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NMRShiftDB / News: Recent posts

NMRShiftDB development slows down

The main NMRShiftDB developer Stefan Kuhn has left our team at the European Bioinformatics Institute. NMRShiftDB will continue to be supported and developed. Later this year, our team will start an extensive new development in the area of metabolomics where the NMRShiftDB technology and data will be of importantce. It is likely that there will be delays in dealing with bug reports in NMRShiftDB.

Posted by Christoph Steinbeck 2010-05-03

Release 1.3.5

Release 1.3.5 is now available. It fixes some bugs and brings some improvments, mainly a all new structure editor applet. See http://nmrshiftdb.sourceforge.net/CHANGELOG for details.

Posted by Stefan Kuhn 2010-01-26

NMRShiftDB training presentation

We made a presentation available at http://nmrshiftdb.sourceforge.net/nmrshiftdbebitraining.pdf, which was made by EBI staff as part of their Bioinformatics Roadshow. It is a very good introduction into NMR and NMRShiftDB.

Posted by Stefan Kuhn 2009-12-03

Standalone client released

The 1.0 release of our standalone client called Speclipse is available for download from https://sourceforge.net/projects/speclipse/files/. It offers offline editing of data and download and submit facilities. It is based on Bioclipse 2.0.

Posted by Stefan Kuhn 2009-09-07

Server Consolidation

We have consolidated the NMRShiftDB servers to run at European Bioinformatics Institute. The URL www.nmrshiftdb.org and all existing server URLs redirect to the server, so users should not notice that except from the URL in the browser.

Posted by Stefan Kuhn 2009-07-08

Bugfix release

Bug fix release 1.3.4 is now available. It fixes some bugs and cleans up ID handling. See http://nmrshiftdb.sourceforge.net/CHANGELOG for details.

Posted by Stefan Kuhn 2009-04-07

NMR prediction paper published

A paper on prediction of 1H-NMR spectra using the data from NMRShiftDB has been published in BMC Bioinformatics.It can be read electronically on http://www.biomedcentral.com/1471-2105/9/400/abstract.

Posted by Stefan Kuhn 2009-01-28

Bioclipse-based client available

Speclipse, the new standalone client for NMRShiftDB, based on Bioclipse and therefore Eclipse, is available for Windows and Linux systems at https://sourceforge.net/project/showfiles.php?group_id=20485&package_id=261040 - it provides convenient access to NMRShiftDB functions including offline editing of entries.

Posted by Stefan Kuhn 2008-06-18

CUBIC NMRShiftDB server moved

The server running at CUBIC was moved to the NMR labs of the University of Mainz, thanks to the help of the NMR department of Organic Chemistry running these facilities.
It can now be reached at http://nmrshiftdb.chemie.uni-mainz.de
Once we've completed the OS upgrade of our main servers at the Max-Planck-Institute for Chemical Ecology in Jena, the Mainz server will be integrated into the load scheduling system and you may get automatically redirected to it again.

Posted by Christoph Steinbeck 2008-04-15

Server Upgrade

The NMRShiftDB servers will get an OS upgrade over the coming weeks. This might lead to delays in replication, but should not affect avaiability.

Posted by Stefan Kuhn 2008-04-15

New NMRShiftDB paper

A paper has been published evaluating the quality of the NMRShiftDB data and using it for comparing NMR prediction tools. Find details at http://www.ebi.ac.uk/citexplore/citationDetails.do?externalId=18293952&dataSource=MED

Posted by Stefan Kuhn 2008-04-05

Bulk data download moved

Since the marburg server is no longer in the NMRShiftDB network, download of bulk data files from the help page is currently broken. Please go to http://nmrshiftdb.svn.sourceforge.net/viewvc/nmrshiftdb/trunk/snapshots/ till further notice.

Posted by Stefan Kuhn 2007-11-21

Bugfix release

Recently we deployed a bugfix release to the servers, mainly fixing a problem with save. See http://nmrshiftdb.sourceforge.net/CHANGELOG for details.

Posted by Stefan Kuhn 2007-07-13

Quality Campaign

Between 2007-3-10 and today, altogether 72 spectra and/or structures in NMRShiftDB have been edited by the community to correct errors identified in analyses by Wolfgang Robien and Antony Williams as well as internal cross-checks.

Posted by Stefan Kuhn 2007-07-02

NMRShiftDB review

Antony Williams published an NMRShiftDB quality review in his ChemSpider blog. See http://www.chemspider.com/blog/?p=13

Posted by Stefan Kuhn 2007-05-03

NMRShiftDB linked in ChemSpider

Structures in ChemSpider are now directly linked to NMRShiftDB. See http://www.chemspider.com/NewFeatures.aspx#NMRSHIFTDB for details.

Posted by Stefan Kuhn 2007-04-23

NMRShiftDB Critique

Prof. Wolfgang Robien from Vienna, maker of the CSearch system, has evaluated NMRShiftDB's data quality and found a number of partly severe errors. Robien's critique is summarized on his own site http://nmrpredict.orc.univie.ac.at/csearchlite/enjoy_its_free.html.
Judge yourself.
We are grateful to Prof. Robien for pointing out these problems and, needless to say, we will carefully investigate the points he makes and correct the errors.
We also feel that this makes a strong case for our open access, open source policy, which gave our reviewer the chance to access our full material and run this test. As Eric Raymond puts it: "Given enough eyeballs, all bugs are shallow"

Posted by Christoph Steinbeck 2007-04-05

NMRShiftDB lab system in use

We extended the NMRShiftDB system to serve as an order administration system of an NMR lab. This system is now in production use at the chemical institutes of Universitaet zu Koeln in Cologne, Germany. For further informations, contact info@nmrshiftdb.org.

Posted by Stefan Kuhn 2007-02-21

SAB meeting

On August 15th the scientific advisory board of NMRShiftDB met in Cologne. Members are J. Bitzer, E. Haupt, T. Kaempchen and H. Kolshorn. We talked about ways of encouraging usage and things to improve. The main point seems to be performance, which we try to tackle asap.

Posted by Stefan Kuhn 2006-08-29

New NMRShiftDB release

Once more we did a new NMRShiftDB release, which is available on the servers. You will notice that it has been heavily redesigned, we hope it looks better now and is easier to use. There are also some new features and bug fixes, see http://nmrshiftdb.sourceforge.net/CHANGELOG for details.

Posted by Stefan Kuhn 2006-07-26

New NMRShiftDB release

A new NMRShiftDB release has been deployed to the servers. A major change is an improved proton prediction. For a complete list of changes see http://nmrshiftdb.sourceforge.net/CHANGELOG. Also a new myNMRShiftDB version, able to synchronize with this release, is available. Downloads are possible from http://sourceforge.net/project/showfiles.php?group_id=20485.

Posted by Stefan Kuhn 2006-02-15

NMRShiftDB data in pubchm

The structure data of NMRShiftDB in pubchem have been updated. The data can be found http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcsubstance.

Posted by Stefan Kuhn 2006-01-25

Major IE problem fixed

It seems that there were problems with latest releases of Internet Explorer. This should be fixed now. We apologize for any inconvenience. If there are still problems, please report them.

Posted by Stefan Kuhn 2005-11-16

More than 15.000 structures

Thanks to further contributions from in-house collections we have now got 15944 structures and 17925 spectra. We have also 1423 proton spectra and about 1500 structures with spectra of different type.

Posted by Stefan Kuhn 2005-08-30

More Corina coordinates

Corina coordinates have been calculated and added for all inputs up to June 2005.

Posted by Stefan Kuhn 2005-07-12