Egon Willighagen

http://chem-bla-ics.blogspot.c... - 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

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

http://blindscientist.genedrif... and http://blindscientist.genedrif... - Paulo Nuin

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

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

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

http://www.embracegrid.info/pa... - Egon Willighagen

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

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

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

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