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Posts: 25
Registered:
February 2006
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Posts: 1
Location:
Dresden
Registered:
December 2004
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Gene regulatory networks, simulations
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25 Apr '06 15:56
 
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Hi,
I am working in a genetics lab, trying to make a genetic network that works in series..I need a software so that i can theoretically corelate my results and find out binding constants etc. I have heard of dizzy, dynetica and celldesigner, but havent ever used them. Kindly comment on their ease of usage..and suggest me a starting point.
Time is of utmost importance, as my thesis will only last for 4 more months... :)
Thanks in advance,
Sikander
Sikander Hayat
Master of Science, Student
Molecular Bioengineering
TU Dresden, Germany
Home: 49 351 4066138
Mobile: 49 176 24656260
Just because you can't see something, doesn't mean it's there.
---------------------------------
Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2¢/min or less.
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Posts: 14
Location:
KGI
Registered:
May 2005
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RE: Gene regulatory networks, simulations
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25 Apr '06 16:30
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Hi Sikander,
Why not try JDesigner 2? It should be very easy to deal with … it also comes
along with a Tutorial Booklet that will explain the basic features:
JD2 :
http://public.kgi.edu/~fbergman/files/latest/SetupSBW.exe
Booklet :
http://public.kgi.edu/~hsauro/sysbio/papers/JDBooklet.pdf
Cheers
Frank
_____
From: sikander hayat [mailto:hayat221@yahoo.com]
Sent: Tuesday, April 25, 2006 3:57 PM
To: SBML Discussion List
Subject: [sbml-discuss] Gene regulatory networks, simulations
Hi,
I am working in a genetics lab, trying to make a genetic network that works
in series..I need a software so that i can theoretically corelate my results
and find out binding constants etc. I have heard of dizzy, dynetica and
celldesigner, but havent ever used them. Kindly comment on their ease of
usage..and suggest me a starting point.
Time is of utmost importance, as my thesis will only last for 4 more
months... :)
Thanks in advance,
Sikander
Sikander Hayat
Master of Science, Student
Molecular Bioengineering
TU Dresden, Germany
Home: 49 351 4066138
Mobile: 49 176 24656260
Just because you can't see something, doesn't mean it's there.
_____
Yahoo! Messenger with Voice. Make
<http://us.rd.yahoo.com/mail_us/taglines/postman1/*http:/us.rd.yahoo.com/evt
=39663/*http:/voice.yahoo.com> PC-to-Phone Calls to the US (and 30+
countries) for 2¢/min or less.
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Posts: 96
Registered:
September 2003
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Re: Gene regulatory networks, simulations
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26 Apr '06 07:31
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Hello Sikander,
Please have a look at COPASI (www.copasi.org) it can deal with gene
networks. It also supports Parameter Estimation, which would allow you
to fit the parameters of your model to your experimental results. In
addition you may choose either stochastic or deterministic integration
depending on you modeling needs.
Thanks,
Stefan
On Tue, 25 Apr 2006 15:56:49 -0700 (PDT)
sikander hayat <hayat221@yahoo.com> wrote:
> Hi,
> I am working in a genetics lab, trying to make a genetic network
> that works in series..I need a software so that i can theoretically
> corelate my results and find out binding constants etc. I have heard
> of dizzy, dynetica and celldesigner, but havent ever used them.
> Kindly comment on their ease of usage..and suggest me a starting
> point. Time is of utmost importance, as my thesis will only last
> for 4 more months... :) Thanks in advance,
> Sikander
>
>
>
> Sikander Hayat
>
> Master of Science, Student
> Molecular Bioengineering
> TU Dresden, Germany
> Home: 49 351 4066138
> Mobile: 49 176 24656260
>
>
> Just because you can't see something, doesn't mean it's there.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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>
>
>
>
> ---------------------------------
> Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+
> countries) for 2¢/min or less.
--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu
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