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Re: Debian for Systems Biology



On Mon, Jan 30, 2006 at 07:27:13AM +0100, Andreas Tille wrote :
> 
> Well, several months ago I suggested that we should start building such
> web pages automatically and started some very basic code (which is far from
> beeing usable and no chance of continuing this for some further months).
> The idea is as follows:
> 
>   1) Obtain the contents of the first part of the web page by parsing
>      Packages.gz file for a list of packages that should be listed on
>      the page.
> 
>   2) Use ddtp translations for translated pages.  (Well, unfortunately
>      the ddtp project is currently in a quite bad state.  It was much
>      more usable before the break into the Debian servers in the end
>      of 2003. :-()
> 
>   3) Build a "fake Package.gz" file containing the projects that should
>      be included into Debian and into the CDD in question to build the
>      list of projects with inofficial packages or are not yet packaged
>      and use the algorithm from 1) to create the other part of the web
>      page.
> 
> If we would have such a system every project could easily build the
> web needed web pages by just compiling a list of projects that should
> be included.  So if the only thing you do not like is the name of the
> page you could compile your own one by just renaming the list name
> (that might lead to a page name) and perhaps add or remove some projects.
> That way we will not double any work but gain maximum flexibility.

That sounds nice, but as you say, it requires some preliminary work
before doing the core work, which is increasing the number of packages
related to biology in debian. Although I warmly welcome anybody who
would code this, I will not do it before it becomes that kind of itch
which one wants to scratch.

In order to create a dynamic, we need some quick results. I want to
start with a simple list, with the program name, the purpose, the
freedom, a rating of the difficulty to integrate to debian, and the
alternatives. Then if we manage to enrich debian of a few packages, we
can think about giving some time to building a better infrastructure...

[By the way, talking about ddtp, it is a shame that it does not work
anymore, because the tranlation of your debian-med pages, which are
mostly descripion of packages or prospective packages, generated a lot
of translations of descriptions of debian packages! So the people who
would like to revive the ddtp will not start with no material.]


> >Also, I wonder how some existing packages could be tweaked. For instance, 
> >the
> >search box of firefox can be used to query very relevant databases,
> >such as pubmed.gov or genbank (http://www.ncbi.nlm.nih.gov/Genbank/),
> 
> You mean mozilla-biofox?

Not sure. It seems that biofox is a toolbar with many functionalities.
In mozilla-derived browsers, there is a small field right of the url
field, from which a google search can be started. Other search engines
can be added, including scientific ones. It is less powerful than
biofox, but on the other hand is not a plugin, but a built-in fuction
that can be configured. But I wonder wether this, and the default
bookmarks, can be easily tweaked in a custom debian distribution.

Best,

-- 
Charles



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