academic collab request

Hi all,
So I'm working on a simple project where I am specifying relatively large sets of chemical reactions (graph transformations) with these things called SMILES strings.

It's kinda neat that once you start working with many strings, it feels like you need to look at the science of programming languages. How does on specify large sets of transformations efficiently in such a way that those specifications are maintainable and debugable etc. I like to think of the SMILES strings as assembly language, and I hope to create something a little higher level to make the job of specification a little easier.

It turns out I am in need of a simple preprocessor type language where I can specify and apply functions in a very "embedded" way. I think it would be pretty simple to do, I should be able to do it myself, but I really want to make sure that I am doing it the "right" way. I.e. under the guidance of someone who really knows a lot about the science programming languages. It'd be really nice to see if this work gives anyone any new good ideas.

Why am I doing this? Well it turns out there is a very important question about chemistry I can answer with this system in don't want to clutter this post, but it has to do with predicting what sorts of molecules will manufactured in the future.

I wonder if there are people other than chemists who would need to specify and maintain large sets of graph transformations and run them on large data sets...

I'm technically a chemistry grad student who does crystallography for living. I've written a lot of of the other parts I need already (i.e. some plumbing to apply a set of rules over the linux cluster at our instiute). I've got a good publication record and I'd be happy to forward my cv to anyone that would be interested in devoting a little time with me to this project. It's weird, I already have enough publications to graduate, but I am kinda using this last little bit of time to try to do something different instead of slumbering into retirement like I see a lot of grad students do.

If you have a strong knowledge of programming languages and would be interested in doing something simple, but unique and very useful, please write me at yadavm with the domain name Maybe your interested in using your talents in something closer to chemistry and biology.

Famous words, but I expect to write the whole thing up in just a month or two, of course just about all I can offer to you is co-authorship. Lunch if you're in San Diego.

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You might want to look into term rewriting systems, and perhaps take a look at Functional Programming and Parallel Graph Rewriting. I haven't cracked it open in a long while, but if I recall correctly, you might find it helpful.