Open source != peer review

I wrote an essay on why I don't agree with the idea that good peer review requires open source. Why is the right to redistribute, on top access to the source code, needed for peer review?

My followup question, once you've answered the first, is to explain how I can review source code and not be accused some time in the future of using that source code in my own code, in violation of copyright and license agreement. This can occur even with free or open source licenses, for various reasons.

Python bug or not?

I posted an example of how
reading 0 bytes from a file can cause Python to run out of memory. Is it a bug?

molecular fingerprints

I wrote a set of essays on molecular fingerprints:

1. Molecular fingerprints, background


2. Generating molecular fingerprints with OpenBabel


3. Computing Tanimoto scores, quickly


4. Block Tanimoto calculations


5. Faster block Tanimoto calculations


6. HAKMEM 169 and other popcount implementations


7. Testing the bitslice algorithm for popcount

Feel free to leave comments about them here.

python4ply

python4ply is a Python parser for the Python language. The grammar definition uses PLY, a parser system for Python modelled on yacc/lex. The parser rules use the "compiler" module from the standard library to build a Python AST and to generate byte code for .pyc file.

This is a place for you to leave comments about python4ply and its documentation.

OpenSMILES and aromaticity

A place to comment about articles I wrote concerning the OpenSMILES specification, which is an attempt to more formally specify how to interpret and generate SMILES strings.

• OpenSMILES and aromaticity

OpenSMILES, molecular formulas and ANTLR

This is the place to comment on the various articles I wrote on parsing molecular formulas and SMILES strings with ANTLR.

• OpenSMILES


• Parser generators and SMILES


• Calculating MW with ANTLR


• Java, and comparisons to PLY and PyParsing

comments on Wide Finder

Comments page for the text I wrote about Fredrik Lundh's notes on Tim Bray's "Wide Finder" Erlang code and a follow-up I did comparing performance.