Tuesday, 17 May 2011

Excel with the Chemistry Development Kit

One of the projects that really astounded me at MIOSS was presented by Kevin Lawson of Syngenta. He has managed to integrate chemistry into Excel, and done so using the freely available and open source toolkit, the Chemistry Development Kit (CDK) (and only using three different programming languages!). The project is called the LICCS System (or Excel-CDK), and the website is at googlecode.

Big deal? Yes - big deal. We may say that R can do everything better than Excel, but the ubuiqity of Excel and the familiarity of everyone with the spreadsheet metaphor, means that targeting Excel brings basic cheminformatic analysis into the hands of non-cinfs like our colleagues, our bosses and our students.

So, what's this all about? Well, once a spreadsheet has been "chemistry-enabled" you can...
  • click on a SMILES strings to see the structure
  • click on a point in a graph and see the structure
  • filter the data by substructure searching (for large datasets you can speed this up by calculating fingerprints first)
  • cluster the data
  • create R group tables
  • calculate molecular properties
If you are at all interested in this, go to the website, and check out the flash video available as a download. This takes you through some of the capabilities of the system.

One interesting aspect is that the software has been cleverly designed for use in a corporate environment. First of all, no installation is required (i.e. admin access is not needed) and secondly, chemistry-enabled spreadsheets can be shared with users who haven't installed the chemistry add-in, so long as they have access to a shared network drive with the required files.

Just a note, to get it all working the first time, you may have to override some security settings in Excel. In Excel 2007, I had to go into the "Trust Center", and in "Macro Settings", enable "Trust access to the VBA project object model". [Update (18/05/11): Kevin says this is only necessary if creating the spreadsheet, not if using one that has already been created.]

Remember - it's an open source project, so get in there and give a hand if you have any ideas for additional features.

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