Egon Willighagen
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Egon Willighagen posted a message
“/me is working on visualizing the Solubility RDF data in Bioclipse...”
20 hours ago - Link
Still in progress, but a first screenshot is being uploaded to my blog... - Egon Willighagen
wow ! I don't think I might be of any help here Egon :-) . I will look carefully your sources to see how you've integrated this into CDK/eclipse. - Pierre
BTW, does someone know of a Java library to interact/read from Google Doc spreadsheets? - Egon Willighagen
very cool! - Jean-Claude Bradley
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Egon Willighagen shared an item on Google Reader
Monday at 3:43 am - Link
If you think progress in scientific publishing is taking long... - Egon Willighagen
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Sunday at 6:33 am - via Reshare - Link
I do that all the time. I can highly recommend it. Add some tagging (or branches) for versions you send around for review, and you're all set. Beats version tracking in Word. - Egon Willighagen
I have always preferred a service like Google Docs, at least for the rough draft stages of a paper that is. Cleaner and faster to get started, especially for people who are new to those things. - Daniel Jurczak
I'll second Egon - though it really shines if you're working in LaTeX. I've never tried to merge two Word docs via subversion. Would it work? - Rajarshi Guha
We are using Google Docs to write a grant, but people who are using it are a little bit skeptical to say the least. It's a slow progress. I never tried to merge Word via subversion, but I guess this is something to check. A quick search showed this: http://nicolas.lehuen.com/inde... - Paulo Nuin
I wish I had posted the whole series I wanted, dunno why I didn't. - Paulo Nuin
multiple editing on a word document can present some issues as it is a binary file, difficult to merge changes via svn. I would recommend LaTex - Frank
If LaTeX is an option then just go for svn. :-) - Daniel Jurczak
@Frank: most of the time, LaTeX is not an option, unfortunately. - Paulo Nuin
Google Docs doesn't seem promising - poor offline version (gears) + inability to tackle anything beyond standard documents (even emf/jpg images do not fit). - Yaroslav Nikolaev
@Rajarshi, Daniel & Frank: what's so special about SVN with LaTeX vs Word? don't have any experience with the former unfortunately...If its only binary vs ascii - one still has ability to track changes/comments from within the Word document, which might be an easier track for an average researcher ;) - Yaroslav Nikolaev
As far as free services are concerned, I've been happy with GoogleDocs for private sharing and Wikispaces for public sharing until the very last formatting step, where we generally use Word. Note that people in my field don't use LaTeX. - Jean-Claude Bradley
@Jean-Claude: what about schemes, images, etc - or you generally don't have a versioning issue on these? - Yaroslav Nikolaev
@Paulo: thanks for the plug, svn-time-lapse looks impressive! - Yaroslav Nikolaev
@Yaroslav, SVN+LaTeX is a nice combination because the latter is plain text. Therefore a simple diff allows you to quickly look at changes etc. I agree that it is not for eveybody - certainly most people in chemistry dept's do not (will not?) use LaTeX. Word's track changes is nice, and indeed I do use that when my collaborators won't use LaTeX - but the lack of branching can be a pain. But in general, I passionately hate Word - anything beyond 5 pages with many figures is simply a pain - Rajarshi Guha
@Yaroslav: My personal caveat with Word+SVN is as you've already guessed the binary vs. ascii thing. Maybe it is just a personal bias. :-) - Daniel Jurczak
More generally, when one writes regularly, the value of focusing on content rather than presentation is a huge boon. And LaTeX documents look sexier than Word documents for the same amount of effort :) - Rajarshi Guha
Its the issue with multiple editors of a binary file in svn - not word vs latex. If two different people check out the same version at 9:00am and work on it. If one person checks back in at 10:00am, the second person trying to check in at 11:00 will get a conflict because svn in not clever enough to resolve or merge conflicts in a binary file. - Frank
LaTeX looks better with LESS effort than Word. Specially now that they abolished menus in Word. - Paulo Nuin
GoogleDocs for the non-Tekkis and LaTeX+VersionControl for the Tekkis, or for the web2.0 freaks a Wiki with RTF export option, this allows post-editing in OpenOffice or Word. One good example is XWiki (Java). - joergkurtwegner
@Frank: this issue is clear! However in non-geeky context it seems easier to resolve it using Word built-in tools, rather than forcing everyone to use LaTeX. - Yaroslav Nikolaev
Any opinions on Git? It sounds more promising in terms of speed & stability (distributed system), however does not seem to have a stable Windows port so far (apart from over-cygwin version)?! - Yaroslav Nikolaev
You could consider using a WYSIWYG LaTeX editor... - Egon Willighagen
Oh, the Git port to Windows is fine, the GUI seems a little bit rough but the command line with SSH included works just fine. The git Eclipse plugin also works fine with most commands, but I had problems pushing things to Github from it. - Paulo Nuin
@Yaroslav For the projects I've been on images and figures don't change enough that it's ever been a problem. On Wikispaces I would just fix the image and replace it. Text is where the massive editing takes place. - Jean-Claude Bradley
One major shortcoming of Google Docs (and most Wikis I've seen) for scientific publications is the lack of support for numbered references - Eric Jain
Eric: that's usually the place were Zotero with its drag and drop comes in. - Daniel Jurczak
Problem with Zotero drag/drop is that it doesn't insert named/numbered citations, just the reference list at the end. The Word/OO plugins are better in that respect, but lag behind the latest Zotero release. I'm sure it wouldn't take too much javascript to get data from Zotero->Google Doc as both citation and reference, if anyone fancies a nice coding project ;-) - Neil Saunders
Neil: Well that's true. To be honest I have never used anything other than LaTeX/BibTeX for "larger" documents, so for me manual adding of references was never a major problem. - Daniel Jurczak
@Eric: exactly the point! that's why file-sharing beats document-sharing in research-paper-writing perspective - one can share a reference library along with the docs.. - Yaroslav Nikolaev
Unfortunately Zotero also suffers from inability to share the library between users/computers..they promise multi-computer sync in Zotero 1.5, and multi-user social sharing in Zotero 2.0...However we're not there yet.. - Yaroslav Nikolaev
Yaroslav: I guess you could use DropBox and put the Zotero library into the shared folder. (??) Have never tried it, so just a guess ? - Daniel Jurczak
The Zotero Sync works pretty well and you can access your database online. - Paulo Nuin
The only thing is, I guess you can't access your papers? Does it also sync up attachments, or at least snapshots? - Chris Lasher
tested Zotero 1.5 Sync (Preview): library metadata and text notes are synced over Zotero servers, while for attachments and snapshots have to use any third-party WebDAV disk (in future developers plan to employ Amazon S3 for this purpose). The problem here is that attachments on WebDAV are stored in own Zotero format (which appears as a collection of .zip and .prop files), so one would have to sync full library with metadata to dig out the appropriate file. - Yaroslav Nikolaev
actually the idea of using Zotero for collaborative paper writing seems very interesting, however currently (v1.5) it only fosters single-user synchronization mode, and hacking for group sharing appears cumbersome...'d have to wait for Zotero 2.0.. - Yaroslav Nikolaev
and rethinking the above discussion (including binary vs ascii part) - it appears that would Zotero or Mendeley extend their desktop clients with a "2.0" text-editing functionality (multi-user + version control), they might actually win over the conventional workflow [Word/OpenOffice <> plugin <> reference repository]. Unless Neil will mashup Zotero with GDocs before that ;-) - Yaroslav Nikolaev
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Help! Unsolved problems with maximized Kubuntu Intrepid windows
Saturday at 12:52 am - Link
OK, that kept me busy for a while :( - Egon Willighagen
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Thomas Lemberger posted a message
“What is better? Comma-separated values (csv) or tab-delimited text? Which one is easier/more robust to import anywhere?”
Friday at 6:46 am - Link
tab-delimited is easier because your fields may already contains some commas - Pierre
Shouldn't make a difference if you're using the appropriate libs. The same problem Pierre mentioned with comma's can occur with tabs - Rajarshi Guha
this is where explicit semantics can be useful :) - Egon Willighagen
No difference at all - it just depends on the quirks of whatever you use to read the file. Spreadsheets have "merge delimiters" and might require quotes around fields, databases likewise, awk has the -F switch, etc. etc. I prefer tabs since they (usually) make the plain text file more readable. - Neil Saunders
can I say neither? Just use something like XML ;) - Allyson Lister
@Allyson absolutely - Duncan Hull
@Allyson: I was anticipating this one a little...But I was thinking of something 'wet biologist'-friendly. Also Google Doc chokes on XML... - Thomas Lemberger
XML is great - where it's available and where it's appropriate for the job. "Wet biologists" love files that they can open in spreadsheets. Delimited files are also good for database import and simple shell script munging using grep, awk, sed, sort etc. - Neil Saunders
(Thanks Duncan!) Yes, I also agree with Thomas and Neil about the right tool for the job. I'm actually involved both in FuGE (http://fuge.sf.net) and ISA-TAB (http://isatab.sf.net). FuGE is a fanastic UML/XSD/(and more) object model for experimental metadata structure & syntax. However, biologists love excel, and that's one of the reasons I'm also involved in the partnered ISA-TAB project, which builds on MAGE-TAB and also leverages FuGE. They are virtually interchangeable - so best of both worlds! - Allyson Lister
a table should stay a table (maybe with a header), not xml, otherwise you are just duplicating the header as xml tags for every single row - Jeremy Leipzig
I agree with Jeremy, if you have a ifxed number of well-defined cols, why add more verbiage? Though if you do want to add it, VOTables is an XML format for tabular data (used in the astro community) - Rajarshi Guha
Do *.csv files open up in Excel without the whole 'choose which delimiter is being used' dialog thing? That'd be a minor edge over tab delimited text. - Euan
Don't use XML if you have something well-structured. XML is powerful when things are *not* well-structured. No XML for a vector of floats, do XML for web pages. No XML for protein sequence, do XML for web/cloud services. - Egon Willighagen
Yes, Euan, they do. - Mr. Gunn
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Pierre posted a message on Twitter
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“Can you see different colors for elements, species and chemicals in this Open Access article..again, only works in Internet Explorer: http://www.chemspider.com/Arti...
November 13 at 10:31 pm - Link
Yes, I can see different colours in IE, not in Firefox. Nice feature :) - arek
I see nothing. Any chance we'll see a FF version? - Egon Willighagen
What tool are you using on the backend for entity extraction? Out of curiosity (I don't have IE handy) how many terms does it highlight in that text? - Rajarshi Guha
here's something that also works in Firefox: http://reflect.ws/Reflection_h... ( http://reflect.ws ). Although I'm on a Mac and so I don't know what actions are linked to the colored items in the posted URL - Michael Kuhn
Works here. What tool is used to extract the terms? - Rajarshi Guha
Michael, cool! That works for me too! But that's not ChemMantis, or is it? Where does this come from? And a very cool TLD, btw! - Egon Willighagen
Oh, and does it use semantic markup, like microformats or RDFa? Would love to see our Userscripts work on it! - Egon Willighagen
I noticed the class="reflect_chemical"... I'll update my userscript to support that (soon) - Egon Willighagen
Reflect is using the STRING/STITCH text-mining engine, plus lots of Java/browser plug-in magic by Evangelos Pafilis et al. I'm sure that if you contact Evangelos or Sean O'Donoghue with an idea about microformats etc. they might be able to embed something. - Michael Kuhn
(the approach is dictionary based, so no fancy recognition of IUPAC names etc.) - Michael Kuhn
Can you give an idea of how many terms it recognizes in that doc? For example, OSCAR (via the Greasemonkey script) gets 150 terms. - Rajarshi Guha
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“Hi, I need some guidance in setting up a webservice (WSDL/REST based) based on an integrated web server that we recently developed. Any links or best-practices on developing webservices ?”
Friday at 6:24 am - Link
if you're programming with JAVA, see the latest implementation of JavaWS. All your methods can be implemented using simple annotations: http://www.netbeans.org/kb/55/... - Pierre
EMBRACE more or less requires you to start with WDSL, not with Java code... - Egon Willighagen
It comes down to following the rules defined by: http://www.ws-i.org/ - Egon Willighagen
@Pierre : Major components of the server is developed in Perl. I am looking for a Perl based solution to implement this at first round. - Shameer Khader
@Egon Thanks for the links - Shameer Khader
The Catalyst web framework makes it easy to expose controller actions as REST targets. It's written in Perl although the learning curve is a bit steep: http://www.catalystframework.o... - Todd Harris
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The Life Scientists: James Watson posted a message
“Hi there”
Friday at 3:53 am - Link
Whoops! Bumped return by accident. What I meant to say was, I'm new to friendfeed and wanted to introduce myself. I am a scientific training officer at the European Bioinformatics Institute and am looking to keep up to date with developments in the field. Look forward to reading and posting in the future. - James Watson
Welcome James - Egon Willighagen
Welcome. Good to see more people from the campus. - Jan Aerts
Welcome. Please, make your feeds public so we can see what is your job about :-) - Pierre
Thanks folks for the welcome. Will update profile make it public! :-) - James Watson
Welcome! I haven't found a better, more fun way to stay up to date, and to discuss science matters than this room.Hope you find it just as enjoyable! - Chris Lasher
Welcome. There is also science online, a room dedicated to science communication, here: http://friendfeed.com/rooms/sc..., please feel free to join. - Maxine
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Egon Willighagen shared an item on Google Reader
November 14 at 1:55 am - Link
Picture of a nearby three-planet (at least) solar system. - Egon Willighagen
giving a 400 bad request though? - Neil Saunders
Mmmm... worked earlier. Try: http://research.operationaldyn... - Egon Willighagen
not working for me either :( - but the second link does! :) - Allyson Lister
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Paulo Nuin posted an entry on Blind.Scientist
November 13 at 11:14 am - Link
good point - Pedro Beltrao
The point about a lack of good highly ranked web presence(s) is a really good one. Talked about it a lot but never actually got something off the ground. - Cameron Neylon
Left my comment in the blog. - Egon Willighagen
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Noel O'Boyle shared an item on Google Reader
November 2 at 3:14 pm - Link
New Dutch coin looks cool - was created by Python. - Noel O'Boyle
and many other open source tools... rather cool blog post, though... really makes me want to buy the coin :) - Egon Willighagen
Ha, my 5 euro coin has arrived :) - Egon Willighagen
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Pawel Szczesny posted a message on Twitter
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Egon Willighagen shared an item on Google Reader
November 13 at 4:48 am - Link
Nice... towards Trust. - Egon Willighagen
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November 13 at 2:47 am - via Bookmarklet - Link
very strong claims: "Intelligence can predict mortality more strongly than body mass index, total cholesterol, blood pressure or blood glucose, and at a similar level to smoking4. But the reasons for this are still mysterious. That needs to change. Reducing health inequalities is a priority, and to do that we need to determine their causes." - Attila Csordas via Bookmarklet
Ummm... don't intelligent people not just take better care of their health? I mean, you have to be pretty stupid to and smoke, and drink much, and eat McDonalds all the time... or... ? - Egon Willighagen
Interesting link, I tweeted it. - Donnie Berkholz
mind over matter :o) - sofarsoshawn
Notably not mentioned: fecundity. Number of offspring is negatively correlated with IQ scores http://is.gd/7A4u (sorry, couldn't find more recent literature--anyone's Google Fu stronger tonight?), and number of offspring is negatively correlated with age of death in most organisms (are humans the exception? I cannot find a published paper to support this; here's the best search I could come up with http://is.gd/7A7f). So if intelligent people have fewer kids, they should live longer, right? - Chris Lasher
Also as an aside, the most intelligent people I know have no kids (with a few exceptions). So in the game of life, being extremely intelligent is bad mark. :-( - Chris Lasher
I am certain that there is also a correlation between number of children and mortality rate. Most certainly 100 years ago, having a child would be one of the top 10 causes of death, although this is not my area of study and I am just guessing. So is it cause or effect? - Jim Hardy
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Neil Saunders posted a message
“More and more, this image sums up how I feel about academia as compared with, you know, cool web stuff”
More and more, this image sums up how I feel about academia as compared with, you know, cool web stuff
November 12 at 1:52 am - Link
I try to combine the two: http://www.iplant.eu - Christopher Harris
hum... may be I would prefer the right side if I was able to publish something.... - Pierre
Neil: where's the cartoon from ? Any copyright ? Can I use it ? - Nils Reinton
http://www.ashersarlin.com/arc...; I've seen it used lots of other places. - Neil Saunders
I like the right side too - not that I am an academic, I just like peace and quiet cf parties with dinosaurs. - Maxine
... and then there is teaching. - Roland Krause
This was my desktop the entire time I was writing my dissertation. - Mr. Gunn
I love how everyone interprets this differently, depending on their personal circumstance. I'm thinking something quite different to many of the comments. - Neil Saunders
I've always interpreted it as the internet being a huge distraction from boring work. Only now do I see that it can also mean "The internet is cool and science is boring" - Eva
... but what about "Web Science" or "Internet Science"? - Duncan Hull
Why do people feel this way? I thought everyone was by now using the Internet to write research papers? At least, I'm having an Internet party when I write a paper... CiteULike, PubMed (with JabRef), FF, Pg, Cb for recent papers, RSS for ToCs, and I think RDF is just around the corner... what more fun would you like? - Egon Willighagen
I have another interpretation. The look on the academic's face says "look at that new and frightening technology! How do I approach it? I know! I'll stand well back and write an old fashioned paper telling everyone what they already know about it." ;) - Joe Dunckley
Well, surely I can answer that myself... Ubiquity: "query-web my-paper limit:2000-NOW", and have RDF, SPARQL summarize all stuff on the internet possibly related to my paper, using the reference list, chemical structures, enzymes, genes, whatever I mention in my paper... trivial, just no one implemented it yet. - Egon Willighagen
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Noel O'Boyle shared an item on Google Reader
November 12 at 5:17 am - Link
I'd forgotten about yubnub. I saw it many years ago. Should work well with several chemistry RESTful webservices that have sprung up since. - Noel O'Boyle
If you actually one of those running Konqueror, these things are called web shortcuts... check out CDK News for some for CDK... - Egon Willighagen
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Egon Willighagen bookmarked a page on delicious
November 13 at 2:04 am - Link
Is this going to be the Skype-killer? - Egon Willighagen
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November 12 at 2:09 pm - Link
Works fine ! (Learned SPARQL Yesterday :-) ) PREFIX myexp: <http://rdf.myexperiment.org/on...> PREFIX dc: <http://purl.org/dc/elements/1....> select ?x ?title { ?x a myexp:Workflow . ?x dc:title ?title } - Pierre
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Egon Willighagen posted a message
“Cameron, an RSS feed for the ONS data require some timestamping in the spreadsheet...”
November 12 at 12:53 pm - Link
Alternatively just read the new rows since the last update? - Rajarshi Guha
Have been thinking about that... setting up a cache of some sort... will do some work on RDF first... - Egon Willighagen
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November 11 at 11:28 pm - Link
Molecule DB support in Bioclipse. - Egon Willighagen
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Egon Willighagen bookmarked a page on delicious
November 12 at 4:42 am - Link
Heated discussion on why access to source code is important to reviewing that code... Feel free to join in. My opinion: OpenSource simplifies the process of peer review. - Egon Willighagen
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Egon Willighagen shared an item on Google Reader
November 12 at 2:07 am - Link
Ha, finally someone who realizes that the USA is *not* the center of the universe. Maybe Obama does manage to make a difference ;) - Egon Willighagen
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