What do we expect from a chemical structure editor applet?
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.
Categorised as: ChEBI, Chemistry Development Kit, Chemoinformatics, JChemPaint, Open Science, Open Source, Scientific Culture
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