My team at the EBI maintains a couple of databases [1,2,3] dealing with various aspects of (bio-) organic chemistry. All of them need chemical structure editor applets where users can specify queries for substructure searches and which are used by our curators for data entry.The development of these databases is funded by the European Union and the BBSRC. We have a long-standing history of promoting open access to scientific publications and data, and of publishing our software as open source projects [e.g. 4,5] and we are therefore delighted that our funding agencies now promote these principles and support us in our goal to make all of our tax-payer funded research and development openly available. In all of our recent grants we have promised to deliver the software infrastructure of our databases as open source software to the scientific community.
Now, this does of course include the chemical structure editor mentioned above. As a pure coincidence 
, I had started a chemical structure editor in the late 1990s, called JChemPaint, which was later influenced a lot contribution from Egon Willighagen and others. JChemPaint experienced several rounds of re-architecture but for some reason it was never really considered to be production-ready.
We are now taking another go at it, at its applet version to be precise. And this time my charming profession team will give it a try and I’m confident that this time we’ll get it right. The fact that we are not alone in developing JChemPaint is both boon and bane. Everyone in an open source project is happy about harvesting the man-power of others but on the other hand you loose some control. While we, for example, are looking at the applet from a usability and GUI perspective, Egon and Arvid at Uppsala do a re-architecturing of the controler (the piece of software dealing with the user input) in order to make it maintainable through modularization.
So, in order to get an idea of what we actually need, we decided to do an analysis of a) existing structure editor applets and what they to well and not so well and b) how our curators do their work. For the latter, we did a screen recording of our curators’ work and looked at the type of functionality they used and how they did this (keyboard shortcuts, mouse, buttons, menus). The preliminary results are available on the JChemPaint wiki and we are more than happy to receive input from the community about this.
As a pure coincidence
my first cheminformatics project (closed source, currently a version of it is within OECD QSAR Toolbox) in 1995 was a structure diagram editor.
A Java (applet )version of it was developed in 2000 and (for my surprise) still runs at http://esc.syrres.com/pointer/default.asp .
The requirements of that time were: less than 100 K , support for Java 1.0 (remember browsers at that time) and response time for the entire substructure search backend < 8ms. The applet did meet the requirement, it does weight about 85K.
And the layout is pretty similar to what is now being designed for JChemPaint.
We are lucky today the constraints low bandwidth connections impose are not around anymore. Are we?
Hi Nina, thanks for your comment.
In fact, I’m currently on the train to the Netherlands, with my laptop and a G3 wireless broadband connection. It took thirty seconds for your applet to load and initialize. Nothing big, but there are still plenty of occasions where I’m glad that an applet has a small footprint. Cheers, Chris
I’m very glad to see this work going on! Some thoughts:
* As well as reviewing applets, it’s probably also good to compare with “offline” drawing applications such as ChemDraw and IsisDraw/SymyxDraw. After all, when many chemists use an applet like this, they don’t think, “This is how I make this bond in MarvinSketch” – they will automatically go to draw as they do in ChemDraw. Any applet shouldn’t be too different in commands & style from the standard drawing packages, esp. ChemDraw.
*Will it accept standard organic abbreviations such as TBDMS, Ts, Boc or Bu? These are a real nuisance to draw out longhand. ACS has a standard list of abbreviations.
Thanks, Martin. Very helpful indeed. We’ll take your comments into account. Cheers, Chris
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