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NMRShiftDB Help
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NMRShiftDB is a web database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users. The NMRShiftDB software is open source, the data is published under an open content license. Currently, only 13C, 1H, 15N and 31P NMR shift data can be stored, but the architecture of the software allows for future extension to other nucleii, e.g., correlated 1H/13C data, 19F, etc. The implemented search algorithms can scan the database for example for the following items: substance name, formula, structure, substructures, chemical shifts, and a Hit List of best matches is generated. Furthermore, a shift prediction algorithm based on the molecular HOSE code and the measured shift data has been included. For proton spectra a prediction based on 3D molecular properties is available. It is the policy of NMRShiftDB to have its content freely available. This means that spectra in NMRShiftDB can be accessed and used without restrictions. Access to single items is possible via the software and we also make available the bunch data (without the personal data). Note that, according to our opinion, NMR spectra do not represent "literary and artistic works" as mentioned in Art. 2 (1) of the Berne Convention, the author of a spectrum is, so to say, nature, and that therefore there is no copyright in NMR data. NMRShiftDB as a database is a protected work in the sense of article 5 of the WIPO Copyright Convention, authored by its contributors and reviewers. It is available under the GNU Free Documentation Licence. The NMRShiftDB data are available as: Questions about NMRShiftDB should be directed to the administrator. You may also subscribe and mail to the NMRShiftDB users mailing list. The software developers will follow the discussions there and comment on them. NMRShiftDB is accessible via the Web interface at www.nmrshiftdb.org. There is also a standalone client called myNMRShiftDB available. This is written in Java and should run on any computer given a Java VM 1.4 or higher exists. Download the latest binary release of myNMRShiftDB from sourceforge.net. After unpacking the zip you should be able to start it by clicking mynmrshiftdb.bat on windows or mynmrshiftdb.sh on Unix-like systems. The use of NMRShiftDB via a Web browser is straightforward, and numerous Help links (symbol  ) are provided. NMRShiftDB will work without any special plugins, but at numerous places you can switch to a Java-based version. This gives additional comfort with entering and viewing data, but a prerequisite for your browser is then that the Java VM (virtual machine) must be installed and JavaScript activated. A major problem in the development of Web-based applications is the wide range of ever-changing capabilities and incompatibilities of the popular browsers in use. In the following we offer some comments and tips concerning browser choice, based on current experience, and we welcome your comments. Internet Explorer The following versions of IE have been tested: 5.5, 6.0. With the original Microsoft VM installed, the applet version does not work. Please install the Sun VM. If you use IE 6, the Sun Java VM should be installed when you want to use the Java version of NMRShiftDB; when necessary, IE should prompt for this the first time you visit the NMRShiftDB site and carry out an automatic installation. Firefox (and Netscape/Mozilla) Firefox is the recommended browser, which we have extensively tested. We recommend the latest release (all 3.x releases are fine). When you want to use the Java Version of NMRShiftDB you should download and install the latest version of the Java 2 VM from the Sun Website. Do not use versions older than 1.4 of the Java VM; your browser may lock up when certain features of NMRShiftDB are used. (This problem appears to be restricted to Linux systems.) If you want to use Mozilla or Netscape, use Version 7. Netscape 4.x should not be used due to problems with nested tables and the Java VM, and Netscape 6.x was just a beta release for Netscape 7 (although it got a major release id). Please upgrade to NS 7, which will solve most problems. Opera With Opera 7.x (we tested 7.11 build 406) and Java VM all functionalities of NMRShiftDB are available. Some versions of Opera 6.x had problems with JavaScript, so the functions Submit, Search and Predict with Java Version do not operate correctly. Please upgrade to Opera 7. Konqueror/Safari Konqueror =>3.1 and Safari >= 1.2 should work. Older versions do not operate correctly for the functions Submit, Search and Predict with the Java version, due to flaws in Konqueror's JavaScript implementation. Macintosh On MacOS 10.1 or higher Safari 1.2, Netscape 7.02 and Opera 7.50 (beta) are reported to work with Java VM 1.4.2. On Classic OS, iCab 2.9.7 should work. With other browsers on Macintosh (OS 9 as well as OS X) the so-called "Live-Connect" feature is not available. This means that Submit, Search, Predict do not operate correctly with the Java Version.
NMRShiftDB is an open-source, open-access application, and users are strongly encouraged to get involved, not only by submitting spectra, but also by reporting bugs and making suggestions for improvements and new functionalities. Bugs should be reported to the administrator; please give details, browser and operating system used, date and time of failure. Interested users are also encouraged to submit code or documentation; please visit the Project Homepage at SourceForge. To see what is planned, visit the Feature Requests Site. If you have any questions, do not hesitate to email the administrator. |
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