Re: [Blue-obelisk] Planet down for the count?
On Tuesday 14 November 2006 16:05, richard apodaca wrote: > Geoff already asked this, but what's the status of the > Planet feed aggregator for Blue Obelisk? I found that > site very convenient. It's working for me: http://wiki.cubic.uni-koeln.de/planetbo/ What URL are you using? Egon -- http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Spread Blue Obelisk
On Monday 13 November 2006 10:49, Jerome Pansanel wrote: > I have added two small icons on BO wiki. This icons (or logo) could be used > on website to promote Blue Obelisk. > > http://wiki.cubic.uni-koeln.de/bowiki/index.php/Logos > > What are you thinking about ? I like them, and would invite all BO affiliated projects to put it on their main pages. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Java press release
On Monday 13 November 2006 17:51, Jerome Pansanel wrote: > http://www.sun.com/smi/Press/sunflash/2006-11/sunflash.20061113.1.xml > > Happy reading ! Note that it is not just GPL to licensed it to, but GPL + the Classpath exception. What this practically means, is that they joined up with the Classpath team, instead of Harmony, the Apache initiative that did not want to be compatible with Classpath. You can read on Planet Classpath what the opensource java community thinks of it: http://planet.classpath.org/ Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Re: blue-obelisk RSS-feed broken
On Thursday 16 November 2006 14:11, Daniel Leidert wrote: > Unfortunately Peters entry breaks the RSS-feed. Any chance to fix this? > > > http://wiki.cubic.uni-koeln.de/planetbo/rss20.xml No, unfortunately not :( I might try to upgrade the planetplanet software, because the version Planet BO currently uses is buggy. Can you recommend good aggregator software? Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] http://www.blueobelisk.org/planetbo/
Hi all, http://www.blueobelisk.org/planetbo/ works again. Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] reported bugs in BODR 4
Hi all, the following two bugs are reported at the CDK SF webpage: [ 1603066 ] acidity of the elements seems weird Seeing helium listed as basic in bodr makes me quite perplex. What kind of acido-basicity this might be? As long as I can't understand this even with the help of my library, I consider all these data as a bug. [ 1603063 ] actinides are listed as rare earths in bodr Rare earths elements are scandium, yttrium and the lanthanides. Actinides are not rare earth elements and should not belong to this family. These bits of data come from Kalzium. Carsten, could you please comment on these two things? Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Re: Python Cheminformatics Framework
On Monday 27 November 2006 22:45, John Stone wrote: > I've had enough discussions with people that have hard-core GPL viewpoints > to know that some people view all non-GPL licenses as insufficient, but my > own situation is one of the cases that GPL doesn't help with and actually > makes life harder than it needs to be. BSD-like licenses I can work with. > Many people can't use GPL licenses due to constraints of their funding > agency, employer, etc. I have trouble understanding this reasoning. Is'nt it actually the agency/employer making things more difficult than needed, here? If you like the color of a car, but your family not, is it the color that is the problem?? > The virality of GPL prevents me (and many others) > from being able to incorporate software licensed with it. I would say that it is your legal deparment (or NIH) preventing you to use to full set of open source software. > Since I see > merits to both sides of the issue, I've been working on finding out about > dual licensing VMD somehow in such a way that we can still report > statistics to NIH (perhaps GPL older versions of VMD ex post facto?), > but even if I dual license adding GPL as an option, I still won't be > able to use GPLed code in the mainline VMD. So while I appreciate the > issues that drive many to use GPL as their license, I probably can't use > their software even if I dual license to play nice, which is a bummer. But many other open source licenses conflict too, e.g. the Apache License and the LGPL (though many overlook this issue, including me). How does the VMD project work around those things? Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] reported bugs in BODR 4
On Friday 01 December 2006 08:58, Carsten Niehaus wrote: > Conclusion: I could remove the familiy-attribute from the actinides and > remove the whole dataset of acidity/basic/neutral/amphoteric. This would be > better then having (possibly) wrong data IMHO. Please fo ahead. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] atom type data into BODR?
Dear Geoff, the atom type list from OB has been on BODR SVN for some time now, and I want to make a start with converting this to CML so that I can add it to the BODR releases. Could you please explain the four txt files in BODR SVN, i.e. aromatic.txt, atomtyp.txt, bondtyp.txt and types.txt and how they relate? types.txt seems to indicate how atom types are interconverted, while atomtyp.txt seems to have the SMARTS queries to perceive atom types. About the atom type perception: what input does that require? In the CDK we have several kinds of input, with combinations of: - no explicit hydrogens - explicit hybridization - missing bond orders (Most notably, atom type perception in SMILES is tricky, where hydrogens are implicitly assumed (with unknown rules), missing bond orders, but with explicit hybridization states.) Does OpenBabel perceive atom types, or just read them from files? If perception is done, do you rely simply on the SMARTS queries, and how well do those work with the above three types of missing input features? Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] BODR 5 released
Hi all, except for the two bug fixes for bugs recently reported by Jean [1,2], nothing really changed in BODR 5. Really a bug fix release, you might say. You can download the new release from CDK's SF page at: http://sourceforge.net/project/showfiles.php?group_id=20024 Egon 1.http://sourceforge.net/tracker/index.php?func=detail&aid=1603066&group_id=20024&atid=120024 2.http://sourceforge.net/tracker/index.php?func=detail&aid=1603063&group_id=20024&atid=120024 -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] atom type data into BODR?
Geoff, (Christian, please read too and comment on the MM2 and MMFF94 atom types in the CDK... thanx!) On Wednesday 03 January 2007 01:42, Geoffrey Hutchison wrote: > > the atom type list from OB has been on BODR SVN for some time now, > > and I want to make a start with converting this to CML so that I can add > > it to the BODR releases. > > Great! The files themselves typically have a few comment lines at the > top to explain their nature. If these don't help, I've provided more > below. OK, thanx. > (And if the comment lines aren't a good explanation, please > let me know so I can change them -- I've added these to help document > the files.) Need to write on my thesis today, but will look at it asap, and report unclear bits. > > Could you please explain the four txt files in BODR SVN, i.e. > > aromatic.txt, > > atomtyp.txt, bondtyp.txt and types.txt and how they relate? > > ... > > > types.txt seems to indicate how atom types are interconverted, while > > atomtyp.txt seems to have the SMARTS queries to perceive atom types. > > * Types.txt is a basic lookup table for converting between different > atom types (e.g., Sybyl to PC Model). I think this is the first, and > best, example needing standardization. For example, we haven't yet > coded MM3 or MMFF94 atom types in Open Babel, but these are in CDK, > right? Indeed we have MM2 (not MM3) and MMFF94. But not sure how complete those lists are. (cc: Christian Hoppe) > The remainder include SMARTS patterns, and it's worth mentioning that > currently Open Babel can involve atom hybridization in SMARTS (e.g., > [#6D2^1] => sp-hybridized carbon with 2 connections). Good. > * Bondtype.txt is used in bond order assignment. It consists of a > SMARTS pattern, followed by a set of triples (index1, index2, order) > where index1 and index2 are atom indexes into the SMARTS. Assignment > is done first to last, so specific matches should be done earlier. > For example allene: > [#6^2][#6D2^1][#6^2]0 1 2 1 2 2 > # bond between 0 and 1 becomes double bond, 1 and 2 becomes double bond Interesting approach. Much more rule based than what CDK has, but that one fails in certain conditions... > * Aromatic.txt is used in aromaticity detection. It consists of a > SMARTS pattern, followed by a minimum and maximum number of pi > electrons on that atom matching the SMARTS. The last pattern in the > SMARTS is chosen, so patterns typically go from more general to more > specific. For example, nitrogen: > [#7rD2] 1 2 > # nitrogen in a ring with two connections can have 1 or 2 pi electrons Ack. > * Atomtyp.txt has three sets of SMARTS for: > - implicit hybridization (sp, sp2, sp3...) > - implicit valence (how many bonds should an atom have) > - external types (determined by other programs) > > > About the atom type perception: what input does that require? In > > the CDK we > > have several kinds of input, with combinations of: > > - no explicit hydrogens > > - explicit hybridization > > - missing bond orders > > > > (Most notably, atom type perception in SMILES is tricky, where > > hydrogens are > > implicitly assumed (with unknown rules), missing bond orders, but with > > explicit hybridization states.) > > Atom type perception is tricky. Period. Open Babel has the same sort > of problems (indeed, I think everything in chemistry does). Depending > on the source of the atoms, lazy perception in Open Babel does > various sorts of work. For example, coming from Sybyl Mol2, atom > types are assumed to be correct(?!). > > I think a better question is perhaps to discuss how to generally deal > with implicit valence. I think there was some discussion a while ago > about coding an open standard of aromatization. That might be a > useful goal here too. If so, perhaps we should start a wiki page and > I'll get some other folks involved from Open Babel. OK, I will soon start with converting the above tables into XML, in one way or another. I'll start with exploring CML, and keep your setup of files for now. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Blue Obelisk ChemoInformatics Data Repository?
On Sunday 07 January 2007 21:58, Stefan Kuhn wrote: > Am Sunday 07 January 2007 22:07 schrieb richard apodaca: > > > > In the BO paper (JCIM 2006, 991), ref. 30 lists: > > > > > > > > http://www.blueobelisk.org/repos/blueobelisk OK, after playing with the Apache cond file a bit more, I got this URL working too now. > > > Try: > > > http://wiki.cubic.uni-koeln.de/repos/blueobelisk/ > > > > Thanks Jean, but I also get 404 with that one. Any > > ideas? > > Works for me. Please try again, I think it was some temporary > server/network problem. No, that was me fiddling with the conf file ;) Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Blue Obelisk ChemoInformatics Data Repository?
On Sunday 07 January 2007 22:21, Jean Bréfort wrote: > > > > In the BO paper (JCIM 2006, 991), ref. 30 lists: > > > > > > > > http://www.blueobelisk.org/repos/blueobelisk > > > > > > Try: > > > http://wiki.cubic.uni-koeln.de/repos/blueobelisk/ > > > > Thanks Jean, but I also get 404 with that one. Any > > ideas? > > It worked 15 minutes ago and does not work anymore. Probably a server > issue... Sorry... was trying to get the URL from the article working... will restore the wiki version for now, until I figure out how to get the paper URL working... After the BO publication the wiki server crashed, and not all got restored... remember the failing www.blueobelisk.org/planetbo/ problem some time ago? I'll try to get the original URL working soon... Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Lanthanides and actinides in BODR
On Monday 08 January 2007 10:52, Jerome Pansanel wrote: > Here's a definition taken from the "Handbook of Chemistry and Physics": OK, that should do. What is the full bibtex entry for that book? Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Java+JavaDoc source code parser?
Hi all, anyone aware of a Java+JavaDoc source code parser? There are some language specs around to be used with parser generators, but I could not find one that supported JavaDoc... Basicallly, what I want to do is create a custom javadoc program. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Re: bodr stuff
Hi Daniel, it's great to hear that BODR might hit Debian soon. On Wednesday 17 January 2007 22:11, Daniel Leidert wrote: > Am Mittwoch, den 17.01.2007, 15:41 +0100 schrieb Egon Willighagen: > > On Wednesday 17 January 2007 15:19, Daniel Leidert wrote: > > > Am Mittwoch, den 17.01.2007, 14:18 +0100 schrieb Egon Willighagen: > > > > Attached. > > > > > > A few comments: > > > > Thanx! That was quick. Will apply them to SVN. > > I did some more changes and now it's linda and lintian clean and IMHO in > a good shape. This could be uploaded to Debian. Michael, your opinion? > > @Egon: The TODO list tells about some XSLT stylesheets you want > > > - add a XSLT to create HTML for the element and isotope lists > > - add help on how XSLT can be used to create TXT > > What do you need? Can I help (you know, I use XML/XSLT for > chemical-mime-data)? I need XSLT to convert the CML based data into human-readable HTML, which would go onto the Blue Obelisk webpage, and likely in the share/docs section. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Fwd: bodr_5-2.changes is NEW
FYI. Egon -- Forwarded Message -- Subject: bodr_5-2.changes is NEW Date: Friday 19 January 2007 11:02 From: Debian Installer <[EMAIL PROTECTED]> To: Egon Willighagen <[EMAIL PROTECTED]> (new) bodr_5-2.diff.gz optional science (new) bodr_5-2.dsc optional science (new) bodr_5-2_all.deb optional science The Blue Obelisk Data Repository Common repository of chemical and physical facts that aim to increase interoperability between chemistry programs. See DOI 10.1021/ci050400b. . Homepage: http://www.blueobelisk.org/ (new) bodr_5.orig.tar.gz optional science Changes: bodr (5-2) unstable; urgency=low . [ Egon Willighagen ] * debian/control: Fixed homepage format in description. (Architecture): Package is architecture independent. (Build-Depends, Build-Depends-Indep): Adjusted build-dependencies. Removed autotools-dev dependency. * debian/copyright: Added missing information - full authors list and the MIT license text. * debian/rules: Cleaned the file by removing commented and unused stuff. Removed stuff related to compiling a program (we don't have to compile anything). Fixed binary-arch/binary-indep targts according to changes in debian/control. * debian/dirs: Removed (unused). . [ Daniel Leidert ] * debian/control (Build-Depends-Indep): Added dpatch. (Uploaders): Added Michael Banck as sponsor. * debian/rules: Added dpatch includes and targets. * debian/patches/00list: Added. * debian/patches/90_dont_install_changelog_and_license_twice.dpatch: Added. - Makefile.in (docs_DATA): Do not install the files mentioned in docs_DATA, because we install these files separately. Override entries for your package: Announcing to debian-devel-changes@lists.debian.org Your package contains new components which requires manual editing of the override file. It is ok otherwise, so please be patient. New packages are usually added to the override file about once a week. You may have gotten the distribution wrong. You'll get warnings above if files already exist in other distributions. --- -- http://chem-bla-ics.blogspot.com/ (new) bodr_5-2.diff.gz optional science (new) bodr_5-2.dsc optional science (new) bodr_5-2_all.deb optional science The Blue Obelisk Data Repository Common repository of chemical and physical facts that aim to increase interoperability between chemistry programs. See DOI 10.1021/ci050400b. . Homepage: http://www.blueobelisk.org/ (new) bodr_5.orig.tar.gz optional science Changes: bodr (5-2) unstable; urgency=low . [ Egon Willighagen ] * debian/control: Fixed homepage format in description. (Architecture): Package is architecture independent. (Build-Depends, Build-Depends-Indep): Adjusted build-dependencies. Removed autotools-dev dependency. * debian/copyright: Added missing information - full authors list and the MIT license text. * debian/rules: Cleaned the file by removing commented and unused stuff. Removed stuff related to compiling a program (we don't have to compile anything). Fixed binary-arch/binary-indep targts according to changes in debian/control. * debian/dirs: Removed (unused). . [ Daniel Leidert ] * debian/control (Build-Depends-Indep): Added dpatch. (Uploaders): Added Michael Banck as sponsor. * debian/rules: Added dpatch includes and targets. * debian/patches/00list: Added. * debian/patches/90_dont_install_changelog_and_license_twice.dpatch: Added. - Makefile.in (docs_DATA): Do not install the files mentioned in docs_DATA, because we install these files separately. Override entries for your package: Announcing to debian-devel-changes@lists.debian.org Your package contains new components which requires manual editing of the override file. It is ok otherwise, so please be patient. New packages are usually added to the override file about once a week. You may have gotten the distribution wrong. You'll get warnings above if files already exist in other distributions. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] "Bug" in BODR
On Monday 22 January 2007 17:39, Carsten Niehaus wrote: > There is a typo in the nameorigin.txt-file. > > --- nameorigin.txt (Revision 242) > +++ nameorigin.txt (Arbeitskopie) > @@ -17,7 +17,7 @@ > 13 Latin 'alumen' > 14 Latin 'silex' > 15 Greek 'phosphoros' for 'carries light' > -16 In sankskrit 'sweb' means 'to sleep' > +16 In sanskrit 'sweb' means 'to sleep' > 17 Greek 'chloros' for 'yellow-green' > 18 Greek 'aergon' for 'inactive' > 19 Arabic 'al qaliy' for potash Please file bug report with patch on cdk.sf.net, or apply it in SVN. Egon -- http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Open Access EU petition
On Monday 29 January 2007, Noel O'Boyle wrote: > I'm forwarding this message from a PLOS announcement list, as I think > several of you will be interested in supporting this... What a shame it is not an Open Data petition... :( Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Teaching Wikipedia Chemistry - We need yout vote
On Tuesday 30 January 2007 22:38, joerg.wegner wrote: > If you would like to see substructure searches and proper SMILES in > Wikipedia it would push the priority, if you 'Vote for this bug' (actually > feature request) at > http://bugzilla.wikimedia.org/show_bug.cgi?id=7514 > Unfortunately you have to create an account, so it's up to you if you > really want to do that. Done. I added two comments too... one about support for InChI, and one about support for semantic markup of chemical information. Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Fwd: [CHMINF-L] RSC Publishing launches Project Prospect
Noel, on the bright side: -- Forwarded Message -- Subject: [CHMINF-L] RSC Publishing launches Project Prospect Date: Thursday 01 February 2007 15:13 From: Valerie Simpson <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Posted on behalf of Richard Kidd February 1, 2007 Dear colleagues RSC Publishing, the publishing arm of the Royal Society of Chemistry, is pleased to announce a new initiative for its journals. From February 2007 electronic RSC journal papers will be enhanced so that their data can be read, indexed and intelligently searched by machine, a first step towards the "semantic web". Readers will be able to click on named compounds and scientific concepts in an electronic journal article to download structures, understand topics, or link through to electronic databases; compounds and ontology terms will be published as RSS feeds enabling automated discovery of relevant research. The initiative, coined 'Project Prospect', is the first of its scope from a primary research publisher. Developed together with UK academics based at the Unilever Centre of Molecular Informatics and the Computing Laboratory at Cambridge University, the Project uses InChIs (IUPAC's International Chemical Identifier for compounds); OBO ontology terms (Open Biomedical Ontologies: a hierarchical classification of biomedical terms) such as the Gene Ontology (GO) and the related Sequence Ontology (SO); terms from the IUPAC Gold Book; and CML (Chemical Markup Language: a means to describe molecular information in a structured form). This is a completely free service for authors and readers of RSC journals. The enhanced articles have an at a glance HTML view with additional features accessed by a tool box. Downloadable compound structures and printer friendly versions will be available via this new service. 'Project Prospect demonstrates our commitment to invest in innovative technologies to provide our authors and readers with the best publishing service available', said the RSC's Acting Managing Director, Robert Parker Midori Harris, GO's editor from the European Bioinformatics Institute (EBI) in Hinxton, UK, welcomes the developments: 'We're delighted by the RSC's decision to use GO and SO terms to annotate scientific papers they publish. It's an exciting application of ontologies that will help researchers search the ever-growing body of scientific literature more quickly and effectively. We hope to see more publishers following the RSC's example in the future.' The RSC intends to develop the Project over the coming months and years to increase the amount of structured science in their research articles. To find out more about the project please contact me at [EMAIL PROTECTED] or visit the project website at http://www.rsc.org/Publishing/Journals/ProjectProspect/index.asp With best wishes, Richard Kidd Manager, Editorial Production Systems DISCLAIMER: This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening. CHMINF-L Archives (also to join or leave CHMINF-L, etc.) http://listserv.indiana.edu/archives/chminf-l.html Search the CHMINF-L archives at: https://listserv.indiana.edu/cgi-bin/wa-iub.exe?S1=chminf-l Sponsors of CHMINF-L: http://www.indiana.edu/~libchem/chminfsupport.htm --- -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Fwd: [CHMINF-L] RSC Publishing launches Project Prospect
On Thursday 01 February 2007 17:24, richard apodaca wrote: > Now comes the tricky part - will they let robots mine > their data? Will they provide an API? Will they offer > their dataset for download? Colin, may I ask you to answer these questions? Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Fwd: [CHMINF-L] RSC Publishing launches Project Prospect
On Thursday 01 February 2007 18:01, Colin Batchelor wrote: > The intended route for that sort of thing is going to be the RSS feeds, > which will contain all of the InChIs and all of the ontology terms, and > will be along in the next couple of weeks. Some questions on these feeds: - will the RSS feeds also contain CML? e.g. spectra with CMLSpec, 3D crystal structures - will each article have its own feed? - to what extent will RDF be integrated? And another questions: - what are the chances I can convince on the use of microformats or RDFa support in the Project View of papers? See Chemical blogspace, or my blog. - the articles seem only processed with OSCAR3(orBetter). What options do authors have to supply InChI's themselves, or even CML? Has anything been formalized in this respect? Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] BODR mentioned in latest Linux Format
On Tuesday 06 February 2007 13:57, Noel O'Boyle wrote: > gElemental (a fork of gPeriodic) got a write up in the latest Linux > Format (available on paper only). One of the coming attractions is > integration of the BODR, which is mentioned in the review as a very > positive idea... :) First we take the world, then the chemoinformatics community.. Egon -- http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] A BODR project on SF?
Hi all, a number of bugs have been reported in the past for BODR, and a few more reports were announced earlier this week. While the BO mailing list is the obvious and true ML to use, and we also have SVN, BODR really needs a BTS too. I have been thinking of simply setting up a SF project for just the BODR project. Now that it is entering the first Linux distribution (Debian), and that it even is mentioned in LinuxFormat, it really seems to take off now, and a separate project page does not seem too bad. If no one disagrees within the next few days, I'll go ahead. If you support this proposal, please let that be know too :) Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] A BODR project on SF?
On Wednesday 07 February 2007 17:30:41 [EMAIL PROTECTED] wrote: > Overall, I think that SF listing is a plus for BODR. I have seen several and positive only messages, so going ahead with this. Will report when the bodr.sf.net is available. Egon -- Radboud University Nijmegen http://www.cac.science.ru.nl/ blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] A BODR project on SF?
On Wednesday 07 February 2007, Egon Willighagen wrote: > If no one disagrees within the next few days, I'll go ahead. If you support > this proposal, please let that be know too :) I only received positive comments, and went ahead. bodr.sf.net is now online. The shell is down right now, so I can't set up a webpage (i.e. link to the wiki) yet... What about SVN? Should I port that to SF? Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Re: Chemical test file repository (was: Chemical MIME <=> Open Babel updates)
cc: Bob/Nico (of Jmol, not sure if they are on the list) On Monday 19 February 2007, Geoffrey Hutchison wrote: > On Feb 18, 2007, at 10:10 PM, Daniel Leidert wrote: > > as own "module" of blue-obelisk)? Such a central repository would also > > allow a strict structuring of the data (valid/invalid formats, testing > > of files with a wrong extension, ...). The test-implementations itself > > (C/C++/XML/XSLT/Java/... code), should then be part of the related > > projects (should be simple, to write the necessary code for ant/ > > make to download the SVN tree of test files). > > Yes, I think this is perfect. One minor note. Open Babel also accepts > some "non-standard" formats, so I'd suggest a structure like: > * valid standard (e.g., PDB 2.2 standard) > * non-standard (e.g., "PDB" files) > * invalid Yes, this seems to be a good thing. Some thoughts... Licensing of the files... ours are LGPL. But OpenBabel's test files are GPL, I assume... so, we either need to get things relicensed to, e.g., MIT license (as we use for BODR), or document thing properly. Another thing that would be interesting is to keep track of the source of the file, that is, which program was used to create the file. Because not completely valid files are often output of some specific program, which we might want to support. This is not common practice, but would be good to keep track off, in terms of interoperability. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] fwd: Molecular Modeler?
Chemical Musings wrote: "OK, this is audience participation time. Does anyone out there know of any good molecular modeling (MM2, MM3, Am1) software that is free (as in beer)? Preferably for Windoze XP. Since leaving my swanky academic position, where the software was bountiful, thanks to grants and site licenses, I have no way to casually minimize molecules. I am looking for something like Spartan or Chem3d, something that will do rudimentary minimizations. It must also export PDB files. A nice GUI is preferred as well." If you have a good suggestion, please leave a comment on his blog: http://chemicalmusings.wordpress.com/2007/02/21/molecular-modeler/ Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Google SoC project ideas: now! (deadline 12 March)
Hi all, those subscribed to the Jmol, Bioclipse or CDK mailing list, will have seen that I put up wiki pages for Google SoC project idea pages. If you work with students, that is, are a teacher as a university (or similar), please consider writing up a project idea, and consider being a mentor. Now, in addition to the ideas for these three projects, we (Carsten, Jerome, Jos and me) proposed semantic desktop/desktop search support for biology and chemistry (see Carsten's blog [1]). The idea is that this will build upon the existing Strigi, kfile-chemical, chemical MIMEs, and OpenBabel projects. One key thing, will be looking up specific molecules via InChIs. Peter MR: OSCAR3 is explcitly mentioned in the proposal, as optional goal. Please comment on this (*or* get a student to apply!). Since this is actually in the KDE set of project ideas, we don't have to wait for having the organization approved. (Ofcourse, there is a small chance that KDE gets rejected :). Egon 1.http://cniehaus.livejournal.com/33639.html -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Google SoC project ideas: now! (deadline 12 March)
On Monday 05 March 2007 16:35:45 Geoffrey Hutchison wrote: > Alas, I can't mentor this particular SoC, since I'll be away during > large parts of July and August. But I will certainly adapt for 2008. :-) > If you think it would be good to post SoC suggestions even if I can't > mentor, I can think of several. Yes, I think this is good. Pick any of the wiki pages. Keep in mind, though, that the project idea has to be with one of the participating organizations. I'll propose CDK and Bioclipse, maybe Jmol if there are ideas there too, but I don't think I can be representative for OB... So, I suggest you should try to link with a project that is participating... (I don't think it is suitable to register BO as organization here... that's not a too well defined community... more an aggregation of similarly minded projects... or...) But, wrapping something into a KDE program, or Bioclipse plugin, should not be difficult to imagine... Egon -- Radboud University Nijmegen http://www.cac.science.ru.nl/ blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] BODR 6 released
Hi all, yesterday I released a new BODR version (6), with these changes: * the elemental masses are updated to a 2006 IUPAC publication (patch by Kevin Daughtridge) * the elements/*.txt now lists "MIT" as license instead of "??" (reported by the Debian FTP team) It can be downloaded from: http://sourceforge.net/project/showfiles.php?group_id=189199 A new .deb has been proposed for inclusion in Debian [1] by people from the debichem project. Daniel, might you upload the .deb for BODR 6 you created to SF? Egon 1.http://ftp-master.debian.org/new.html -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Google Starts Summer of Code 2007
Hi all, On Friday 16 February 2007, Geoffrey Hutchison wrote: > I think we should apply -- we obviously have nothing to lose, and a > lot to gain. I applied with Bioclipse and the CDK yesterday, and via the KDE there is some chemistry involved too. Geoff, did you apply with OpenBabel? Anyone else? Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Google SoC project ideas: now! (deadline 12 March)
On Monday 05 March 2007 16:44:28 Egon Willighagen wrote: OK, CDK and Bioclipse tried, and lost :( Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Google SoC project ideas: now! (deadline 12 March)
> Was there any feedback for next time? It's always good in such > competitions to aim to improve to get approval next year. Not yet, at least. If I get feedback, I'll report... Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Re: Blue Obelisk Firefox toolbar
On Tuesday 20 March 2007, Noel O'Boyle wrote: > On 17/03/07, Noel O'Boyle <[EMAIL PROTECTED]> wrote: > > (2) Click on the little blog button, and all DOIs or article names > > that have been 'chemical blogspaced' get text like "[2 blog > > comments]", which is hyperlinked to chemical blogspace. (Relies on a > > chemical blogspace API...does this exist?) This would be especially > > useful when used on the ACS TOC pages on the web. > > In fact, I found that this has already been done for postgenomic.com, > and with a few tweaks it now works for ACS TOC pages at least and > chemical blogspace...see > http://www.redbrick.dcu.ie/~noel/PDB/findPDB.html for the Greasemonkey > script and installation instructions. It's pretty cool, actually :-) > but praise should go to the original author Pedro Beltrao. Nice indeed. Thanx for hacking that up, I never came around to that. Similar things have been done for PubMed: http://www.ghastlyfop.com/blog/2006/09/postgenomic-pubmed-mashup.html Will blog about this in 'Chemical blogspace' shortly... Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Re: Blue Obelisk Firefox toolbar
On Tuesday 20 March 2007, peter murray-rust wrote: > At 10:34 20/03/2007, Noel O'Boyle wrote: > >In fact, I found that this has already been done for postgenomic.com, > >and with a few tweaks it now works for ACS TOC pages at least and > >chemical blogspace...see > >http://www.redbrick.dcu.ie/~noel/PDB/findPDB.html for the Greasemonkey > >script and installation instructions. It's pretty cool, actually :-) > >but praise should go to the original author Pedro Beltrao. > > Sensational! I would like to exhibit this in my talk at ACS on Sunday > - in the Gary Wiggins symposium. Any comments? The most interesting of Noel's script as compared to the greasemonkey script I wrote earlier for InChI's and SMILES [1], is that it checks first if information is really present. It's a bit in efficient, but nowadays machines should have no problem with that, and the advantages are clear. I should adapt my user script to check first too, if the InChI is present in PubChem. BTW, Noel, it might be interesting to look at that script I linked to in the other reply, which actually puts content from PG in the TOC of the journal. Since Cb is based on the PG software, the API should be the same. Egon 1.http://chem-bla-ics.blogspot.com/2006/12/smiles-cas-and-inchi-in-blogs.html -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Re: Re: Blue Obelisk Firefox toolbar
On Tuesday 20 March 2007, Noel O'Boyle wrote: > Will do - it would be nice to have a central location for > Chemistry-related Greasemonkey/Javascript scripts, so that next time I > won't overlook work that you or someone else has already carried out. > Maybe somewhere on the BO wiki. Yes, that would be a good idea. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Fwd: Strigi: chemistry and biology support
> Alexandr Goncearenco applied for GSoC and here is his proposal. He's a CUBIC student, and did quite well in the course part. > I am able (as > I am a GSoC-mentor) to ask "official" questions in the GSoC-forum so that > Alexadnrs answer can be seen by others Mentors. The more precise the > application is the higher the chances he'll get a chance that his > application is picked. I think the proposal is quite ambitious, but he has a good programming track, and might just actually make it happen. Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Blue Obelisk Dinner and obelisk migrations
> * Jean Claude Bradley for services to promoting all sorts of Openness > and being brave enough to do it. > > JC wasn't physically present so we hope we shall have photographic > evidence of the transfer. JC was not in the CINF session in the morning, but fortunately ran into him in the hallway when heading back to the hotel. We handed him the BO officially, and Christoph took pictures. Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Re: BOwiki site
On Saturday 31 March 2007, Martin Walker wrote: > I meant to mention, the BOwiki has been out of order all this > afternoon. Are you upgrading something, or is there something wrong? Sorry for that... forgot to warn the mailing list. It was a long scheduled outage of power. I thought to do that when I got back to NL from the ACS meeting (which was great, and very nice meeting you!), but should have realized before that I would be sleeping on friday/saturday :) Everything should be back to normal now. Sorry for the inconvenience. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Fwd: bodr_6-1_i386.changes ACCEPTED
FYI. BODR is now part of the Debian GNU/Linux distribution. Did not make 4.0, so scheduled for 4.1, or 5.0, or whatever is next. Egon -- Accepted: bodr_6-1.diff.gz to pool/main/b/bodr/bodr_6-1.diff.gz bodr_6-1.dsc to pool/main/b/bodr/bodr_6-1.dsc bodr_6-1_all.deb to pool/main/b/bodr/bodr_6-1_all.deb bodr_6.orig.tar.gz to pool/main/b/bodr/bodr_6.orig.tar.gz Override entries for your package: bodr_6-1.dsc - optional science bodr_6-1_all.deb - optional science Announcing to debian-devel-changes@lists.debian.org Thank you for your contribution to Debian. -- -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 Accepted: bodr_6-1.diff.gz to pool/main/b/bodr/bodr_6-1.diff.gz bodr_6-1.dsc to pool/main/b/bodr/bodr_6-1.dsc bodr_6-1_all.deb to pool/main/b/bodr/bodr_6-1_all.deb bodr_6.orig.tar.gz to pool/main/b/bodr/bodr_6.orig.tar.gz Override entries for your package: bodr_6-1.dsc - optional science bodr_6-1_all.deb - optional science Announcing to debian-devel-changes@lists.debian.org Thank you for your contribution to Debian. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Blue Obelisk in the Google Summer of Code
Two chemistry projects have made it into the Google Summer of Code: 1. a 3D viewer/editor for KDE 2. desktop searching for (bio)chemical documents see: http://code.google.com/soc/kde/about.html Both are mentored by BO members: Carsten and me, respectively. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list [EMAIL PROTECTED] http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Re: Chemical test file repository (was: Chemical MIME <=> Open Babel updates)
On Sunday 15 April 2007, peter murray-rust wrote:
> FWIW it has taken us some time to sort of (in Java) how to manage
> test files in unit tests. They cannot have absolute filenames or they
> fail on different machines. So they tend to live with the test suite
> and be accessed by relative URLs. This works fine, but it is slightly
> more difficult with files not in the test system.
>
> For Java, therefore, we need a URI server for the test files. We
> would load a Java BO test module under Java/maven so the libraries
> were managed. Then we would be able to load input and sample output
> files and compare them.
If you puth them in the classpath, then you can load them with:
String filename = "data/mdl/prev2000.sd";
logger.info("Testing: " + filename);
InputStream ins =
this.getClass().getClassLoader().getResourceAsStream(filename);
Egon
--
[EMAIL PROTECTED]
Cologne University Bioinformatics Center (CUBIC)
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6
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Re: [Blue-obelisk] Re: Chemical test file repository
Based on Daniel's good proposal, I would like to propose a slightly different hierarchy: Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Re: Re: Blue Obelisk Firefox toolbar
On Tuesday 20 March 2007, Rajarshi Guha wrote: > On Tue, 2007-03-20 at 22:08 +, peter murray-rust wrote: > > Do we envisage many scripts or (better IMO) a single script with > > options. Yes, I am in favor of several/many scripts too. > > Here are my immediate thoughts from my viewpoint: > > - OSCAR-extracted terminology. (Some one else raised this). This > > requires a set of lexicons for the various terms - but VERY powerful. > > David Jessop (here) did a summer project on this in the Polymer area > > using GreaseMonkey. Worked beautifully. > > - OSCAR extracted compounds. Might have to link through to a site > > such as WWMM or PubChem to resolve some of the names. We can't easily > > cache 10 million names Correct, see below. > > - Nick's CrystalEye database (for papers with crystal structures). > > Very powerful - can be linked through DOI in the same was as Cb. > > I've been trying to play around with Javascript and web services so that > I can pull database hits, 2D images and whatever else is a web service > and annotate a page. Yes, I saw you make that bookmark... SOAP via JavaScript. OSCAR integration would indeed require a webservice, and I would certainly split that of as separate userscript. > However I'm hitting a wall when it comes to web services that return > anything but a String when using the Mozilla SOAP api. That does not sound uncommon. SOAP libraries are often only partial implementation. > Does anybody have any experience with the Mozilla SOAP api? No, not yet. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] BO Award page (was: Revamp of the wiki)
On Friday 27 April 2007, Noel O'Boyle wrote: > I don't see any mention of the Blue Obelisk Awards... Page added, but is incomplete (did I get the list correct?), and I think we need to add the pictures. Because I did not exactly know the exact reasons for the award, I guessed something. Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] [ bodr-Bugs-1713504 ] Please prune unnecessary .pc file entries
Forwarded: Bugs item #1713504, was opened at 2007-05-05 08:50 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=928367&aid=1713504&group_id=189199 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: Please prune unnecessary .pc file entries Initial Comment: As bodr is noarch, and the .pc file is installed into %datadir, it should not containf %libdir and friends. -- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=928367&aid=1713504&group_id=189199 If you reply to this message, keeping the Subject: header intact, Mailman will discard the held message. Do this if the message is spam. If you reply to this message and include an Approved: header with the list password in it, the message will be approved for posting to the list. The Approved: header can also appear in the first line of the body of the reply. -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Relocation of mailing list?
On Tuesday 08 May 2007, Daniel Leidert wrote: > Am Dienstag, den 08.05.2007, 13:52 +0200 schrieb Christoph Steinbeck: > > As the owner of the domain "blueobelisk.org" and current host of the BO > > sites, I agree with all that has been said. > > The most important thing: We need a stable location. > > My choice would be SourceForge and I've taken the freedom to register > > the project *blueobelisk* at SourceForge. > > Egon already registered bodr.sourceforge.net. > http://sourceforge.net/projects/bodr That one is specific for the BO data repository of isotope, element, atom type data. I think they can coexist without any problem. Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] CML RSS
> I think this way will be easier for clients and servers alike. It would not be too difficult to support this in Bioclipse. > If the link resolves to an RDF description or a GRDDL-able HTML page you > could retrieve additional metadata as well. > > Any thoughts? Yeah, I have seen CMLRSS used at more occassions to publish a full database. I do not feel this appropriate use of CMLRSS. Maybe it is, but running it on a large database is going to give problems. I my view, the area of application of RSS and CMLRSS is news, either about publishing new blog items or news headlines or new additions to molecular/crystal databases. For other applications, we need to look at true RDF. Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] CML RSS
> Peter wrote: > Had a chance to play with the latest Bioclipse and although there > were bugs (which we may sort out tomorrow) the OPML tool is able to > feed CrystalEye stuff to Bioclipse and display it. One thing that would already help a lot is a proper XML editor. The Eclipse Web Tools Package has a very good one (syntax highlighting, visual error reports, autocompletion, a tree view and a 'plain text' view, ...), but that has not been available as a separate tool sofar... let's see what Eclipse RCP 3.3 does in this respect... Additionally, I plan a (RCP) Forms based approach, or maybe a simple table based approach for a non plain text XML editing, but a GUI for adding and editing feeds. Help is always most welcome and *much* appreciated. > So I favour the > traditonal idea of a feed with a fairly short list of back items - > e.g. last 30 entries. If you miss them you have to look elsewhere for > the archive. So the RSS feed should be a FIFO. (Note to myself: Jean-Claude has code that allows local archiving of older feed content. I hope to see that integrated into the CMLRSS reader in Bioclipse. :) > I am convinced that we should promote Bioclipse as the rich client > and I think that it could work well for NCI. Will require quite a lot > of work in quality assurance, etc. - testing different platforms etc. Indeed... anyone can help here. A growing number of cheat sheets are being written to guide new users through available functionality, and we are exploring to use these as testing framework... > but then the CMLRSS could be very exciting. Bioclipse has "features" > (bad name - really pluginSets) Sorry about that. This is inherited from the Eclipse RCP framework, so blame IBM :) > which can be customised to provide > task-oriented collections of plugins. Thus NCI could have a > "submisson" feature, or a "latest compounds" CMLRSS feature. Please check the below Bioclipse wiki page to see which features are being set up. Use of this RCP technology is really very new in Bioclipse, and was started only 3 weeks ago, so there are still some rough edges. The idea is that a 'feature' defines a minimal set of 'plugins'. The plugins provide the actual functionality, and the feature defines what functionality is required to perform a specific task. So, you can expect a CMLRSS feature, which will extend the core Bioclipse with just that functionality to allow CMLRSS reading. Another feature example would be the structure elucidation feature, which will likely even be split up in NMR based and MS based CASE. One feature for each of them. This allows users to get a Bioclipse interface tuned to what they need to do. Of course, you may install all features you like. Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Relocation of mailing list to Google Groups + rant
On Wednesday 16 May 2007, Sanford Dickert wrote: > > I vote against this and the reasons are as easy: Google (groups) has > > nothing to do with Open Source, Data or Standards and their services > > also have technical problems (I don't want to blame them, but that's the > > situation). I would very much concentrate our services in one place. SF.net does our SVN, has forums, mailing lists, basically all we need. > Actually, google has been a supporter of open source efforts for quite some > time. They also fail to have any interest in chemistry what so ever. Even when it is indexing chemistry. > Their news service has nothing to do with the google groups, and > they have been steadily improving this service (full disclosure: I am > personal friends with the lead engineer at gGroups and was heavily involved > with eGroups). If you can get Google to provide proper support for indexing InChIs or chemistry in general, it could be tempting to have a BO group with Google. > > I don't understand, why accessing a mailing list or a newsgroup shall be > > a barrier for people wanting to join an (also) technically oriented > > project? Why do you think, you wouldn't have the problem, when you host > > the discussion forum via Google Groups service? > > The reason is that gGroups allows for easy click-thru joining - and offers > other ways of joining WITHOUT having to become a member of google or google > Accounts (e.g. you can add your email address to the list without signing > up for google Accounts) How is that different from the click-through on SF when registering with a SF mailing list? > With gGroups, you should be able to set moderation such that you have total > control over who joins, who posts, etcetera. Same on SF. SF also provides archives which people can browse. Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Blue Obelisk SF project approved. Ready to start moving.
On Wednesday 16 May 2007, Christoph Steinbeck wrote: > A minor question: Is [EMAIL PROTECTED] ok for our new > mailing list. It needs to be [EMAIL PROTECTED] We can > only choose the "something" part :-) Sounds good to me. Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Subversion access
On Monday 28 May 2007, Noel O'Boyle wrote: > I would appreciate being added as a developer to the BO project on SF. Could not find your account name... what is it? > I will use this to version any Greasemonkey scripts I'm working on. > I'll make a top-level Greasemonkey folder if this is okay with > everyone (I'll put trunk, branches, tags inside this). Personally I would prefer trunk/greasemonkey/ and tags/greasemonkey-0.5/ for tags for the releases... Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Subversion access
On Monday 28 May 2007, Egon Willighagen wrote: > On Monday 28 May 2007, Noel O'Boyle wrote: > > I would appreciate being added as a developer to the BO project on SF. > > Could not find your account name... what is it? Never mind... found it. Added as devel with SVN access. Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Subversion access
On Monday 28 May 2007, Daniel Leidert wrote:
> Am Montag, den 28.05.2007, 22:56 +0200 schrieb Egon Willighagen:
> > Personally I would prefer trunk/greasemonkey/ and tags/greasemonkey-0.5/
> > for tags for the releases...
>
> Based on the short discussion via IRC, that we had recently, I would
> suggest package/{trunk,branches,tags}, if the blueobelisk SVN is
> considered as a kind of collection place.
That would be the same as Noel suggested, right?
Egon
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[Blue-obelisk] BODR SVN moved to bodr.svn.sf.net
Hi all, the SVN for BODR has now been moved to bodr.svn.sf.net. CIA commit messages got to #cdk. Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] opendata QSAR data sets?
Hi QSAR-interested among us, should we attempt to set up a repository for opendata QSAR data sets, like [1] but then just the truely opendata ones (proper license). This repository would be one big set of CML documents with properly annotated properties. I think it would be interesting to see RDF/SPARQL or similar things in place to allow creating subsets for one specific property as input to statistics software. Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] opendata QSAR data sets?
On Tuesday 29 May 2007, Rajarshi Guha wrote: > On May 29, 2007, at 5:57 AM, Egon Willighagen wrote: > > Hi QSAR-interested among us, > > > > should we attempt to set up a repository for opendata QSAR data > > sets, like [1] > > What is [1]? sorry :) 1. http://cheminformatics.org/datasets/index.shtml Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Re: Chemical test file repository
On Tuesday 17 April 2007, Egon Willighagen wrote: > Based on Daniel's good proposal, I would like to propose a slightly > different hierarchy: > > notest="gchempaint" test="kfile-chemical" > content-test="mixed"/> > > > > > > > > >producedBy="X" license=""/> > > > > OK, started setting this up in BO's new SVN on SF. I can use some help with adding the LGPL-ed test files from the CDK project. Additionally, some XSLT sheets need to be set up to create HTML pages, or, alternatively, we use some PHP magic to dynamically convert the XML to HTML or so... Egon -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Chemical blogspace move
Hi all, my CUBIC machine is getting deinstalled as we speak... so I moved Cb to: http://blueobelisk.sf.net/cb/ This is a temporary solution as I found no way to update the MySQL database content. The old wiki machine at the CUBIC redirects the old root dir to the new one. However, direct links to particular pages (such as userscripts!) need to be update manually: s/wiki.cubic.uni-koeln.de/blueobelisk.sf.net/g Sorry for the inconvenience... Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Chemical blogspace move
> On Jun 14 2007, Egon Willighagen wrote: >>my CUBIC machine is getting deinstalled as we speak... so I moved Cb to: >> >> http://blueobelisk.sf.net/cb/ > > Is the BO greasemonkey working? I would like to demo it tomorrow at 0800 - > please let me know if not - and don't worry... Ah, no. Sorry about that. But the fix is easy (I hope you read this in time... it's 7:28 here, so that should give you 92 minutes...): find all occurrences of url: "http://wiki.cubic.uni-koeln.de/pg/api.php?type=paper&ids_only=1"; (e.g. in the get_DOI_list) and replace wiki.cubib.uni-koeln.de/pg/ by bluobelisk.sf.net/cb/ The version I have has three URLs pointing to the CUBIC. After doing that, the script works again. At least for the JCIM homepage, which has one discussed paper (the one by Agrafiotis). Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Chemical blogspace move
>> On Jun 14 2007, Egon Willighagen wrote: > Ah, no. Sorry about that. But the fix is easy (I hope you read this in > time... it's 7:28 here, so that should give you 92 minutes...): > > find all occurrences of To do that in FireFox, choose Tools -> Greasemonkey -> Manage Script. Then click the relevant script (one by one) in the left list, and then the Edit button in the lower left corner. This effects both the script to add comment to DOIs, as well as the script that does the same on the PubChem webpage for InChIs. See also: http://chemicalblogspace.blogspot.com Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Two summer-of-code like projects for Bioclipse and Jmol
Hi all, I just received confirmation that Bioclipse and Jmol both have a summer student assigned in a Dutch variant of the Summer of Code. Details will follow in my blog later this weekend. Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Chemical blogspace move
>> On Jun 14 2007, Egon Willighagen wrote: >> Is the BO greasemonkey working? I would like to demo it tomorrow at 0800 >> - >> please let me know if not - and don't worry... > > Ah, no. Sorry about that. But the fix is easy (I hope you read this in > time... it's 7:28 here, so that should give you 92 minutes...): Peter, did the message reach you in time? > find all occurrences of > > url: "http://wiki.cubic.uni-koeln.de/pg/api.php?type=paper&ids_only=1"; > > (e.g. in the get_DOI_list) > > and replace > > wiki.cubib.uni-koeln.de/pg/ > > by The new location is: cb.openmolecules.net/ Thanx to Geoff for hosting this! At this location I can run the update scripts for Cb, which I could not at SF. Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Chemical blogspace move
> On 6/17/07, Egon Willighagen <[EMAIL PROTECTED]> wrote: > Sorry to be a pest, though, but is this completely replacing Planet > Blue Obelisk? That's what I had in mind, because I have no place to run the PlanetPlanet software right now. > It's just that I thought Planet Blue Obelisk was a > really good face to show, actually - better even than the wiki, > because it emphasised us as a community of real people with real > interests, rather than as some abstract. Had not thought about that bit... the BO section of Cb suits me well, except for some missing entry titles... I even have the BO headlines on my blog front page now. > That felt really approachable > to me, compared to a "faceless", relatively-speaking, MediaWiki > install. Maybe that's just me, though! Noel wanted to reinstate the original planet BO... maybe it is a good idea. Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Chemical blogspace move
>> I'll second that. > Third? I definitely miss the Planet aggregation service. The software I used is PlanetPlanet, buggy, but does a fair job. http://www.planetplanet.org/ > Well, if Egon can give me some pointers on Planet Blue Obelisk, it can > definitely be resurrected at openmolecules.net. Suggested URLs are welcome > (planet.openmolecules.net ?) planetbo ? > I bought the domain with the intention of a chemical database aggregation > service. (Rich, please let me know if you want to hook into that.) > Clearly that never got off the ground, but I'm now thinking it would be > cooler as an additional Blue Obelisk site -- places to host open chemistry > projects. I have one docking project in the works(?) and will host > ChemSpotlight there soon. Maybe we can also set up the qsar.openmolecules.net with open data QSAR data sets... (haven't actually gotten around to open sourcing the QSAR data sets from my PhD thesis, but that should happen fairly soon... the most difficult part is to come up with a suitable CML convention to hold all info (structures *and* activities/properties), such that we can easily build webpages that can extract the info. I am thinking of a SDF equivalent, including the relevant DC fact etc... Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Mailing list move?
> On the subject of moving Blue Obelisk services... > > Let's first just get everyone using the new mailing list. Can someone > (Egon?) send me the address list for the current list? We can import that > into the new SourceForge list and switch. Christoph is already working on that... > If anyone can point me to the SF.net Support Request for the archive move, > I can bug some people. Already done, AFAIK. But SF is being slow, it seems... Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] RE: Blue-obelisk wiki redesign and planet BO
> I also find it rather intriguing > that the Blue Obelisk manifesto is published in a journal which > only subscribers (aka da club) can access. > The Blue Obelisk - Interoperability in Chemical Informatics, J. Chem. Inf. > Model., 2006, 46, 991-998. http://dx.doi.org/10.1021/ci050400b > Is there any way to liberate the content? Well, there would be no reason in targeting the readers who already are into ODOSOS :) Seriously, we should have a link that allows 50 free downloads, and unlimited downloads after a year or so (as reprints). I guess Rajarshi knows those details. Egon ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] RSS extension...
Noel, I wanted to experiment with an RSS extension [1], so that the Planet Blue Obelisk feed can be put on the front page, but discovered that the extensions/ dir is RO for group members. Can you please fix that? Egon 1.http://www.mediawiki.org/wiki/Extension:GISWiki/RSS ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
