comments on Andrew Dalke's writings

f2pypy

2011-11-09T14:39:00.000-08:00

I posted about f2pypy my mini-project to make a new backend to f2py which generates a ctypes-based extension module for Python. The goal is to see if that is a viable path for PyPy support of the existing shared libraries already wrapped by f2py. I think it is.

Feel free to comment!

Where free software and peer-review software differ

2011-07-12T13:02:00.000-07:00

In this essay I point out while free software and scientific peer-review have many characteristics in common, they come from different philosophies. There are requirements for free software (free ability to redistribute modified code to anyone) which are not essential to effective peer review, and there are requirements for effective peer review (getting access to the source code in order to evaluate it) which are directly contrary to the free software ideals of the GNU project (which lets you distribute free software for any price you may wish).

Here is the place to leave comments about that essay.

Code review

2011-07-12T12:51:00.000-07:00

I believe the literature shows that code review is a effective way to find defects in software and to promote knowledge transfer. I think it's easier to put into place than pair programming. Unfortunately it's also socially stressful.

In my essay on code review I outline some of ways I've done code review and some reasons that people don't do it.

I want to promote the use of code review in general, and also more specifically in cheminformatics. I'm not sure how. I described a few in that essay. If you have more, let me know.

Dealing with SSSR

2011-06-04T15:38:00.000-07:00

Here's the place to leave comments about my "Dealing with SSSR" article. In it I describe my experience in trying to develop a toolkit-indendent means of specifying some of the PubChem bits which require ESSSR. I concluded saying that I couldn't - without reimplementing ESSSR myself for each toolkit - handle those bits so I would be ignoring them.

I also wondered why people use SSSR, and how well they've tested their SSSR-based algorithms, including testing in the face of differing atom order.

Implementing the CACTVS/PubChem substructure keys

2011-01-19T16:19:00.000-08:00

Here's the place to leave comments about my rather lengthy article on the problems I ran into while implementing the PubChem/CACTVS substructure keys, with background, pointers to the MACCS definitions, and other chunky nuggets of feature key wisdom.

subgraph enumeration

2011-01-10T05:39:00.000-08:00

I've started a series on subgraph enumeration. In Part 1 I present a brute force enumeration algorithm, modify it to remove duplicates, and post-process the results to generate canonical SMARTS for each subgraph. In Part 2 I develop a new algorithm which is about 3.5 times faster.

Reordering SMILES atom order

2010-12-28T08:37:00.000-08:00

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.

Ontologies of Algorithm Implementations

2010-11-13T15:12:00.000-08:00

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."

KNIME, Pipeline Pilot, and visual programming languages

2010-03-15T17:10:00.001-07:00

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

Instrumenting the AST

2010-02-22T07:41:00.000-08:00

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.

Project hosting options?

2010-01-29T18:51:00.000-08:00

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

Fingerprint File Format

2010-01-10T17:29:00.000-08:00

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

Content-Disposition

2010-01-03T22:16:00.001-08:00

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

2009-12-28T22:36:00.000-08:00

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

2009-11-15T05:23:00.000-08:00

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

2008-11-11T03:19:00.000-08:00

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?

2008-08-08T18:35:00.000-07:00

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

2008-06-27T13:13:00.000-07:00

I wrote a set of essays on molecular fingerprints:

Molecular fingerprints, background

Generating molecular fingerprints with OpenBabel

Computing Tanimoto scores, quickly

Block Tanimoto calculations

Faster block Tanimoto calculations

HAKMEM 169 and other popcount implementations

Testing the bitslice algorithm for popcount

Feel free to leave comments about them here.

python4ply

2008-03-09T04:02:00.000-07:00

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

2007-11-30T10:25:00.001-08:00

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

2007-10-31T09:53:00.000-07:00

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

2007-10-07T16:46:00.000-07:00

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.