BioSmalltalk win ...almost
Hi Hernan, apparently BioSmalltalk is the faster in the field of Bio* platforms (BioPerl, BioPython, BioJava, ...) and the more trendy: http://www.ijcseonline.org/spl_pub_paper/PID%2023.pdf I would love to believe in that ;-) But if you read carefully the paper, you will found that authors has made a dramatic mistake ... They think that Pharo was the name of BioSmalltalk ... and then they compare with Google Trends, Pharo against BioPerl, BioPython, ... Anyways the statement that BioSmalltalk is the faster is maybe true :-) Hernan did you know this paper ? Regards, -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
:) This is supercool to see BioSmalltalk being mentioned and analysed. May be hernan should contact the authors.
Hi Hernan,
apparently BioSmalltalk is the faster in the field of Bio* platforms (BioPerl, BioPython, BioJava, ...) and the more trendy: http://www.ijcseonline.org/spl_pub_paper/PID%2023.pdf
I would love to believe in that ;-)
But if you read carefully the paper, you will found that authors has made a dramatic mistake ... They think that Pharo was the name of BioSmalltalk ... and then they compare with Google Trends, Pharo against BioPerl, BioPython, ...
Anyways the statement that BioSmalltalk is the faster is maybe true :-) Hernan did you know this paper ?
Regards,
-- Using Opera's mail client: http://www.opera.com/mail/
Hi Serge, 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 2016-11-30 11:31 GMT-03:00 Serge Stinckwich <serge.stinckwich@gmail.com>:
Hi Hernan,
apparently BioSmalltalk is the faster in the field of Bio* platforms (BioPerl, BioPython, BioJava, ...) and the more trendy: http://www.ijcseonline.org/spl_pub_paper/PID%2023.pdf
I would love to believe in that ;-)
But if you read carefully the paper, you will found that authors has made a dramatic mistake ... They think that Pharo was the name of BioSmalltalk ... and then they compare with Google Trends, Pharo against BioPerl, BioPython, ...
Anyways the statement that BioSmalltalk is the faster is maybe true :-) Hernan did you know this paper ?
Regards, -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
On Thu, Dec 1, 2016 at 12:11 AM, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
Hi Serge,
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.
For me this paper is crappy and this kind of journal not really good. So I'm not surprised,
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.
It would be nice to do as real benchmark between the different platforms on real examples. A paper for IWST 2017 ? ;-) Regards, -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
Yes, a +1 on the assessment of the paper. The research methodology does not really result in any representative or generalisable data, so the conclusions are unfounded. (I have no experience with the journal, but my gut tells me to stay away from it.) -- Does this mail seem too brief? Sorry for that, I donât mean to be rude! Please see http://emailcharter.org . Johan Fabry - http://pleiad.cl/~jfabry PLEIAD and RyCh labs - Computer Science Department (DCC) - University of Chile
On 01 Dec 2016, at 12:56, Serge Stinckwich <serge.stinckwich@gmail.com> wrote:
For me this paper is crappy and this kind of journal not really good. So I'm not surprised,
participants (4)
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Hernán Morales Durand -
Johan Fabry -
Serge Stinckwich -
stepharo