Tuesday, December 28, 2010

Reordering SMILES atom order

I wrote a rather long essay about how to generate SMILES strings where the atoms are in arbitrary/user-defined order. The first two implementations use RDKit but in the last I couldn't work around an RDKit bug so I switched over to OpenBabel. (Edit: Greg commented here that the bug has been fixed in version control and will out as part of the Q4 2010 release.)

This is the place to leave questions and comments about what I wrote.

Saturday, November 13, 2010

Ontologies of Algorithm Implementations

A place for you to leave comments about my essay Ontologies of Algorithm Implementations wherein I gave examples of how it's not simple to say "this data set was generated by algorithm X."

Monday, March 15, 2010

KNIME, Pipeline Pilot, and visual programming languages

I presented a talk at CUP 2010 in Santa Fe on KNIME, Pipeline Pilot and visual programming languages in general, with comparison to other visual programming languages and text-based toolkit approaches. I've broken the talk up into parts, which are published on my technical writings blog.

This is the place to leave comments on those writings. The relevant postings are:

  • KNIME and beginners, where I walk through my problems trying to get heavy atom counts working in KNIME

Monday, February 22, 2010

Instrumenting the AST

Here is the place for you to leave comments on "Instrumenting the AST" wherein I describe an way to modify the AST for Python code in order to insert new code for things like line and branch tracing and ways to add tests which aren't otherwise easily possible.

Friday, January 29, 2010

Project hosting options?

This is a place to comment about my post "Project hosting options?"

Sunday, January 10, 2010

Fingerprint File Format

I proposed a fingerprint file format for small molecule chemistry. Here's the place to leave comments or suggestions.

Sunday, January 3, 2010


I think there's a problem in how several web browsers fail to escape the filenames for Content-Disposition. I reported the problem and put a call out for people to verify the problem and either enlighten me or to submit bug reports to the relevant trackers.