The Blue Obelisk: A volunteer!

I flew back from SF to Heathrow yesterday and, as usual, was hacking on the laptop (with difficulty as Virgin doesn’t seem to give enough space to open a laptop). After a while my neighbour (S) asked:
S: “do you mind saying what you do?”
P: “not at all – I’m a chemist at Cambridge, working in informatics”
S: “I saw you using Eclipse. I’m a software developer for [a company that tests devices] and we use it a lot”.
P: “Ah, we not only use it for testing, we have a rich client (Bioclipse) – it’s great – do you want to see it working?”
P shows Steve Bioclipse, Jmol and he is impressed…
S: “I’d like to help with that – I enjoy software challenges and would like to do some of that in my spare time”
S is a computer scientist and I tell him that Miguel Howard – a compsci – created the stunning graphics on Jmol without knowing any significant amount of chemistry. And we started to discuss the sorts of contribution that can be made towards the Blue Obelisk movement. S would be happy to look at developing machine learning methods, distributed threading, image processing, etc. where the project didn’t require an in depth knowledge of chemistry and where the project is reasonably self-contained.
So – by chance – we have a volunteer who can bring a lot to the project. I shall mail the BO suggesting that we promote a wish-list on the site that such volunteers can choose from. There must be quite a lot of potential volunteers out there in all sorts of disciplines who would enjoy – and that is the key word – contributing to the BO.  Because it’s FUN – not a bar on a Gantt chart. I understand S – Often I tackle software problems for relaxation – it’s creative and fun (if there isn’t a deadline). The satisfaction of creating a bit of working software can be enormous (although the pain of debugging it is the opposite!).
So if you think you have something to contribute to BO, have a look at the site, download and try the software and see if it excites you.
I have worked with virtual volunteers for many years. It’s a different ethos from a managed project – you have no right to expect anything from anyone. The demands of real life (RL) must take precedence. Sometimes there are problem with employers or supervisors. And many volunteers offer something and then are never heard from again. But we now have a substantial software and information architecture and there are opportunities in many aspects besides software: BO Data curation, tutorials, advocacy, documentation (not as boring as it sounds if you don’t do it all at once, or if you have a new slant on it), examples, integration, mashups, applications, etc.

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2 Responses to The Blue Obelisk: A volunteer!

  1. If he’s interested in machine learning and image processing, perhaps he might be interested in something like 2D image -> structure code? It’s actually not much chemistry for a first go — turn it into a graph, recognize a few typical element characters, know that a vertex without a label is a carbon atom.
    Other bits are obviously complicated — dealing with overlapping bonds, pseudo-3D representations, etc.
    But I don’t think anything in open source chemistry offers even a framework for this yet.

  2. petermr says:

    I had a hack at image2structure a few years back. My approach was to try to find consistent local patterns that represented common artifacts of the drawing program. This is rings, “Me”, “COOH”, etc. I reckoned that this would allow identification of core fragments and decorations, especially if people were using the same tool consistently. My problem cam in that the images were mor blurred than they looked – it could be quite difficult to separate characters even after some image processing. Maybe it’s better now.
    Mixtures of text and graphics will always be a problem as positioning will be arbitrary.

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