Re: [Blue-obelisk] Planet down for the count?
I've moved BO to a new domain hoster, but that should not make a difference. The URL http://blueobelisk.org gave no problems for me. http://blueobelisk.org/planetbo might indeed be a problem now, but I wonder how it might have worked before, because the redirection rule stayed the same. Cheers, Chris richard apodaca wrote: > That's strange. The URL I had always used is: > > http://blueobelisk.org/planetbo > > It redirects to: > > http://wiki.cubic.uni-koeln.de/bowiki/planetbo > > Which apparently no longer works - thus my confusion. > > Even: > > http://blueobelisk.org > > gives me a "Bowiki has a problem" page as it redirects > me here: > > http://wiki.cubic.uni-koeln.de/bowiki/ > > The link you gave does work. > > --- Egon Willighagen <[EMAIL PROTECTED]> wrote: > >> 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 > > > > Richard Apodaca > Blog: http://depth-first.com > > > > > Do you Yahoo!? > Everyone is raving about the all-new Yahoo! Mail beta. > http://new.mail.yahoo.com > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Looking for structure enumeration code
Rich,
this is just wonderful :-)
Thanks so much.
If we only had more of these articles.
I certainly begin to realize the value of scripting languages for using the CDK,
especially in teaching.
Cheers,
Chris
richard apodaca wrote:
> I've just written a tutorial on using the
> GENMDeterministicGenerator class from Ruby CDK:
>
> http://depth-first.com/articles/2006/11/15/diversity-oriented-chemical-informatics
>
> --- Christoph Steinbeck <[EMAIL PROTECTED]>
> wrote:
>
>> Additionally, the CDK features a stochastic (Random)
>> constitutional isomer
>> generator. Might also be a nice feature when you
>> just want some examples and not
>> all isomers of a given formula. Example code is here
>> at [1]
>>
>> Cheers,
>>
>> Chris
>>
>> [1]
>>
> https://svn.sourceforge.net/svnroot/cdk/trunk/cdk/src/org/openscience/cdk/test/structgen/RandomStructureGeneratorTest.java
>> Egon Willighagen wrote:
>>> On Wednesday 08 November 2006 19:24, Alex
>> Henderson wrote:
>>>> Does anyone know of any available source code
>> (any language, but prefer
>>>> Java, C/C++, Perl) that can enumerate chemically
>> correct structures given a
>>>> molecular formula?
>>> The Chemistry Development Kit [1] is want you
>> need. It has a deterministic
>>> structure generator; I think [2] is the class to
>> use. The code should be:
>>> GENMDeterministicGenerator gdg = new
>> GENMDeterministicGenerator("C4H10","");
>>> Vector smiles = gdg.getSMILES();
>>>
>>> Other code examples can be found in [3].
>>>
>>> Egon
>>>
>>> 1.http://cdk.sf.net/
>>>
> 2.http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.html
> 3.https://svn.sourceforge.net/svnroot/cdk/trunk/cdk/src/org/openscience/cdk/test/structgen/deterministic/GENMDeterministicGeneratorTest.java
>>
>> --
>> PD Dr. Christoph Steinbeck
>> ([EMAIL PROTECTED])
>> Head of the Research Group for Molecular Informatics
>> Cologne University BioInformatics Center
>> (http://almost.cubic.uni-koeln.de)
>> Zülpicher Str. 47, 50674 Cologne
>> Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
>> ___
>> Blue-obelisk mailing list
>> Blue-obelisk@hardly.cubic.uni-koeln.de
>>
> http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
>
>
>
> Richard Apodaca
> Blog: http://depth-first.com
>
>
>
>
> Sponsored Link
>
> $420k for $1,399/mo.
> Think You Pay Too Much For Your Mortgage?
> Find Out! www.LowerMyBills.com/lre
> ___
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> Blue-obelisk@hardly.cubic.uni-koeln.de
> http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
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Re: [Blue-obelisk] Visualizing Cheminformatics Algorithms
Peter Ertl wrote:
> The article features (or better featured, the IJC site seems to be
> dead) a nice applet allowing people to run interactively various types
> of diversity selection algorithm and compare the results.
>
> As I said, the IJC site is now dead. Maybe this is one reason why
> authors do not trust too much the new open access journals. Which of
> them will be alive in 10 years?
Peter,
thanks a lot for contributing to the Blue-Obelisk List :-)
I can only second what Rich already replied. Open Access *is* the model of the
future since it gives us back the rights for our work.
The problem with disappearing content is also one of the regular publishers -
where are their archives going when they die. It's just a question of likelihood
of dying :-)
Also, I think, it is a responsibility of societies (as in: all the people in
Germany) to make sure their knowledge doesn't die. Certainly if they consider
themselves to be a "Wissensgesellschaft" ("knowledge societies").
One way towards this is putting things in institutional repositories - the
University of Cologne has a much higher likelihood of being around in 100 years
than any of the regular publisher that I know.
A second way is national libraries and their archival initiatives. The German
National Library is now required by law to archive whatever appeares on the net
in Germany (Within certain boundaries, but scientific articles certainly are
part of this mission).
On remark at the end: the fact that the IJC site is down and that the archive
has not been made accessible somewhere else is *very* depressing.
Cheers,
Christoph
--
PD Dr. Christoph Steinbeck ([EMAIL PROTECTED])
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de)
Zülpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
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Re: [Blue-obelisk] Re: 3D structure generator
I would like to add that the CDK *did* develop a 3D generator in the mean time. It works similar to the the Bustr3d approach and can be tested on http://www.chemistry-development-kit.org Note that there is currently a bug with the ring perception. Cambridge and the CDK team had plans of merging the two approaches, but so far we did not do that. Cheers, Chris peter murray-rust wrote: > At 21:08 13/01/2007, Dan Willenbring wrote: >> Dear Dr. Peter Murray Rust, > > Thanks very much - I'm taking the liberty of copying your message to the > Blue Obelisk list > >> I ran across a pretty old Cdk-devel message ( http://sourceforge.net/ >> mailarchive/message.php?msg_id=5267361 ) where you were discussing a >> possible open source implementation of 3D structure generation. I am >> working on a project where I need to generate several thousand sets >> of crude 3D coordinates (for further optimization with Gaussian03) >> from structures presently in a ChemDraw document. > I am assuming these are primarily organic > > Sam Adams here created Bustr3D - which used a fragment-based approach > derived from the NCI dataset. BUSTR is being rewritten to allow for > easier distribution and maintenance. > > Nick Day has a library of many thousand fragments from the > crystallographic literature which we are soon going to release. > >> Do you know if there has been any progress made in this area? Is >> there a project I have yet to run across that I could work on to suit >> my needs? > > We would be delighted if you were able to give some help in this area. > It might be an idea to see the sorts of molecules you have. Our approach > is particularly geared to ring nuclei joined by short linkers - it is > not a conformational analysis system. > > Best > > P. > > >> Thank you, >> Dan Willenbring >> >> Tantillo Group >> University of California, Davis >> Department of Chemistry >> One Shields Ave >> Davis, CA 95616 >> >> [EMAIL PROTECTED] >> 530 304 0971 > > Peter Murray-Rust > Unilever Centre for Molecular Sciences Informatics > University of Cambridge, > Lensfield Road, Cambridge CB2 1EW, UK > +44-1223-763069 > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ 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 Meeting in Chicago
Hi everybody, we are in the process of setting up a Blue Obelisk meeting in Chicago - same style as last time (beer, food, fun). Rajarshi, Egon, Stefan and myself will be there - who else will join us? Rajarshi suggested a Chinese Sezchuan Restaurant in Chicago's Chinatown. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ 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 Meeting in Chicago
Dear All, our planning for the Blue Obelisk meeting in Chicago has yielded first results. The following people have confirmed their participation: - Jean-Claude Bradley - Warren Delano - Rajarshi Guha - Peter Murray-Rust - Stefan Kuhn - Henry Rzepa - Christoph Steinbeck - Egon Willighagen It looks like Tuesday, 7 pm, would be a good time for the meeting. I suggest that we now collect suggestions for a nice place to meet. Rajarshi has suggested a Chinese restaurant already. And additional ideas for nice places in Chicago (beer, food, fun, but not too loud, so we can talk)? Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] New Blue Obelisk Home?
Geoff, yes, the Cologne Servers will continue for a while. If there where problems with mailing lists and the wiki, they were only temporary. I'll take care of things as soon as a move is neccessary. Cheers, Chris Geoffrey Hutchison wrote: > > Just writing to inquire about the Blue Obelisk servers. I've noticed > some problems with the wiki and mailing list webpages. > > A while ago, I offered to host BlueObelisk.org since my webhost provides > considerable bandwidth and disk allocations, along with mailing lists, > SVN, etc. > > Are the Uni-Koeln.de servers going to continue? > > Thanks, > -Geoff > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Second call: Date, time and place for Blue Obelisk Meeting in Chicago
Dear all, as I wrote earlier, the Blue Obelisk meeting in Chicago will be quite well visited. Confirmed participants are: - Jean-Claude Bradley - Warren Delano - Rajarshi Guha - Peter Murray-Rust - Stefan Kuhn - Henry Rzepa - Christoph Steinbeck - Egon Willighagen It looks like Tuesday, 7 pm, would be a good time for the meeting. Who (besides Rajarshi, who already made a suggestion) is familiar with Chicago and can make a suggestion for a nice place to meet (beer, food, fun)? Rajarshi, can you specify your suggestion in greater detail (address)? Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Announcement: Blue Obelisk meeting in Chicago
Dear all, I'm glad to announce date, time and place for the Blue Obelisk meeting in Chicago. We plan to meet on Tuesday, March, 27th, 7 pm at the restaurant South Water Kitchen 225 North Wabash Avenue Chicago, IL 60601 Tel: 312.960.8507 Currently, the following people (alphabetic order) have confirmed their participation: - Jean-Claude Bradley - Warren Delano - Sandford Dickert - Rajarshi Guha - Peter Murray-Rust - Stefan Kuhn - Henry Rzepa - Christoph Steinbeck - Egon Willighagen Rajarshi has reserved a table for ten. If you are not listed above but would like to join in, that's great. Every additional participant is highly welcome. But in this case, please notify me ASAP. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Revamp of the wiki
Noel O'Boyle wrote: > The Blue Obelisk wiki is the public face of the BO to the world. There > has been some talk recently about promoting the BO, and this is the > website that people come to if they are curious or want to get > involved. Since it has grown organically as wikis tend to do, it is > now in need of a major revamp. > > The front page should focus on key information (i.e. readers should > not be distracted by a multitude of links to information that may not > be relevant to them), the most important links (e.g. mailing list, and > RSS feeds), as well as a small number of table of contents links (e.g. > one for developers, one for general users, one for curious chemists). > > If nobody has any objections, I will reorganise it today/tomorrow. I'm happy with it. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ 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?
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. SF allows us to assign as many admins, developers, etc. as we like. Everyone has access and the stability is excellent - certainly better than any of our local sites. Provided that the project gets approved, we can start moving things over, if everyone agrees. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ 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?
Daniel Leidert wrote: > Am Dienstag, den 08.05.2007, 13:52 +0200 schrieb Christoph Steinbeck: > Egon already registered bodr.sourceforge.net. > http://sourceforge.net/projects/bodr Sure, but this has a different and more limited scope (dr) as the name implies. > You should talk with Egon and decide, which project of both to > use/remove :) Not necessary - we are in telepathic connection :-) Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ 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?
Egon Willighagen wrote: > 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. Right - thanks. Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ 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 SF project approved. Ready to start moving.
Our SF project blueobelisk.sf.net has been approved and we now have a SF-based platform. Let me know who wants to take responsibilities. I have added PeterMR and EgonW to the project as project admins, but clearly, we need more here. 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 :-) I' going to submit a support request regarding the move of the archives. Hope that'll work, but since both systems are mailman based, it might. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Status on SF.net move?
Geoff, I added you as an admin. I did not have time to do anything else. Cheers, Chris Geoffrey Hutchison wrote: > Hi guys, > > I'd be happy to help with the SF.net migration (ghutchis) -- are we > waiting for a mailing list archive migration? > > Thanks, > -Geoff > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] Move of mailing list to SourceForge
Dear all, I've created the mailing list "blueobelisk-discuss" on sourceforge and will file a support request to mass-add the members of the current list to the new one (SF does only allow to add one member at a time to prevent misuse of the platform for SPAM). Just in case: Please let me know if you do *not* want to be a member of the new list. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] WIKI content and design
Hi Tobias, Noel, and everybody when we move this to Sourceforge, which will require some investigation, we can take care of these things. Currently, the Wiki lives on my site at Cologne. I remember that there were some limitations for running mediawiki on SF. Not sure if they still exists. If someone has time to install mediawiki in our bo webspace on SF, I'll really appreciate it. Then, the existing MySQL tables can easily be move from Cologne to into the SF MySQL. cheers, Chris Tobias Kind wrote: > Hi Noel, > > Thanks for the links. Regarding the BO WIKI I think it should be possible > to edit content for registered and known and active people. Web 2.0 time! > > So if I want to add some stuff on the news page > It should posibble for me to do that after I was cleared by the BO WIKI > admin. > I would not add spam and the admin always has the right to remove content > anyway. > Maybe this would bring more life into the BO website. > Some important parts like agenda, aims and strategies can be protected from > edit by users, > I think most input comes from blogs anyway, but a clear collection > of aims, links, agendas on the BO website is needed. > > Regarding the Blueobelisk.org style (is this the main site?) > I like it to have stome static LINKs, like the old plone page from CUBIC > http://almost.cubic.uni-koeln.de/jrg/ > You have Strategy and Agenda, People, Projects, News etc. > These plone templates for research groups are usually well designed. > > Kind regards > Tobias > > > > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Wiki has moved to sourceforge
Thanks, Noel, for doing the work :-) BOers: It should be mentioned that if you use the same username, the system will connect this username with your old edits! It worked nicely for me. So, if you want to keep connected with your past, there is a good reason for choosing the same username :-) I have switched the BO wiki at CUBIC to read-only but will keep it online as long as possible for reference. I've redirected http://www.blueobelisk.org to http://blueobelisk.sourceforge.net, a switch which may take a while to be recognized by the name servers. Cheers, Chris Noel O'Boyle wrote: > Dear all > > The Blue Obelisk wiki/website has moved to http://blueobelisk.sf.net. > There were some difficulties so all user accounts will have to be > recreated. You should use the same user name for your account as > originally used, if possible. > > Please let me know if there are any problems. For the record, the > Admin password is the same as that for the mysql database (SF admins > have access to this). > > An attempted install of bad behavior (spam filtering) didn't work. > Maybe Geoff or someone can look at this at a later date. > > Regards, >Noel > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
[Blue-obelisk] SourceForge and WikiSpaces
sorry for crossposting. SourceForge now provides a Wiki for every project. http://web.sourceforge.com/news_archive/2007/1820.php The cdk wiki would, for example, be at cdk.wiki.sourceforge.net. It's not Mediawiki, but maybe it is usable. If we can find tools for migrating things from Wiki type to another, maybe it is easier to use the build-in one for the new CDK wiki. Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ 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: paradigm shift in data sharing in chemistry and the BO (PMR)
Tobias Kind wrote: > Well if you have 80% coverage and 90% accuracy - it rocks! Regarding > the NMRShiftDB, well the keyword is curation. The same for mass spectral > data, I would still buy the NIST mass spectral database, because its > curated, but there will be a shift towards machine curation, so in this > case its good to have open data. Anyway every database vendor should be > happy to have a free and open machine readable format available. I just want to mention here - although this is a bit off-topic - that NMRShiftDB *is* curated. A reviewer looks at every dataset entered by a user. You may argue it is not *well* curated (if you want to be nasty), but that accusation hold for any kind of curation. :-) Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Lecturer in Chemoinformatics Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ 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: paradigm shift in data sharing in chemistry and the BO (PMR)
Tobias Kind wrote: > Hi Christoph, > I did not argue about curation of the NMRShiftDB, I think the NMRShiftDB is > a great thing and I am happy that somebody started and developed it. I was aware of that but I just could not resist to make my (pointless) point :-) > I was also very happy that I did not comment on the accusations by > Wolfgang Robien, because a nice BlogWar was developing afterwards. > http://nmrpredict.orc.univie.ac.at/csearchlite/hallofshame.html > http://acdlabs.typepad.com/my_weblog/2007/05/update_robien_o.html Same here - although I will finally have to summarize things and comment. > You could also argue; how could Wolfgang perform such a statistics > in the first place? Because he could freely download the data :-) > In this way he morphed into an open data spectral curator > in the second place, which was very interesting to watch. That's why I can't get that smile out of my face when I read the respective blog fight. I take the reports about errors very seriously, but not the ones about our model. That was exactly the moderately original point in our grant proposal for NMRShiftDB - can we transfer the ideas of open source development to communally developed databases. It did not work until Wolfgang jumped in :-) I will blog about this. > What could have happen in NMR research if Wolfgang Robien would > have opened his NMR database with 80,000 carbon NMR spectra and > structures in 1993? We will never know. Maybe we would now talk about > 2D NMR spectra prediction errors instead of talking about 1D NMR errors > like: Oh my algorithm is 0.19 ppm better than yours. > Maybe everybody would use comprehensive algorithms like SENECA or StrucEluc? > Such algorithms are innovative and exciting! And instead of 12 publications > which mention CSearch in the abstract; or 70 at all; there would be 700 > publications which made use of CSearch and Wolfgangs algorithms and > databases? Very well said. I have nothing to add here :-) Cheers, Chris -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Lecturer in Chemoinformatics Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ 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 don't seem to have this information, but I contacted Wendy Warr to see if we can recover it. Very soon, the manuscript will be freely accessible anyway. Cheers, Chris Rajarshi Guha wrote: > > On Jun 19, 2007, at 1:54 AM, Egon Willighagen wrote: > >>> 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. > > Actually I think Christoph will have those details (he was the > corresponding author) -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Lecturer in Chemoinformatics Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
