Fingerprint File Format

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

Content-Disposition

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.

Problems with TDD

This is the place to comment on my essay "Problems with TDD." In that essay I pointed out that there's still very little evidence that TDD is an effective development technique. I explained why TDD was not a good technique for me, and made the stronger claim that TDD is a weak development technique because it does not include essential unit tests. To show that it wasn't because I don't understand or practice TDD well enough, I pointed out worked-out examples done with TDD by two of the leading TDD experts. They contained implementation weakness which were not identified by TDD nor even mentioned by the implementors.

100,000 tasklets: Stackless and Go

This is the place to leave comments regarding my essay 100,000 tasklets: Stackless and Go. I repeated a timing test from Go using Stackless and showed that Stackless was faster than Go, yet Go should have the advantage of being a compiled language designed for just this task. I also questioned why the performance of the Go compiler was interesting, given that it seems to be slower than gcc.

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.