Review of all the Debian Med debtags, and questions.

[Charles Plessy]

Hi Enrico,

Le Thu, Jan 22, 2009 at 11:58:52PM +0100, Enrico Zini a écrit :
> On Sun, Jan 11, 2009 at 02:48:40PM +0900, Charles Plessy wrote:
> 
> > Many of our programs work on biological sequences. I know we discussed
> > this before, but I really think that works-with:sequence would make
> > sense. In combination with field::biology, it would fully replace
> > field::biology:bioinformatics. I volunteer to do the transition by hand
> > if necessary. We currently have 84 field::biology:bioinformatics
> > packages.

> I'm worried about is that "works-with::sequence" seems to be an unclear name
> if we take it outside of the biology context.  Would
> "works-with::biological-sequence" be acceptable as well?

No problem. Let's consider renaming if there is later a request for a
"works-with::foo-sequence" tag.


> > works-with::trees
> >   We would use this for our phylogeny packages, and many other tools not
> >   related to biology could use it. works-with::graphs could be an
> >   alternative, but potentially confusing.
> 
> works-with::graphs would probably make more sense considering we have
> loads of graph theory and visualisation software around.  We may fix the
> confusion by describing the tag as "Trees and Graphs".

Perfect.


> > works-with::temperature
> >   We would have three candidate packages, but criticall mass would
> >   probably attained with sensors and weather packages.
> 
> I see the need, but I'm looking for a better name: sensors and weather
> packages wouldn't just measure temperature, but also pressure, light,
> wind and whatnot.  So maybe something along the line of
> "works-with::physical-measurements".  "works-with::measurements", even?
> That may include benchmark tools as well, and instinctively I'd say "why
> not?"

Actually, works-with::measurements would not describe some of our candidate
packages. We have "oligonucleotide design" applications that can either predict
the "melting temperature" of short DNA molecules, or generate arbitrary DNA
sequences whose melting temperature matches. Similarly, a weather forecasting
program would works-with::temperature but not works-with::measurements. On the
other hand, works-with::measurements would fit pondus (body weight management).
In addition to this sensors packages perform the measure themselves, which
would more fit "use::measuring".
 

> > made-of::data:examples, or role::example
> 
> Is it worth to separate examples from documentation?

Not necessarly. In my hands however, example packages contain example data, not
text documentation, but arguably the purpose is similar (although in addition
it can be used to check if the program is working correctly).


> > use::calculating
> 
> Definitely needed.  "calculating" or "computing" ?

Better ask a native speaker ;)


> > uitoolkit::xulrunner (in our case: biofox)
> 
> This makes a lot of sense: how many packages do we have?  iceweasel,
> biofox, then?

Difficult question… Biofox actually performs some operations within the browser
(like translating a DNA sequence into a protein sequence), while some other
add-ons have a much simpler interface, which may not desserve description with
a uitoolkit tag…


> > Executive summary: please create works-with::sequence and delete
> > field::biology:{bioinformatics|molecular|structural} and
> > field::medecine:imaging.
> 
> Will do as soon as we have an agreement about the
> "works-with::(biological-)sequence" name of the tag.

Since you prefer works-with::biological-sequence, let's go for it.


Have a nice sunday,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan