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.

 
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

 
 

 

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!
Please contact us, Sebastian (mostly regarding the installation) or Laurence (about how to use the program) under
email: software (at) cardoso-lab.org

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:
for 32 bit Linux: Priithon_25_lin#20090615.tbz
for 64 bit Linux: Priithon_25_lin64#20090615.tbz
for Mac: Priithon_25_mac_2009-06-18.dmg
for Windows: Priithon_25_win#20090615.zip

  • note for Linux: you will need Python 2.5 (!) installed.
  • 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 !!
  • note for Windows: The Priithon_25_win zip file includes a version of Python (32bit, which also works on a 64-bit windows)

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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