I didn't knew that paper. You are right, in the community analysis they seem to compare Bio* projects against Pharo and not BioSmalltalk. That's weird because the paper is very clear about BioSmalltalk is the name of the library and Pharo is the supporting platform. I will contact the authors because the BioSmalltalk community is very small and I expected that when developing the library. On the other side they use 99% Pharo code... I remember someone asking me about how to do in BioSmalltalk the task proposed in the paper. I answered the analysis is strange, because the flat-file they are parsing (intended for human reading) can be downloaded in XML and parsed easily with a XML pull parser. Or even ASN.1.

BioSmalltalk is faster for some tasks, for example reading/filtering BLAST alignments. I have put special emphasis on that. Maybe I should prepare a post comparing speeds for additional tasks. Thank you for the link.

Cheers,

Hernán