Re: History behind pkgsrc 'biology' category

2016-02-08 Thread Rene Hexel 
> On 6 Feb 2016, at 11:19 PM, matthew sporleder  wrote:
> 
> On Fri, Feb 5, 2016 at 6:09 PM, Swift Griggs  wrote:
>> 
>> Again, not complaining. I think it's quirky and cool. I'm just curious.
> 
> […]
> If you recall, the late 90's and early 2000's saw a big push in
> bioinformatics, and especially with perl as a processing language.

  What Matthew said: not sure if, in hindsight, I would have made the same
decision today, but at the time, this appeared to be the trend …

  René

Re: History behind pkgsrc 'biology' category

2016-02-07 Thread Aleksej Saushev 
  Hello!

Swift Griggs  writes:

> I am curious (only curious - this is not a complaint): Does
> anyone know why there ended up being a pretty well-fleshed-out
> 'biology' section in pkgsrc but there isn't "chemistry",
> "physics", "engineering" etc...
>
> Was there some prodigious pkgsrc maintainer/hacker who was a
> biologist or is it just that there happen to be more
> biology-related programs which justify the discrete category?
>
> Again, not complaining. I think it's quirky and cool. I'm just curious.

  date: 2000-11-25 23:10:55 +0300;  author: jtb;  state: Exp;  lines: +0 -0;
  Initial import of new "chemtool" package:
  Program for drawing organic molecules


  date: 2008-03-09 20:52:57 +0300;  author: tnn;  state: Exp;  lines: +0 -0;
  Import mopac-7.0 as pkgsrc/biology/mopac.

  Mopac is semiempirical molecular energy calculation program for
  chemistry and physics.

This is how "biology" started including organic and computational chemistry.

When the question arose what to do with GROMACS, it was added to biology
category since it is definitely closer to biology than MOPAC7.
Right now there's understanding shared between at least two developers
that "biology" is to pkgsrc what "physics" was to Aristotle and followers.


-- 
HE CE3OH...

Re: History behind pkgsrc 'biology' category

2016-02-06 Thread matthew sporleder 
On Fri, Feb 5, 2016 at 6:09 PM, Swift Griggs  wrote:
>
> I am curious (only curious - this is not a complaint): Does anyone know why
> there ended up being a pretty well-fleshed-out 'biology' section in pkgsrc
> but there isn't "chemistry", "physics", "engineering" etc...
>
> Was there some prodigious pkgsrc maintainer/hacker who was a biologist or is
> it just that there happen to be more biology-related programs which justify
> the discrete category?
>
> Again, not complaining. I think it's quirky and cool. I'm just curious.
>
> Thanks,
>   Swift


I wasn't around then but the cvs history pretty much confirms my suspicions:

René Hexel  (rh@)  started the category in 1999 with the message:
"Enable bioperl."

If you recall, the late 90's and early 2000's saw a big push in
bioinformatics, and especially with perl as a processing language.

Matt

p.s. I have cc'ed René to see if more details can be shared.

History behind pkgsrc 'biology' category

2016-02-05 Thread Swift Griggs 


I am curious (only curious - this is not a complaint): Does anyone know 
why there ended up being a pretty well-fleshed-out 'biology' section in 
pkgsrc but there isn't "chemistry", "physics", "engineering" etc...


Was there some prodigious pkgsrc maintainer/hacker who was a biologist or 
is it just that there happen to be more biology-related programs which 
justify the discrete category?


Again, not complaining. I think it's quirky and cool. I'm just curious.

Thanks,
  Swift