Jean-Claude Bradley has blogged JSpecView Article on Chemistry Central
Robert Lancashire has just published an article in Chemistry Central Journal:
The JSpecView Project: an Open Source Java viewer and converter for JCAMP-DX, and XML spectral data files
Our lab has found this software to be key for communicating organic chemistry results within an Open Notebook Science environment. All NMR raw data and metadata are automatically recorded and users from anywhere can mine the spectra by expanding and integrating at will from a browser interface. This is an enormous improvement over the traditional method of storing and publishing spectra as images that cannot be expanded.
The article describes other useful applications, such as the integration of JSpecView with Jmol, to show the assignment of specific peaks.
The other reason I really like this article is that Robert has used some UsefulChem blog posts as primary references. This is an important way for the scientific blogosphere to get incorporated and accepted by the mainstream.[RL] Abstract
The JSpecView Open Source project began with the intention of providing both a teaching and research tool for the display of JCAMP-DX spectra. The development of the Java source code commenced under license in 2001 and was released as Open Source in March 2006. The scope was then broadened to take advantage of the XML initiative in Chemistry and routines to read and write AnIML and CMLspect documents were added. JSpecView has the ability to display the full range of JCAMP-DX formats and protocols and to display multiple spectra simultaneously. As an aid for the interpretation of spectra it was found useful to offer routines such that if any part of the spectral display is clicked, that region can be highlighted and the (x,y) coordinates returned. This is conveniently handled using calls from JavaScript and the feedback results can be used to initiate links to other applets like Jmol, to generate a peak table, or even to load audio clips providing helpful hints. Whilst the current user base is still small, there are a number of sites that already feature the applet. A tutorial video showing how to examine NMR spectra using JSpecView has appeared on YouTube and was formatted for replay on iPods and it has been incorporated into a chemistry search engine.
PMR: Congratulations to Robert, both on publishing JSV and choosing an Open Access journal to do it in. I predict that he will get many downloads and hopefully not a few citations. JSV was not always Open Source and Robert has had to be tenacious to extract it.
We have collaborated with Robert for some years and are two of the co-authors of the CMLSpect pape. There are now several, interoperating standards for 1-dimensional spectra – JCAMP-DX, AnIML and CMLSpect. There is really no excuse for publishers not to encourage authors to deposit these. They aren’t enormous, they can be deposited as supplemental data and can then by re-used by the scientific community. At present the publishers force readers to measure spectra with rulers if they want any numerical information.
And others deserve mention – Stefan Kuhn, who has helped to develop much of the spectral software, Christoph Steinbeck and the authors of JCAMP and the software library at sourceforge. We have benefitted from this in the SPECTRa project which allows groups in academia and elsewhere to reposit their spectral and crystallographic information.
Peter, as you saw from my other posts at http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=854 I have followed the SPECTRa project with interest and read the “final report” recently.
BAsed on your comment “We have benefitted from this in the SPECTRa project which allows groups in academia and elsewhere to reposit their spectral and crystallographic information.” the system is up and running somewhere. Can you point me to the system to test as I am interested to see it in action.
As you likely know we have implemented spectral uploading onto ChemSpider already (http://www.chemspider.com/docs/Uploading_Spectra_onto_ChemSpider.htm) and use JSpecView for the purpose of viewing. It took about 8 hours of work to deliver the minimalistic implementation and there is definitely work to be done to improve it. I know that a lot of time was spent interviewing users and I am therefore interested in seeing the interface you developed for people (I have not interviewed lots of people re ChemSPider uploading and am going on the feedback of people like Bob Lancashire himself and JC Bradley, both on the ChemSPider advisory group (http://www.chemspider.com/Advisory.aspx).
Thanks
Peter, When we unveiled uploading of analytical data to ChemSPider you commented that we were assuming copyright over the data (http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=682). We weren’t of course but we did then respond as fast as possible to your comments with OUR view of Open Data declaration (http://www.chemspider.com/blog/?p=208). Based on some of your later posts this is not consistent with your own definitions of Open Data and I’ll work that out in the future. In any case people can download the data and reuse if it is labeled Open Data on submission (our definition).
Since you are directing the SPECTRa project allowing for the deposition of spectral data I have to assume that you have not assumed copyright over the data and the data are declared as Open Data at submission. I look forward to reviewing the data and potentially reusing if appropriate. Please let me know where to find the data. Thanks
(2) The area of Open Data is very complex and I doubt any two humans have exactly the same view! I have tried to create consensus by kicking off the SPARC Open Data mailing list, by creating a Wikipedia entry on Open_Data and by being part of the Open Knowledge foundation. Many others – John Wilbanks at Science Commons and Paul Miller of Talis for example have worked hard at trying to devise licences. When I started I didn’t think we needed licences, now I do.
I am not directing the project – and never did – that was Peter Morgan from the library. But even if I had the data would not necessarily be Open. Some may, of course, but the project was to archive all sorts of data and some of this may be confidential (e.g service structures for pharma companies) and even I am not allowed to see it.
I would hope that the data passes through escrow and ends up finally in the University IR. But I am not part of that process in either institution. Our project researched into the feasibility and developed the tools. I argue for, and expect, that theses will increasingly be Open Access in Universities. But that is a policy for provosts and faculty boards. At least they can’t argue they don’t have the tools.
Because tools are Open Source it doesn’t follow that the data are. In general all the data I create or aggregate is Open. (But not all – we do industrially financed research here and are bound by confidentiality and IP). And I am not the departmental crystallographer, or the spectroscopist. Sorry!
I’m fully aligned with you that theses should be open. The tools are coming…very close in many ways and i acknowledge your efforts in leading the charge.
I was wondering whether SPECTRa was an online system for all to use but see that it is an institutional repository at Cambridge (?). Thanks
(4) The tools aren’t the problem – it’s the business process 🙂
SPECTRa is (or rather was) a *project” funded by JISC. JISC funds many projects and a lot are to research into practices. SPECTRa did this, but it also produced a toolkit. Th report – and the tools – should enable any institution or department to build a system for capturing chemical data. We have talked to a number who are interested. In particular I hope to spark this off in Australia. But I cannot force people to archive data 🙂
As I said, the tools are Open. You are very welcome to use them if it helps.