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LinuxScience


Applications
Description:

A group for those doing science work with Linux, including (but not restricted to) data analysis, visualisation.

Members:16
Comments:10
Created:Aug 19 2009
Changed:Aug 19 2009
Readability:readable for everybody
Membership:everybody can join

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 just for me

 
 by bongoMan on: Sep 3 2009
 
Score 50%

hey, i am a computational biologist, this group sounds just right for me! So let me write the first comment :) My favourite scientific linux apps:

-gnuplot (plotting data)
-pymol (visualising proteins)
-kalzium (periodic table of elements)
-bkchem (drawing chemical structures)
-clustalw (multiple alignments)
-latex + kile (writing papers or thesis, drawing formulas)

else, most programs i use are written by myself ;)

chemdraw is better than bkchem, I miss it on linux. Sigma plot is great too, would also be nice to have this on linux. Apart from those, I could never imagine doing scientific work on another os!


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 Re: just for me

 
 by flerant on: Sep 3 2009
 
Score 50%
flerantflerant
Institute of Applied Physics RAS
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Artem Korzhimanov 0

Institute of Applied Physics RAS
Russian Federation, Nizhniy Novgorod
Last visit Oct 6 2009
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I prefer to use mathgl (http://mathgl.sourceforge.net/) for drawing. It's more flexible and the pictures look much smarter.

As for visualizing molecules, I like VMD the most.


Physics is like sex. Sure, it may give some practical results, byt that's not why we do it.
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 Re: Re: just for me

 
 by bongoMan on: Sep 3 2009
 
Score 50%

Thank you for the MathGL Tip, it looks very interesting, and I didn't know about it :)

VMD is a great viewer too, it makes very beautiful pictures. But I got used to pymol since so long...

cheers!


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 Simulation software

 
 by bogdanc on: Sep 4 2009
 
Score 50%

I am interested in digital communications and related software applications. I have extensively used IT++ library as a free replacement for Matlab. Unfortunately IT++ lacks graphical capabilities and Octave has limited capabilities wrt Matlab.
I would like to have a tool to graphically represent the trellis of a convolutional code, given the generator polynomials. Do you know such a tool?


Bogdan
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 Re: Simulation software

 
 by jgomezdans on: Sep 4 2009
 
Score 50%

I tend to use Matplotlib, as it is pretty much equivalent to Matlab when producing plots. However, I don't know about your specific plot type....


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 Re: Re: Simulation software

 
 by bogdanc on: Sep 4 2009
 
Score 50%

I have forgotten to mention: it is possible to load results from IT++ into Matlab or Octave, while in matplotlib I don't know how to do it. Without some API for loading results from another app, this plotting tool is not too useful.


Bogdan
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 Re: Re: Re: Simulation software

 
 by jgomezdans on: Sep 4 2009
 
Score 50%

I guess the point i was trying to make is that python+scipy+numpy+matplotlib+etc is roughly equivalent to Matlab or Octave, but with a nice programming language ;D

Additionally, scipy is able to read matlab files (I guess that with some limitations): http://www.scipy.org/doc/api_docs/SciPy.io.mio.html


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 Re: Simulation software

 
 by flerant on: Sep 4 2009
 
Score 50%
flerantflerant
Institute of Applied Physics RAS
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Artem Korzhimanov 0

Institute of Applied Physics RAS
Russian Federation, Nizhniy Novgorod
Last visit Oct 6 2009
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look at mathgl. It works with octave, rather simple and makes smart graphs.


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 Re: Simulation software

 
 by shakes76 on: Sep 8 2009
 
Score 50%
shakes76shakes76
Discrete Geometry 3D Viewer
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Shekhar Chandra 1

Discrete Geometry 3D Viewer
Australia
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I have written Discrete Geometry Viewer which handles 3D/2D/1D plots and does convolutions. You can find it on this site.

http://www.qt-apps.org/content/show.php?content=95201&PHPSESSID=9bb769cd119b1cac24c6f8bf9cdde5e8


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 Linux related thesis

 
 by bogdanc on: Sep 5 2009
 
Score 50%

Just wondering: are there thesis proposals (PhDs) working on issues related to Linux ? For example, I have begun to use KDE4.3 and I am quite astonished by the level of complexity already achieved: one can define activities in top of desktops, etc. Desktop usability issues requires quite a research IMHO.


Bogdan
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