I am delighted to report Egon’s announcement of the new work on JChempaint – one of the open Source chemical drawing tools from the Blue Obelisk community
22:24 19/05/2008,A quick screenshot, after some work on the JChemPaint code based on CDK trunk/. Nothing much to see, but a rather small code base, which is good. Today, I have set up cdk/cdk/trunk/ and cdk/jchempaint/trunk as Eclipse plugins, allowing the second to depend on the first. So, no more use of svn:externals. This is what it now looks like, and basically formalizes the end result of Niels‘ work of last year:
A possible spin of is that Bioclipse2 can use these plugins too, instead of defining plugins itself.
To reproduce the above screenshot, just import cdk/cdk/trunk and cdk/jchempaint/trunk into Eclipse, and run the TestEditor from the JChemPaint plugin.
PMR: There is a LOT going on quietly and relatively unuannounced in the Blue Obelisk world. Bioclipse continues apace. CDK is being seriously refactored. So is JUMBO. Many of the incompatibilities are being removed. We’re introducing mavenization to most of the Java programs so that they can be combined without breaking the libraries.
This has several benefits. It allows people to combine functionality without worrying about implementation. It helps to identify and define the functionality. To provide use cases and tutorials. To get rid of methods which have been superseded by better ones.
None of this is dramatic. But the overall effects will be dramatic.
You will wake up one morning – whether in academia, government, or industry and say “The Blue Obelisk gives us more or less everything we need. It works. Why aren’t we using it?”
Chemoinformatics is now not rocket science. It’s clear what the mainstream activities are. And the Blue Obelisk is catching up rapidly on most of the current functionalities and is ahead in some:
- high-quality semantic representation of chemistry
- dictionaries and ontologies
- transformation of molecules
- descriptors
- sub-structure search
- collections of data
- totpological analysis
- 3D structure generation
- 2D diagram generation
These can be combined with other Open Source offerings in text-mining, machine-learning, etc.
What is there new in chemoinformatics in the last 10 years that the BO has to catch up with? I can’t think of very much. There are a few things we don’t have:
- top rank name to structure (but there’s OPSIN from Peter Corbett and PMR and it can be extended)
- image to structure (but there are growing points, OSRA)
- structure elucidation (SENECA…)
And we’ll address these. There is enough critical mass of collaborators, and they are working together. Different projects, but a shared vision.
And there is more in the pipeline.
So, those of you who spend lots of money on commercial tools – maybe it’s worth thinking about Blue Obelisk. But unfortunately we don’t wear suits, so you will have to work to take us seriously.
PMR: A minor quibble. Please don’r reproduce the above screenshot – which makes horrible use of stereochemical indicators. Throw it in the bin. Find something beautiful instead.
Hear hear,
I’m glad I already woke up some time ago. I can share with you that I already found a great benifit in combining the tools from Blue Obelisk group and some others with the gradulately diminishing commercial tools. Keep it up and keep us posted.
Peter.
(1) Thanks Peter.
This is very helpful. Open Source benefits from knowing that their tools are being used. We appreciate that some requirements are commercial so users cannot always tell us how and why. Even apparently simple things can help – for example some use cases and accounts of what has been achieved.
Reporting bugs is also very valuable. We WANT people to report bugs. (OK, we do not actually rejoice at midnight when another bug is reported but we’re glad you reported it.) And, over the years, bugs start to disappear. (New ones take their place, of course).
So other users of BO, please let us know if there are things you are doing and things you would like to and aren’t. BO is now large and it can be difficult to find your way around. We’re happy to try to help.
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