NMRShiftDB / News: Recent posts

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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

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.

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

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

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"

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.

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.

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.

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.

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.

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.

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.

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