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Software shared by Cardoso Lab
1. Open Source Software to Model DNA replication
Software: This application combines a 1D Simulation of DNA replication with a 3D random loop DNA model. The simulations can be performed online at http://sim.bio.tu-darmstadt.de/. Original author: Dr. Daniel Löb.
The program specific files can be downloaded in one zip file: DNA replication master.zip or here
Installation: The instructions for each application can be found in the subdirectories.
License: This application is released under the GPL License version 3.
2. Open Source Software to Measure Colocalization Using the H Coefficient
Software: Here you will find a software needed to calculate colocalization coefficients, among them the H-coefficient, written in python to run in combination with priithon (see in the instructions for the Randomizer how to install priithon). In the compressed files you can find further instructions on how to run it. It should run on Windows, Linux and MacOS X. A detailed description of the this new colocalization coefficient can be found in our recent publication “New image colocalization coefficient for fluorescence microscopy to quantify (bio-)molecular interactions.” Journal of Microscopy, 249, 184, (2013) doi: 10.1111/jmi.12008
The program specific files can be downloaded in one zip file: H-coeff.zip
3. Open Source Software for the Randomizer Program
Software: Here you find the software needed to run the program described in our recent publication “3D-Image analysis platform monitoring relocation of pluripotency genes during reprogramming” Nucl. Acids Res. (2011) doi:10.1093/nar/gkr486.
It should run on Windows, Linux and MacOS X. Feel free to contact us in case you encounter any problems or if you would like to give any kind of feedback... we really appreciate it!
Installation:
The program specific files can be downloaded in one zip file: Randomizer.zip
This file works for all operating systems.
To run this, you will also need Priithon. Priithon is hosted
separately at priithon.googlecode.com
Please download the file that fits your platform:
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for 32 bit Linux: |
Priithon_25_lin#20090615.tbz |
note for Linux: you will need Python 2.5 (!) installed
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for 64 bit Linux: |
Priithon_25_lin64#20090615.tbz |
note for Linux: you will need Python 2.5 (!) installed
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for Mac: |
Priithon_25_mac_2009-06-18.dmg |
note for Mac: you will need Python 2.5 (!) installed. Even if you
have a 64-bit OS-X, you can use Randomizer as long as you have a 32-bit Python 2.5 installed. Make sure that self-installed versions of Python
should go into the /usr/local area of your system,
to not interfere with the health of your system!
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for Windows: |
Priithon_25_win#20090615.zip |
note for Windows: The Priithon_25_win zip file includes a version of
Python (32bit, which also works on a 64-bit windows) |
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Last but not least you will have to download the file Priithon_py_update_20110521.zip and put the one folder inside (named "Priithon") into the
Priithon_25_(win/mac/lin) area, overwriting the existing "Priithon"
folder.
Starting Randomizer:
- Double click priithon_script (or priithon_script.bat)
- drag & drop the randomizer.py file into the "Priithon shell" windows,
an choose "execute py-file"
- drop an image sequence files
For a detailed instruction on how to use the program please watch our tutorial movie explaining the main functions.
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