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Bug#295078: marked as done (RFP: stochastirator -- an accelerated discrete reaction event simulator)

Your message dated Thu, 16 Feb 2006 11:59:44 -0700
with message-id <E1F9oLw-0006zO-VL@merkel.debian.org>
and subject line WNPP bug closing
has caused the attached Bug report to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what I am
talking about this indicates a serious mail system misconfiguration
somewhere.  Please contact me immediately.)

Debian bug tracking system administrator
(administrator, Debian Bugs database)
--- Begin Message --- 
Package: wnpp
Severity: wishlist

* Package name    : stochastirator
  Version         : 0.0.1
  Upstream Author : Eric Lyons
* URL             : http://opnsrcbio.molsci.org/stochastirator/
* License         : GPL
  Description     : an accelerated discrete reaction event simulator

The Stochastirator represents the time-dependent behavior of biochemical
reaction networks in accordance with stochastic chemical kinetics.
Briefly, for a user-specified reaction netwrok, the program works by,

   1.      computing the "next time" each reaction will execute based on
the unique number of substrate molecules (or combinations) and reaction
propensity.
   2.      sorting the "next (reaction) time(s)" to determine which
reaction next occurs.
   3.      executing the next reaction, thereby advancing the simulation
time and updating the number of products and substrates involved in the
reaction.
   4.      computing a new "next time" for the executed reaction and
reactions whose number of substrate species (or combinations) were
changed by the just executed reaction.
   5.      repeating steps 2-4 until the end time of the simulation is
reached 

The next reaction time, t, is computed using the First Reaction Method
developed by Gillespie in 1976.

t=(1/a)ln(1/r)

where,

"a" is the reaction "propensity" (the product of the reaction "rate" and
the number of unique reactant combinations), "r" is a random number
drawn from a uniform distribution in the unit interval. 

-- System Information:
Debian Release: 3.1
  APT prefers unstable
  APT policy: (500, 'unstable'), (500, 'testing')
Architecture: i386 (i686)
Kernel: Linux 2.6.8-1-686
Locale: LANG=it_IT@euro, LC_CTYPE=it_IT@euro (charmap=ISO-8859-15)

-- 
Luca Brivio

Web:		http://icebrook.altervista.org
Jabber:		lucab83@jabber.org

________________________________________________________________________

"Homo sum: humani nil a me alienum puto" (P. Terentius Afer)
________________________________________________________________________

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--- End Message ---
--- Begin Message --- 
Hello,

This is an automatic mail sent to close the RFP you have reported or 
are involved with.

Your RFP wnpp bug is being closed because of the following reasons:
- It is, as of today, older than 365 days.
- It hasn't had any activity recently.

As this is an automatic procedure, it could of course have something
wrong and probably it would be closing some bugs that are not 
intended by owners and submitters (like you) to be closed, for
example if the RFP is still of your interest, or there has been 
some kind of activity around it. In that case, please reopen the
bug, do it, DO IT NOW! (I don't want to be blamed because of
mass closing and not let people know that they can easily reopen
their bugs ;-).

To re-open it, you simply have to mail control@bugs.debian.org
with a body text like this:

reopen 295078
thanks bts

Further comments on the work done in the bug sent to
295078@bugs.debian.org would be truly welcomed.
Anyway, if you have any kind of problems when dealing with
the BTS, feel free to contact me and I'd be more than happy to help
you on this: <damog@debian.org>.

A similar process is being applied to other kind of wnpp bugs.

Thanks for your cooperation,

 -- David Moreno Garza <damog@debian.org>.

--- End Message ---
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