Smalltalk › Pharo › Pharo Smalltalk Users

BioSmalltalk win ...almost

_‹ Previous Topic Next Topic _›

Classic

List

Threaded

5 messages Options

SergeStinckwich

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/

stepharo

Re: BioSmalltalk win ...almost

:)
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/

hernanmd

Re: BioSmalltalk win ...almost

In reply to this post by SergeStinckwich

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 <[hidden email]>:

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/

SergeStinckwich

Re: BioSmalltalk win ...almost

On Thu, Dec 1, 2016 at 12:11 AM, Hernán Morales Durand
<[hidden email]> 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/

jfabry

Re: BioSmalltalk win ...almost

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 don’t 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 <[hidden email]> wrote:
>
> For me this paper is crappy and this kind of journal not really good.
> So I'm not surprised,