Re: [Blueobelisk-discuss] [Fwd: Re: gperiodic: Some issues and improvements]

2007-07-30 Thread Egon Willighagen
Dear Jonas, I did not receive your email directly, but as the one who made the recent BODR releases, I do feel obliged to respond; if you are angry at the BODR development, I take that personally. That's fine, but I was not aware that I had let you down. On 30 Jul 2007 14:34:21 +0100, Dr P.

[Blueobelisk-discuss] You got RDF?

2007-08-02 Thread Egon Willighagen
Hi all, I have been cooking up a RDF provider service [1], and can easily add RDF bits from external sources. If you run a webservice and provide, or interested in providing, RDF interface to your database, please let me know. The InChI is used as common identifier. Egon

[Blueobelisk-discuss] Help needed with cmake-ing or autotool-ifying OSRA

2007-08-12 Thread Egon Willighagen
Hi all, We have all seen OSRA, the GPL-ed library to convert images to connectivity tables. My GSoC student wrote up an extensive blog about his experiences with it (all comments to any of his blogs are much appreciated):

Re: [Blueobelisk-discuss] PMR on /.

2007-09-04 Thread Egon Willighagen
On 9/4/07, Rajarshi Guha [EMAIL PROTECTED] wrote: Open Access gets more attention! http://yro.slashdot.org/article.pl?sid=07/09/04/1341248 Go Peter! Egon -- http://chem-bla-ics.blogspot.com/ - This SF.net email is

Re: [Blueobelisk-discuss] Bugs in elements.pl

2008-01-30 Thread Egon Willighagen
On Jan 30, 2008 2:13 PM, Carsten Niehaus [EMAIL PROTECTED] wrote: If you give me a thumbs up I will changes the Perl-script to change this. Looks fine to me. Please update the changelog for the things you changed. Egon -- http://chem-bla-ics.blogspot.com/

Re: [Blueobelisk-discuss] [PATCH] elements.xml

2008-03-01 Thread Egon Willighagen
On Thu, Feb 21, 2008 at 12:08 AM, Peter Murray-Rust [EMAIL PROTECTED] wrote: I am starting to work with Geoscience Australia who need to capture isotope information in CML and I was very grateful that I could point to the BODR for elements. Many thanks Daniel and anyone else who helped.

[Blueobelisk-discuss] BODR 8 released: fixes the distcheck issues

2008-03-02 Thread Egon Willighagen
Hi all, I have just released BODR 8, which is a quick bug fix version of BODR 7 I released yesterday. Here are the changes: Release version 8 2008-03-02 * Uses CML 2.5, with two tweaks: missing Rg and Ds; allow scalar inside isotope * Fixes the distcheck errors: correct

Re: [Blueobelisk-discuss] ACS New Orleans: FOAF Expt

2008-03-10 Thread Egon Willighagen
On Mon, Nov 12, 2007 at 9:44 AM, Rzepa, Henry [EMAIL PROTECTED] wrote: For this to work, can I ask as many of you as have the time to consider making available a FOAF entry. These are being collected at http://blueobelisk.sourceforge.net/wiki/Members where you can see three entries

[Blueobelisk-discuss] Fwd: [Jmol-users] future Jmol questions

2008-03-17 Thread Egon Willighagen
FYI. Please reply to the Jmol users mailing list. Egon -- Forwarded message -- From: Bob Hanson Date: Mon, Mar 17, 2008 at 1:54 PM Subject: [Jmol-users] future Jmol questions To: [EMAIL PROTECTED] Jmol users, I'm ready to tackle two big Jmol feature requests: 1) automatic

Re: [Blueobelisk-discuss] ACS New Orleans; FOAF presentation

2008-03-30 Thread Egon Willighagen
for Obelisk... n backends: 1 Friend's project: Egon Willighagen (see http://www.blueobelisk.org/) Friend's project: Henry Rzepa (see http://www.blueobelisk.org/) Friend's project: Rajarshi Guha (see http://www.blueobelisk.org/) Friend's project: Jerome Pansanel (see http://www.blueobelisk.org/) Friend's

Re: [Blueobelisk-discuss] ACS New Orleans; FOAF presentation

2008-03-30 Thread Egon Willighagen
On Mon, Mar 31, 2008 at 3:13 AM, Egon Willighagen [EMAIL PROTECTED] wrote: Meanwhile, I have been working on a FOAFdigger ... which you can download from SVN (GPL3): https://blueobelisk.svn.sourceforge.net/svnroot/blueobelisk/foafdigger/trunk Egon -- http://chem-bla-ics.blogspot.com

Re: [Blueobelisk-discuss] About editing wiki...

2008-04-14 Thread Egon Willighagen
On Mon, Apr 14, 2008 at 6:23 AM, Vlad [EMAIL PROTECTED] wrote: I'm a principal developer JMolEditor (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html) and I would like to ask a permission to be able to edit blueobelisk wiki pages. Might you please add the license information to

Re: [Blueobelisk-discuss] Revised Covalent Radii

2008-05-01 Thread Egon Willighagen
On Thu, May 1, 2008 at 8:47 PM, Geoffrey Hutchison [EMAIL PROTECTED] wrote: Here's something to consider for the data repository. There's now a much more complete and systematic analysis of covalent radii -- just published: Covalent radii revisited

Re: [Blueobelisk-discuss] The Blue Obelisk is challenged: predicting solubility

2008-07-31 Thread Egon Willighagen
On Thu, Jul 31, 2008 at 3:43 PM, Rajarshi Guha [EMAIL PROTECTED] wrote: Reproducible is definitely a worthy model. But equally important is quality. Surely we aim at the most statistically sound *and* most predictive model. But anyone can do that. You're right that given the small training

Re: [Blueobelisk-discuss] The Blue Obelisk is challenged: predicting solubility

2008-07-31 Thread Egon Willighagen
On Thu, Jul 31, 2008 at 4:10 PM, Rajarshi Guha [EMAIL PROTECTED] wrote: First need the appropriate structrues See: http://www-jmg.ch.cam.ac.uk/data/solubility/ BTW, the file has 3D coordinates, and look at the first entry, the planar napthol: 1-Naphthol MOE2005 3D

Re: [Blueobelisk-discuss] The Blue Obelisk is challenged: predicting solubility

2008-07-31 Thread Egon Willighagen
On Thu, Jul 31, 2008 at 4:19 PM, Egon Willighagen [EMAIL PROTECTED] wrote: On Thu, Jul 31, 2008 at 4:10 PM, Rajarshi Guha [EMAIL PROTECTED] wrote: First need the appropriate structrues See: http://www-jmg.ch.cam.ac.uk/data/solubility/ BTW, the file has 3D coordinates, and look at the first

Re: [Blueobelisk-discuss] The Blue Obelisk is challenged: predicting solubility

2008-07-31 Thread Egon Willighagen
On Thu, Jul 31, 2008 at 4:37 PM, Rajarshi Guha [EMAIL PROTECTED] wrote: http://www-jmg.ch.cam.ac.uk/data/solubility/ BTW, the file has 3D coordinates, and look at the first entry, the planar napthol: Hmm, where did they come from? They can't be CCDC structures (?). If not, how were they

Re: [Blueobelisk-discuss] GNU-Darwin: Molecules and Molecule of the Day, [EMAIL PROTECTED] .org

2008-08-21 Thread Egon Willighagen
On Thu, Aug 21, 2008 at 1:43 PM, [EMAIL PROTECTED] wrote: We have 4 million small molecules in pdb format, with many more to come. Check it out. http://molecules.gnu-darwin.org/ Might you please add some copyright/license information to those pages? Under what conditions can these PDB files

Re: [Blueobelisk-discuss] Recent Drop In to Group

2009-02-12 Thread Egon Willighagen
Hi Norman, On Thu, Feb 12, 2009 at 5:04 PM, Norman L Reitzel nreit...@swbell.net wrote: I'm looking for a MOL/SDF tool that I can compile/run/fix on *nix, specifically linux but I also am coerced to support Solaris platforms. MDL molfiles can be edited with JChemPaint and Bioclipse2 (which

Re: [Blueobelisk-discuss] Google Summer of Code

2009-02-12 Thread Egon Willighagen
On Fri, Feb 13, 2009 at 4:42 AM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: No, it's not even spring yet. (Although it has been very warm here in Pittsburgh.) But it's close to time for Google Summer of Code. Over the last few years, we have been reasonably successful with chemistry

Re: [Blueobelisk-discuss] Hi! I'm lurking here too... and me too

2009-02-13 Thread Egon Willighagen
Hi Johan, On Fri, Feb 13, 2009 at 9:18 AM, Johan Henriksson jo...@student.chalmers.se wrote: I'm half through my phd at karolinska institutet Nice! Not too far from several other Blue Obelisk members... doing c.elegans (totally not molecules). background in mechanical engineering and math.

Re: [Blueobelisk-discuss] Open Standards in cheminformatics

2009-04-02 Thread Egon Willighagen
On Thu, Apr 2, 2009 at 10:09 AM, Daniel Leidert daniel.leidert.s...@gmx.net wrote: Rajarshi Guha wrote: Hi, while working on a presentation, I was wondering: are there any open standards in cheminformatics? Standard may be too strong a term - an alternative might be to ask if there are any

Re: [Blueobelisk-discuss] Open Standards in cheminformatics

2009-04-02 Thread Egon Willighagen
On Thu, Apr 2, 2009 at 1:35 PM, Jean-Claude Bradley jeanclaude.brad...@gmail.com wrote: I second Christoph - JCAMP-DX is an open standard that could do a lot more good in the chemistry community if the word gets spread more about its utility Let's summarize this in the BlueObelisk wiki, and

Re: [Blueobelisk-discuss] Open Standards in cheminformatics

2009-04-02 Thread Egon Willighagen
On Thu, Apr 2, 2009 at 4:05 PM, Craig James craig_ja...@emolecules.com wrote: Egon Willighagen wrote: Let's summarize this in the BlueObelisk wiki, and annotate things with homepage, mailing list, etc. It's always good to define our terms. Open definition:  - Public participation

Re: [Blueobelisk-discuss] Wikipedia page

2009-05-18 Thread Egon Willighagen
On Mon, May 18, 2009 at 10:11 AM, Noel O'Boyle baoille...@gmail.com wrote: Not to discourage you, but several (if not the majority) of the references to the BO paper are by people trying to find a citation for OpenBabel. I am hoping that this problem will eventually be resolved :-) Sure. But

[Blueobelisk-discuss] Anyone in Frankfurt on Monday Afternoon?

2009-08-29 Thread Egon Willighagen
Hi all, I'm giving a presentation at the GDCh meeting in Frankfurt on Monday morning, and have time in the afternoon to talk about CDK, Bioclipse and/or the Blue Obelisk movement. Or about Open Data, Open Standards and Open Source in chemoinformatics. If you happen to be around the Frankfurt

Re: [Blueobelisk-discuss] XML Summer School: Oxford 20-25th September 2009

2009-09-07 Thread Egon Willighagen
Hi Duncan, On Mon, Sep 7, 2009 at 1:22 PM, Duncan Hullduncan.h...@cs.man.ac.uk wrote: The XML summer school which returns this year at St. Edmund Hall, Oxford from 20th-25th September 2009. As always, it's packed with high quality technical XML training for every level of expertise, from the

Re: [Blueobelisk-discuss] Very sad news

2009-11-07 Thread Egon Willighagen
On Sat, Nov 7, 2009 at 8:28 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: I will also think about physical Blue Obelisk - any suggestions would be appreciated. I was wondering about that too... he has been awarded a Blue Obelisk yet, has he? Egon -- Post-doc @ Uppsala University Homepage:

Re: [Blueobelisk-discuss] Introducing Ganesh Venkateshwara and MeTA Studio

2009-11-10 Thread Egon Willighagen
Hi Ganesh! On Tue, Nov 10, 2009 at 5:34 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: This is to introduce Ganesh (copied) who has developed an Open Source framework for computational chemistry (MeTA Studio). Ganesh presented this at the Australasian eResearch conference and it's a wide-ranging

Re: [Blueobelisk-discuss] Linked Open Data BoF at #eraust09

2009-11-10 Thread Egon Willighagen
On Tue, Nov 10, 2009 at 11:48 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: Thanks - I will show this if we have time. (The msg was primarily aimed at people actually here but this is fun...) Yes, locational boundaries disappear... :) Egon -- Post-doc @ Uppsala University Homepage:

Re: [Blueobelisk-discuss] Introducing Ganesh Venkateshwara and MeTA Studio

2009-11-10 Thread Egon Willighagen
On Tue, Nov 10, 2009 at 12:38 PM, Ganesh V tovgan...@gmail.com wrote: Thanks for your mails. Yup I would like to join the community and also would like MeTA Studio to be included in the Blue Obelisk category. Great! Welcome :) Have subscribed to the BO mailing list... does this enable me to

Re: [Blueobelisk-discuss] Introducing Ganesh Venkateshwara and MeTA Studio

2009-11-10 Thread Egon Willighagen
On Tue, Nov 10, 2009 at 1:21 PM, Noel O'Boyle baoille...@gmail.com wrote: Only an admin can create an account. I'll contact you off list with a username and password Thanx! I did not remember how this was done... Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/

[Blueobelisk-discuss] Web-based Community Forum: http://blueobelisk.stackexchange.com/

2009-11-11 Thread Egon Willighagen
Hi all, again grant writing is blocked by that nasty writers block phenomenon... (well, still have a few hours before deadline...) There is something called StackOverflow, and the beta of that is free to use. Not Open, though. Consider it sort of a MS-Windows or MS-Word on which we build. I like

Re: [BlueObelisk-discuss] What is an Open Standard?

2009-12-11 Thread Egon Willighagen
On Fri, Dec 11, 2009 at 10:44 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: The intention of all the BO contributors of code and specs is to make them available, and re-usable without inappropriate restrictions. There is no intention to restrict fields of endeavour or people or organizations.

[BlueObelisk-discuss] Open Standards - Open Specifications

2009-12-11 Thread Egon Willighagen
Hi all, in reply to the other thread... one thing we seem to agree on, is that standards cannot be Open or not... something is a standard or not, and this is decided by the uptake really... Instead, what the discussion was really about is: Open Specifications. Shall we rename ODOSOS to: Open

[BlueObelisk-discuss] Fwd: Bounty Ending Soon - Blue Obelisk Exchange

2009-12-27 Thread Egon Willighagen
Hi all, there are a three questions on the BOx that have a bounty of 100 points... if you give the best answer, you both boost your karma and help the community... Egon -- Forwarded message -- From: Blue Obelisk Exchange i...@blueobelisk.stackexchange.com Date: Sun, Dec 27, 2009

Re: [BlueObelisk-discuss] Input needed: Open Standards or Open Specifications?

2010-02-16 Thread Egon Willighagen
On Tue, Feb 16, 2010 at 9:41 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: I do not see a requirement that anyone can take the specification and redistribute modified versions as useful. That is what has led to some of the proliferation of incompatibilities that we already have Quite so. But at

Re: [BlueObelisk-discuss] Input needed: Open Standards or Open Specifications?

2010-02-16 Thread Egon Willighagen
On Tue, Feb 16, 2010 at 5:23 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Tue, Feb 16, 2010 at 3:23 PM, Daniel Zaharevitz zahar...@mail.nih.gov wrote: One of the most valuable sets of specifications is the IETF drafts. They have no legal force but they are explorations of whether a

Re: [BlueObelisk-discuss] Input needed: Open Standards or Open Specifications?

2010-02-16 Thread Egon Willighagen
On Wed, Feb 17, 2010 at 12:58 AM, Geoffrey Hutchison geo...@pitt.edu wrote: One of my (unstated) goals with Open Babel is to support as many file formats as possible. Leave no chemical data behind and process it as accurately as possible. Let there be no mistake here... I do not like to

Re: [BlueObelisk-discuss] Input needed: Open Standards or Open Specifications?

2010-02-19 Thread Egon Willighagen
On Fri, Feb 19, 2010 at 2:08 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: GeoffH has made a useful suggestion (on the BO Stack Overflow, http://blueobelisk.stackexchange.com/questions/231/what-formats-fall-into-open-specification) which I'd be happy to take as a starting point. Likewise...

Re: [BlueObelisk-discuss] Input needed: Open Standards or Open Specifications?

2010-02-19 Thread Egon Willighagen
On Fri, Feb 19, 2010 at 2:58 PM, Andrew Dalke da...@dalkescientific.com wrote: Nowadays [Weininger] doesn't even do chemistry. He's started a recording studio. Does he or Daylight have obligations to continue the development of SMILES, and if so, for how long? Freedom to redistribute and

Re: [BlueObelisk-discuss] Input needed: Open Standards or Open Specifications?

2010-02-19 Thread Egon Willighagen
On Fri, Feb 19, 2010 at 3:06 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: This does not mean that there is a universal absolute right to absolute modification, but that the process of modification should be formalized. Within that some things will be permitted or encourgaed and others will be

Re: [BlueObelisk-discuss] Input needed: Open Standards or Open Specifications?

2010-02-19 Thread Egon Willighagen
On Fri, Feb 19, 2010 at 3:40 PM, Andrew Dalke da...@dalkescientific.com wrote: On Feb 19, 2010, at 9:23 AM, Egon Willighagen wrote: Freedom to redistribute and modify is used in Open Source to make that a non-issue. (just saying ... I think people understand where I'm getting at :) You

Re: [BlueObelisk-discuss] Input needed: Open Standards or Open Specifications?

2010-02-19 Thread Egon Willighagen
On Fri, Feb 19, 2010 at 6:04 PM, Craig James craig_ja...@emolecules.com wrote: My posting to BO and OB earnestly requesting help with the SMILES aromaticity definition got ... zero replies on this forum, and one on OpenBabel, from Geoff. Aromaticity is a really nasty topic... I might have

Re: [BlueObelisk-discuss] OOChemistry 0.1 released!

2010-03-06 Thread Egon Willighagen
Konstantin, On Sat, Mar 6, 2010 at 2:17 PM, Konstantin Tokarev annu...@yandex.ru wrote: We therefore have some experience of OOXML documents. We use CML as the native data structure within the DOCX and have a schema that validates it. We'd like to help make sure that - as far as possible -

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

2010-03-31 Thread Egon Willighagen
On Wed, Mar 31, 2010 at 11:29 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: I believe that it would be very valuable to have commodity QM code(s) that are Open [libre, NOT gratis] and can be used by scientists who want common calculations such as ground state geometries and energies and

[BlueObelisk-discuss] moving Blue Obelisk Exchange to Shapado

2010-03-31 Thread Egon Willighagen
the StackExchange engine to Shapado... I very much like to see the old data ported to the Shapado subdomain I just set up: http://blueobelisk.shapado.com/ Very much looking forward to hearing from you, with kind regards, Egon Willighagen 0.http://en.wikipedia.org/wiki/Blue_Obelisk 1.http

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

2010-03-31 Thread Egon Willighagen
On Wed, Mar 31, 2010 at 12:23 PM, Noel O'Boyle baoille...@gmail.com wrote: The biggest barrier to general usage is setting up the job. Do these have user interfaces? If not, can Avogadro bump this up their priority list? I'll work on it from the cclib end. Bioclipse1 has a plugin [0] to run

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

2010-03-31 Thread Egon Willighagen
On Wed, Mar 31, 2010 at 5:03 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: More accurately, however, I have watched while a compchem syadmin expert has spent an hour compiling MPQC. Debian and Ubuntu users can do: sudo aptitude install mpqc Egon -- Post-doc @ Uppsala University

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

2010-03-31 Thread Egon Willighagen
Hej Noel, On Wed, Mar 31, 2010 at 5:07 PM, Noel O'Boyle baoille...@gmail.com wrote: u...@ubuntu904desktop:~/Tools/cinfony$ apt-cache search mpqc libopenbabel-dev - Chemical toolbox library (development files) libopenbabel3 - Chemical toolbox library gabedit - graphical user interface to Ab

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

2010-03-31 Thread Egon Willighagen
On Wed, Mar 31, 2010 at 6:19 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: The point I am trying to make is that I am suggesting the BO try to make it easy for chemists, not Linux / Ubuntu / Debian experts, Apt-get is a package management system. It takes care of dependencies. Together with rpm

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

2010-03-31 Thread Egon Willighagen
On Wed, Mar 31, 2010 at 6:19 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: Is there a way the BO can help? A long time ago, when live bootable CD we're new and novel, I played with a Debian (or Ubuntu?) Live CD with Blue Obelisk software. Some of it was prepackaged, other was not. Users would

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

2010-03-31 Thread Egon Willighagen
On Wed, Mar 31, 2010 at 6:52 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Wed, Mar 31, 2010 at 6:46 PM, Egon Willighagen This is why I mentioned earlier in this thread, and several times in the past, that it is important that BO tools get adopted by (Linux) distributions (I am not aware

Re: [BlueObelisk-discuss] moving Blue Obelisk Exchange to Shapado

2010-03-31 Thread Egon Willighagen
Hi all, On Wed, Mar 31, 2010 at 12:09 PM, Egon Willighagen egon.willigha...@gmail.com wrote: I very much like to see the old data ported to the Shapado subdomain I just set up: http://blueobelisk.shapado.com/ This transition is currently in progress. It will take a while, as it seems

Re: [BlueObelisk-discuss] moving Blue Obelisk Exchange to Shapado

2010-04-02 Thread Egon Willighagen
Hi all, On Wed, Mar 31, 2010 at 8:50 PM, Egon Willighagen egon.willigha...@gmail.com wrote: On Wed, Mar 31, 2010 at 12:09 PM, Egon Willighagen egon.willigha...@gmail.com wrote: I very much like to see the old data ported to the Shapado subdomain I just set up: http://blueobelisk.shapado.com

[BlueObelisk-discuss] Maintainer needed: the CDK command line applications

2010-04-07 Thread Egon Willighagen
Hi all, a long time ago, the CDK came with a number of command line utilities... a 'babel' alternative, descriptor calculator, format guesser, etc: http://cdk.svn.sf.net/viewvc/cdk/cdk-clapps/trunk/src/main/org/openscience/cdk/applications/ These command line utilities are useful to enrich your

Re: [BlueObelisk-discuss] Blueobelisk QA at shapado

2010-04-20 Thread Egon Willighagen
Hi Noel, On Tue, Apr 20, 2010 at 10:13 AM, Noel O'Boyle baoille...@gmail.com wrote: I want to bring the new BlueObelisk QA site to the attention of the members of this list: http://blueobelisk.shapado.com/ Please help answer questions such as: (1) What skills/background is necessary to

Re: [BlueObelisk-discuss] SMARTS substructure search benchmark set

2010-04-21 Thread Egon Willighagen
Hi Christian, On Wed, Apr 21, 2010 at 12:14 PM, Noel O'Boyle baoille...@gmail.com wrote: Do you mean a validation test set? I don't think there is any standard set. You could take a look at the test suites of the various BO projects (OpenBabel, CDK, RDKit, even JOELib) and put one together.

Re: [BlueObelisk-discuss] BODR 9 released

2010-04-25 Thread Egon Willighagen
2010/4/25 Konstantin Tokarev annu...@yandex.ru: Your configure script doesn't fail if xsltproc is missing, only warning is shown Please file as bug report at http://sf.net/projects/bodr Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg

Re: [BlueObelisk-discuss] Ontology for chemical reactions

2010-05-18 Thread Egon Willighagen
On Tue, May 18, 2010 at 1:23 PM, Jean-Claude Bradley jeanclaude.brad...@gmail.com wrote: Thanks Peter - this is helpful.  What software packages currently support the ontology you describe? The CDK has CMLReact support (thanx for asking :). Egon -- Post-doc @ Uppsala University

[BlueObelisk-discuss] Fwd: Jmol viewer in Accelrys Pipeline Pilot for viewing materials

2010-05-25 Thread Egon Willighagen
Hi all, I though this was nice news: -- Forwarded message -- From: Stephen Todd st...@accelrys.com Date: Tue, May 25, 2010 at 1:23 PM Subject: Jmol viewer in Accelrys Pipeline Pilot for viewing materials To: jmol-developers-ow...@lists.sourceforge.net

[BlueObelisk-discuss] help needed: unanswered Blue Obelisk eXchange questions

2010-06-03 Thread Egon Willighagen
Hi all, some unanswered BOx questions: * Modify user defined protein model using the mouse? * Which (open) electronic lab notebook (ELN) tools do you use? * How can I 'tag' a web page as containing incorrect chemistry, and share this observation socially? * Open source software for DNA and RNA

[BlueObelisk-discuss] Fwd: [Jmol-users] Jmol 12.0.RC19 released

2010-06-11 Thread Egon Willighagen
FYI Congrats to Bob and the others! -- Forwarded message -- From: Robert Hanson hans...@stolaf.edu Date: Fri, Jun 11, 2010 at 2:35 PM Subject: [Jmol-users] Jmol 12.0.RC19 released To: jmol-us...@lists.sourceforge.net Thank you, Nico, for releasing 12.0.RC19. I know the idea of

Re: [BlueObelisk-discuss] BODR: Nuclear spin values

2010-06-17 Thread Egon Willighagen
at the time. When I made the release last month, I already planned to bring up relicensing as CC0, but been too busy and forgot. There should be no concept of owner, though you should attribute the authorship. The current copyright owners are: Geoff Hutchinson Carsten Niehaus Egon Willighagen Jörg

Re: [BlueObelisk-discuss] BODR: Nuclear spin values

2010-06-17 Thread Egon Willighagen
On Thu, Jun 17, 2010 at 9:30 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: I would prefer not to use the phrase copyright owner unless it is clear what is being copyrighted. You cannot formally copyright the data (although people do). You can copyright the database under European law though I

Re: [BlueObelisk-discuss] Chemical blogspace future? (was: More strangeness)

2010-06-17 Thread Egon Willighagen
Hi Jordan, On Thu, Jun 17, 2010 at 5:03 PM, Jordan Mantha jordan.man...@gmail.com wrote: Have you guys considered using Planet as a Chemistry blogspace aggregator? It's pretty easy to setup and scales well. Ubuntu[1], GNOME[2], and Debian[3] are some common examples that I know of. We used to

[BlueObelisk-discuss] Program for the RDF symposium at the American Chemical Society fall meeting

2010-06-26 Thread Egon Willighagen
is in XHTML+RDFa, the source is also available on GitHub (well, you really download the source code anyway), allowing people to happily fork, make changes, and perhaps make the page as triple-dense as is possible. Hoping to have informed you well, with kind regards from Uppsala, Egon Willighagen

Re: [BlueObelisk-discuss] BO dinner at the Boston ACS?

2010-07-21 Thread Egon Willighagen
On Wed, Jul 21, 2010 at 4:27 PM, Noel O'Boyle baoille...@gmail.com wrote: How about asking on the CCL in advance? Or posting on your blogs? And via the social networks... Blue Obelisk eXchange, Friend Feed rooms, more blogs, mailing lists for particular conferences... I'll try to remember to

Re: [BlueObelisk-discuss] BO dinner at the Boston ACS?

2010-07-21 Thread Egon Willighagen
On Wed, Jul 21, 2010 at 5:13 PM, David Wild djw...@indiana.edu wrote: Alternative would be to *not* publicize the dinner, but to print up some leaflets to leave outside the CINF and COMP rooms. But then we no longer have the actual goal of the dinner in mind... Which is to get new people to

[BlueObelisk-discuss] An Ubuntu Blue Obelisk meta package

2010-07-24 Thread Egon Willighagen
Hi all, there was some talk recently about Blue Obelisk software available as Blue Obelisk / Debian packages... This morning I had trouble waking up, so hacked up a metapackage, so that you can now do: sudo add-apt-repository ppa:egonw sudo aptitude install blueobelisk Ideas, feature requests,

Re: [BlueObelisk-discuss] An Ubuntu Blue Obelisk meta package

2010-07-24 Thread Egon Willighagen
On Sat, Jul 24, 2010 at 2:31 PM, Egon Willighagen egon.willigha...@gmail.com wrote: there was some talk recently about Blue Obelisk software available as Blue Obelisk / Debian packages... Ummm... Ubuntu / Debian packages, of course :) Egon -- Post-doc @ Uppsala University Proteochemometrics

Re: [BlueObelisk-discuss] Fwd: [InChI-discuss] Licensing of InChI software

2010-08-01 Thread Egon Willighagen
On Sun, Aug 1, 2010 at 5:00 AM, Andrew Dalke da...@dalkescientific.com wrote: On Jul 31, 2010, at 12:30 AM, Egon Willighagen wrote: some legal framework kicks in to overcome this problem... I'm pretty sure it works something like that with copyright on books too... not? Not. Orphan works

Re: [BlueObelisk-discuss] Silicos NV releases Sieve v3 under GNU GPL version 2

2010-08-04 Thread Egon Willighagen
Dear Gert, On Wed, Aug 4, 2010 at 10:00 AM, Gert Thijs gert.th...@silicos.com wrote: Silicos is pleased to announce the release of version 3 of its molecular filtering software Sieve. Thank you for another contribution to the community! • Selection criteria by means of smarts patterns;

Re: [BlueObelisk-discuss] Distributing Blue Obelisk Propaganda at ACS

2010-08-10 Thread Egon Willighagen
On Fri, Jul 30, 2010 at 4:38 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: Maybe we can come up with something for CDK, and maybe an overview sheet with a list of open source chemistry packages (courtesy of the Blue Obelisk)? Then we'd have three little piles of sheets to compete

[BlueObelisk-discuss] PDF 2 text parsing?

2010-08-14 Thread Egon Willighagen
Hi all (and Peter's team in particular), Converting PDF back into text is a somewhat tricky exercise, as words can actually be characters rendered in approximately word format... Strigi [0] does a decent but not perfect recovery of text... is there someone here who has experience with PDF 2 text

Re: [BlueObelisk-discuss] PDF 2 text parsing?

2010-08-14 Thread Egon Willighagen
On Sat, Aug 14, 2010 at 4:26 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Sat, Aug 14, 2010 at 11:41 AM, Egon Willighagen Converting PDF back into text is a somewhat tricky exercise, as words can actually be characters rendered in approximately word format... This understates the problem

[BlueObelisk-discuss] Open Standards: Resource Description Framework

2010-08-17 Thread Egon Willighagen
Cheminformatics should have special interest in these three sessions, and I am very much looking forward to seeing you all next Sunday and/or Monday! The full program can be found at: http://egonw.github.com/acsrdf2010/ (please retweet and share with friends otherwise) with kind regards, Egon

[BlueObelisk-discuss] Nina Jeliazkova awarded a Blue Obelisk Award

2010-08-23 Thread Egon Willighagen
Hi all, on behalf of Peter, Christoph awarded Nina Jeliazkova the Blue Obelisk Award for her contributions to ODOSOS cheminformatics at the Blue Obelisk dinner tonight at the ACS meeting in Boston. Egon PS. the award is not for any particular achievement, but I do like to mention some of Nina's

[BlueObelisk-discuss] making video's and podcasts more semantic

2010-09-03 Thread Egon Willighagen
Hi all, I just ran into this interesting video: http://www.drumbeat.org/content/popcorn-js-semantic-video-demo Should be able to make video's and podcasts less hamburger-like... Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse

[BlueObelisk-discuss] CDK 10 year anniversary

2010-09-26 Thread Egon Willighagen
Hi all, tomorrow, September 27-29, it is exactly 10 years ago that Dan Gezelter (the Jmol inventor) hosted a meeting at Notre Dame (South Bend) where he, Christoph Steinbeck (the CompChem and JChemPaint inventor), and me founded the Chemistry Development Kit, loosely named after the 'Java

[BlueObelisk-discuss] Fwd: [Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties

2010-10-25 Thread Egon Willighagen
FYI -- Forwarded message -- From: P.Canepa pc...@kent.ac.uk Date: Mon, Oct 25, 2010 at 10:09 AM Subject: [Jmol-users] J-ICE a Jmol interface for crystallographic and electronic properties To: jmol-us...@lists.sourceforge.net jmol-us...@lists.sourceforge.net,

Re: [BlueObelisk-discuss] [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk

2010-10-25 Thread Egon Willighagen
On Sun, Oct 24, 2010 at 10:13 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Perhaps we can collaborate with reusing/extending existing OpenTox REST services with similar functionality and sharing experience with development of  web services based on RDF . Perhaps as a start the data can

Re: [BlueObelisk-discuss] [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk

2010-10-25 Thread Egon Willighagen
On Mon, Oct 25, 2010 at 11:13 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Perhaps as a start the data can just be pulled and put in one of the current OpenTox servers? No problem with this - do you have in mind particular piece of data to start with ? Check here...

Re: [BlueObelisk-discuss] [quixote-qcdb] Re: [OTDev] Quixote project for computational chemistry and future possibilities for Blue Obelisk

2010-10-25 Thread Egon Willighagen
Nina, On Mon, Oct 25, 2010 at 12:28 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: On Mon, Oct 25, 2010 at 10:33 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: For gaussian files it should be feasible as well, does CDK reads gaussian files ? JUMBO does and the transofrmation is

Re: [BlueObelisk-discuss] Chemical MIME types

2010-10-28 Thread Egon Willighagen
Hi Martin, On Thu, Oct 28, 2010 at 8:20 PM, Martin Peeks martin...@googlemail.com wrote: On 28 October 2010 16:36, Peter Murray-Rust pm...@cam.ac.uk wrote: From looking at the update-desktop-database package's website http://www.freedesktop.org/wiki/Software/desktop-file-utils, it appears

Re: [BlueObelisk-discuss] Chemical MIME types

2010-10-28 Thread Egon Willighagen
On Thu, Oct 28, 2010 at 11:23 PM, Peter Murray-Rust pm...@cam.ac.uk wrote: If KDE and Debian are treating chemical/ as an upperlevel type then it may well be worth trying IETF/IANA  again. I am trying to collect real world adoption on the Blue Obelisk eXchange... Ubuntu supports it too, and

Re: [BlueObelisk-discuss] Chemical MIME types

2010-10-28 Thread Egon Willighagen
On Fri, Oct 29, 2010 at 12:22 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: Things have changed a lot in the last hours (including some private correspondence) and I am now quite optimistic so I would certainly support it. We can make a very good case including - I suspect:  * many 100s of

Re: [BlueObelisk-discuss] [Kalzium] Re: [Bug 255854] Element 117 (UUs) has wrong discovery date

2010-11-02 Thread Egon Willighagen
On Wed, Nov 3, 2010 at 12:09 AM, Rebetez Etienne etienne.rebe...@oberwallis.ch wrote: Am Dienstag, 2. November 2010, 20:19:46 schrieb Carsten Niehaus: Have you already contacted BO? It is important to fix those things upstream. I used to sync the dataset every few month. It is just a matter of

[BlueObelisk-discuss] CC0 RDF hosting service

2010-12-29 Thread Egon Willighagen
Hi all, Mark Hahnel has extended his Science 3.0 website with a CC0 RDF hosting service. The purpose is small data sets, like results from experiments. http://www.science3point0.com/opendata/ It is still new, and most certainly not in its final form. Yet, this should be of such interested to

Re: [BlueObelisk-discuss] Dummy element in bodr elements.xml

2010-12-30 Thread Egon Willighagen
On Fri, Dec 31, 2010 at 2:57 AM, Neumann, Steffen steffen.neum...@ipb-halle.de wrote: but is it bodr's job to take care of implementation details about indexing ? What if someone is coding in pascal (where arrays start from 1 ...) Dummy atoms are at the level of atom types, and do not really

Re: [BlueObelisk-discuss] [FYI] Java API for PubChem

2011-01-14 Thread Egon Willighagen
Hi Jun, On Fri, Jan 14, 2011 at 11:58 AM, Jun Zhao jun.z...@zoo.ox.ac.uk wrote: This might be of interest to someone! Sure is! A Java API for working with PubChem data-sets. Mark Southern and Patrick Griffin Bioinformatics 2011 published 6 January 2011, 10.1093/bioinformatics/btq715 Thanx

[BlueObelisk-discuss] Fwd: [Jmol-users] Jmol integrated with chemCanvas

2011-01-22 Thread Egon Willighagen
Looks really interesting! -- Forwarded message -- From: Dimitris Dimitropoulos ddimit...@gmail.com Date: Sat, Jan 22, 2011 at 12:26 AM Subject: [Jmol-users] Jmol integrated with chemCanvas To: jmol-us...@lists.sourceforge.net Hi, I though that some people may find interesting

[BlueObelisk-discuss] what the CDK really needs...

2011-02-06 Thread Egon Willighagen
are the CDK could really need help with, and also hope to have clear that anyone is most welcome to help out, and shape the future of the project! With kind regards from a sunny Uppsala, Egon Willighagen -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska

Re: [BlueObelisk-discuss] Wiki

2011-02-10 Thread Egon Willighagen
On Thu, Feb 10, 2011 at 9:14 AM, Noel O'Boyle baoille...@gmail.com wrote: SourceForge have just changed everything on their server, so the wiki is down. I'll sort it out by and by... :( SourceForge-- (for not giving a warning...) Noel++ (for looking into getting it fixed...) Egon -- Dr

Re: [BlueObelisk-discuss] Wiki

2011-02-10 Thread Egon Willighagen
Hi Greg, On Thu, Feb 10, 2011 at 9:46 AM, Greg Landrum greg.land...@gmail.com wrote: On Thu, Feb 10, 2011 at 10:21 AM, Egon Willighagen SourceForge-- (for not giving a warning...) This criticism is unjustified. After the attacks on the site, the folks at sf.net did send around an email

Re: [BlueObelisk-discuss] Open data platform beta testers.

2011-02-14 Thread Egon Willighagen
Hi Mark, On Mon, Feb 14, 2011 at 2:20 PM, Hahnel, Mark m.hahne...@imperial.ac.uk wrote: All figures are licensed under a Creative Commons Attribution 3.0 Unported License. - with the CC-BY logo. Perhaps this isnt prominent enough. I personally would prefer CC0 but I know that 'normal

Re: [BlueObelisk-discuss] Wiki

2011-02-15 Thread Egon Willighagen
On Tue, Feb 15, 2011 at 12:03 PM, Noel O'Boyle baoille...@gmail.com wrote: The wiki is now back up at http://sourceforge.net/apps/mediawiki/blueobelisk/index.php?title=Main_Page. There's still a bit more work to do fixing the redirects, and sorting out images, and so forth. Thanx! To make

[BlueObelisk-discuss] DataONE

2011-03-15 Thread Egon Willighagen
Hi all, just wanted to make you aware of this: https://www.dataone.org/content/2011-summer-internship-program M.Sc. students, PhD, and even post-docs seem eligible... tough competition, or very well funded. #opendata #science Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för

[BlueObelisk-discuss] unanswered hot questions on the Blue Obelisk eXchange

2011-03-25 Thread Egon Willighagen
Hi all, I know I need to this more frequently, but here's again a shortlist of hot questions (most upvoted) that have not received any answer yet: - Which (open) electronic lab notebook (ELN) tools do you use? -

[BlueObelisk-discuss] Fwd: CCL: OpenTox Online Tutorial: Predict the toxicity of a molecule using ToxPredict. (Wed, 20 April, 15:00 CEST)

2011-04-16 Thread Egon Willighagen
Hi all, I was just wondering... how (un)common are tutorials like this in the Blue Obelisk community? Egon -- Forwarded message -- From: Roman Affentranger roman#%#douglasconnect.com owner-chemis...@ccl.net Date: Thu, Apr 14, 2011 at 9:38 AM Subject: CCL: OpenTox Online

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