mistakes I make. 13. Why should I deal with an encyclopedia if I have access to primary sources?" Update: Beta version of a survey on the matter is at http://bit.ly/AcaWP . - Daniel Mietchen from Bookmarklet
@achimraschka @fischblog here we go with a first draft of the ten reasons that keep experts off of wikis. - Daniel Mietchen
another possibility: involved in too many other projects already and can't handle another area of focus. Similar to #2, but more about fragmented focus than time constraints. - Heather Piwowar
Negative perceptions: I don't want to be associated with those nasty "wiki" things... - Cameron Neylon
another: I already do lots of writing and editing and don't want to do any more. - Heather Piwowar
another one: "Really !? I can edit an article in wikipedia ?" - Pierre Lindenbaum
@ Cameron I would consider that as being part of #3 above. Added in all the rest plus some rough categories. Current version: "Lack of incentives 1. Wiki edits do not count for tenure. 2. I do not know what that would be good for. 3. None of my peers does it. 4. None of my peers comes here to read about my research. [edit] Disincentives 1. Wiki edits take away time from my research. 2.... more... - Daniel Mietchen
One that might be a variant of #9, but probably counts as its own thing: "I don't want the hassle of dealing with Wikipedia's local culture." More people than have edited Wikipedia articles have heard horror stories about nonsensical edit wars, and don't want to deal with that. Having to argue for the significance of an academic scientist whose page is a stub, while lengthy and lovingly detailed pages exist for fictional characters strikes a lot of people as absurd, bordering on Kafkaesque. - Chad Orzel
I found that people who are inclined to blog tend to avoid community-driven activities like wikis and vice versa. I guess many people look at wikipedia and simply decide that it's not their style. - Lars Fischer
I could see at least five items in that original list where you could substitute almost any other Science 2.0 tool and it still would hold. With some tweaking probably the rest too. I'm starting to think about what the list of corresponding come-backs might be. - Dan Hagon from Android
Thanks for all these comments. I've added Dan's. Now off to #glamwiki . Will get back to this upon return. - Daniel Mietchen
And here comes the seemingly inevitable request for deletion: http://en.wikiversity.org/wiki... . - Daniel Mietchen
I am sure WikiEducator would be happy to host the page - Kubke
shouldn't it be turned into a web poll ? - Pierre Lindenbaum
The request for deletion debate ended with "keep" this time. @ Pierre: Yes, and help with setting one up is welcome. - Daniel Mietchen
@Daniel I'll create the poll on G-Docs in the evening - Pierre Lindenbaum
@Daniel I just send you an invitation for editing the document. - Pierre Lindenbaum
Here is the poll : http://goo.gl/5GvXC - Pierre Lindenbaum
Cool - can you add a "Tick all that apply" notice? Merci! - Daniel Mietchen
Awesome, why not a 5-point likert scale then? (5 radio buttons) - that would make it so much useful! - ReaderMeter
I guess we should do some test runs before announcing it far and wide. - Daniel Mietchen
Folks, bear with us while we reformat the poll - ReaderMeter
Survey in beta: Reasons why academics do (not) contribute to Wikipedia http://bit.ly/AcaWP . Please provide feedback here. - Daniel Mietchen
I left most of the "I DO contribute to wikipedia" section blank, because I seldom do contribute there. It didn't return an error, but it wasn't exactly clear what I should do there. - Bill Hooker
I also left the 'I DO contribute to wikipedia' section blank, although I contribute to other wikis. - Kubke
Bill Hooker, Kubke -- yes that's what we are expecting. - ReaderMeter
Done the survey. I answered both sets of questions because I have done some edits but not a whole lot. - Cameron Neylon
Thanks to all those who filled it in so far. We have made some adjustments. Further beta testers welcome. - Daniel Mietchen
Done :) - science3point0
The survey is live now at http://survey.nitens.org/... . Thanks for filling it in or spreading the word. - Daniel Mietchen
I heard the #1 yesterday in a conf call: "what is a wiki?" - Egon Willighagen
Can Mendeley not include the "Wikipedia edit count" in their user profiles? That is easily done and would certainly disarm some'motivational aspects'. - joergkurtwegner
Not as easily done as you think, Joerg. What would count as an edit? Do you subtract from the count if your edit gets reverted? How often do you check? Do big edits count for more than small edits? - Mr. Gunn
We fixed a design flaw in the survey, now the "individual motivation" section should be unambiguous. - ReaderMeter
Noel O'Boyle
POV-Ray input format (pov) — Open Babel v2.3.0 documentation - http://openbabel.org/docs...
Added an image to the POV-Ray docs for Open Babel. The POV-Ray format was fixed in OB v.2.3.0. I took the opportunity to add options for checkerboard, etc. :-) - Noel O'Boyle
Roderic Page
Web Hooks and OpenURL: the screencast - http://iphylo.blogspot.com/2011...
Pawel Szczesny
Science Blogging and Tenure - Science Careers - http://sciencecareers.sciencemag.org/career_...
Reason no. 103 to have an online presence - you get your ugly photo reposted on well-known websites :) - Pawel Szczesny from Bookmarklet
Not only photos are re-posted, but also Twitter details http://twitter.com/#!... - joergkurtwegner
Thanks Joerg. I'm making a fun of it (of course, I cannot take 'online fame' seriously), but indeed it's nice to be featured in Science Careers anyway. However, interaction with Vivienne (author of this piece) deserves a separate post - I was impressed by the amount of material she wanted to collect before writing these two sentences on my case. We were even discussing extensively which word can be used as description of interviewers reaction to my online collaborations. - Pawel Szczesny
Interesting to hear, I think that is what they call serious journalism. - joergkurtwegner
Lars Juhl Jensen
Commentary: The GPU computing fallacy - http://larsjuhljensen.wordpress.com/2011...
Modern graphics processors (GPUs) deliver considerably more brute force computational power than traditional processors (CPUs). With NVIDIA’s launch of CUDA, general purpose GPU computing has become greatly simplified, and many research groups around the world have consequently experimented with how one can harvest the power of GPUs to speed up scientific computing. This is also [...] - Lars Juhl Jensen
Facebook CTO Bret Taylor On HTML5, Mobile As The Future, And Yes, FriendFeed - http://techcrunch.com/2011...
Facebook CTO Bret Taylor On HTML5, Mobile As The Future, And Yes, FriendFeed
"Finally, I asked Taylor about the Turkish use of FriendFeed sustaining it against U.S. traffic loses. He said it has been amazing to see it rise there and in a few other countries organically. He also said that before he left Facebook, fellow FriendFeed co-founder Paul Buchheit did a few things to ensure that FriendFeed will be able to run completely autonomously indefinitely." - AJCann from Bookmarklet
We're all still here, aren't we? :) - Benjamin Tseng
Someone must be around looking after the service. After all, it didn't go down and stay down earlier this week. - Scoble, Alex Scoble
Pawel Szczesny
Trying to persuade academic publisher (in Poland) to adopt CC instead of All Rights Reserved.
Journal (non-scientific) is freely available and I was asked to write an essay for it. I hope at least I can sublicense my piece under CC-BY, but maybe they would go for adopting CC for all texts. - Pawel Szczesny
My text will be licensed under CC and I was told they will reconsider adopting CC for all content. It's always worth to ask :) - Pawel Szczesny from iPhone
Interestingly so far they didn't insist on non-commercial clause, so it's going to be CC-BY. Already started to wonder what of I ask for CC0 next time. - Pawel Szczesny from iPhone
Egon Willighagen
Egon Willighagen - LinkedIn Labs | InMaps - Visualize your LinkedIn network - http://inmaps.linkedinlabs.com/share...
Crosslinks between groups are interesting. Also illustrative: there is no clear Uppsala University group. - Egon Willighagen
My map consists of two groups - real life connections and online connections. The service somehow figured out (mostly, but accurately) which of my online friends I have met in person. - Pawel Szczesny
It separates quite well between online, work and the various hobbies. Interesting how little cross-connected these groups are. - Björn Brembs
@Folks - Can you share links to your maps? Here is mine http://inmaps.linkedinlabs.com/share... - joergkurtwegner
What is HCLS standing for? - joergkurtwegner
here is mine: http://inmaps.linkedinlabs.com/share... -- it doesn't discriminate between work, OA/OS related, blogging and old friends. It does make a separate network for my wife and two friends I know through her. - Bill Hooker
Jill O'Neill
Beyond the PDF … is ePub | Gobbledygook - http://blogs.plos.org/mfenner...
Does ePub actually serve the needs of the research community more than the standard PDF file? - Jill O'Neill
That post is really interesting. Tell me how I can read or write ePub from Word? Otherwise, "oh, just use ePub throughout the process" is nonsense. It's saying "IF everyone adopted a set of tools that doesn't, by and large, exist yet, THEN these problems would be solved." Which might be true but is somewhat irrelevant. - walt crawford
Well the conversation we had included both how hard it would be to read and write epub in Word but also how to make sure epub would open properly in a browswer. It seemed plausible and the people who could make it happen (or at least identify what the problems would be) were there at the breakfast table. - Cameron Neylon
Walt, we already have a good number of ePub clients. And ePub support for Word and Excel documents is certainly on the agenda. - Martin Fenner
And when ePub works nicely with everyday tools, I'll be happy to use it as appropriate. I'm not putting down ePub as a good idea; it's just not there yet. For that matter, it's not there yet on OpenOffice either, at least last time I checked. "On the agenda" is great, as far as it goes. - walt crawford
I've been using an ePub plugin in Firefox that works quite nicely. I haven't looked at the creation side for things though (because for myself at the moment I don't need to). - Deborah Fitchett
But aren't any of you more concerned about the ePub being a standard developed to suit the needs of trade publishers rather than the needs of researchers and scientists. At least w/ PDF, you get the meat of the article (tables as well as text) in the most efficient design layout possible. That may not sound important, but PDFs offer a legibility that I haven't seen in most ePub files offered to the public. - Jill O'Neill
Jill, I listed some of the things I don't like about PDF in the blog post. And ePub/HTML is catching up fast in legibility. - Martin Fenner
Rich Apodaca
We’ll be retiring our support of OpenID on May 1 - http://productblog.37signals.com/product...
"The promise was grand. Life would be simpler if we only had one login, but in this case, the cure was worse than the disease." - Rich Apodaca
Jonathan Eisen
Wondering if I should finally bite the bullet and switch my blog from blogger to wordpress ...
textpattern! - Bosco Ho
well, will play around with WP but not sure when/if I will switch yet - Jonathan Eisen
I wondered the same thing myself over two years ago, but never made the switch. http://igotgenes.blogspot.com/2008... I'm curious about your motivation. Mine was primarily a gripe with code formatting (now handled by SyntaxHighlighter http://blog.cartercole.com/2009... ) and LaTeX for math markup, which I haven't solved yet. - Chris Lasher
Also, I only need to see things like this to decide I don't have the gumption to host my own WP instance: http://python.genedrift.org/2010... - Chris Lasher
Chris - motivation was simply that I have been hearing lots of glory stories about WP - so I figured I should at least check it out - Jonathan Eisen
Wordpress is nice if you are interested in plugins and themes, e.g. for reference management. I will also start work on a epub plugin. - Martin Fenner
First moving to WP.com, then self-hosted WP, then writing custom plugins for WP, then writing custom CMS... You're starting a long journey ;) - Pawel Szczesny
@ananelson has the ultimate geek blog: she writes her posts with vim using her dexy (http://dexy.it) language. - Martin Fenner
Noel O'Boyle
"Without the use of free and/or open source software cited or running quietly on the backend of the server this effort would not have been possible. In this regard, we especially want to thank the developers of Jmol (http://jmol.org), CDK (http://cdk.sf.net) and OpenBabel (http://openbabel.sf.net)."
Why thank you, Bauer et al. "Superimpose´ : a 3D structural superposition server" http://dx.doi.org/10... - Noel O'Boyle
Wondering how they used the CDK... cannot find that in the paper. - Egon Willighagen
Michael Nielsen
U.S. Department of Labor and Department of Education commit $2 billion to create open educational resources for community colleges and career training; CC BY required for grant outputs - Creative Commons - http://creativecommons.org/weblog...
I didn't see that coming so early (expected such thing to be announced next year). I like it very very much. - Pawel Szczesny
John Resig
Learning from Twitter's performance problems: http://ejohn.org/blog...
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