Polonator G.007 source

The Polonator Source has gone github. MIT license on everything

Release Background

The Wyss Institute is funding improvements to the Polonator source. Much of the Polonator source code was originally a rush job, so the code is a bit rough around the edges. As a commitment to the project, and generally building open software and hardware I'm majorly refactoring the code base.
This is the start of an organization process of the code, which has been slowly accumulating over the last year.

The fundamental things we are doing:

1. More Python
2. Python gets access to C data structures through swig'd numpy arrays (open to anyone changing this, to Boost.Python, or whatever)
3. The result is a more scriptable automated microscope
4. Accelerating and multithreading the image processing and basecalling
5. Updating the user interface.
6. Code prettying

If you want to contact me mail: nick.conway at wyss.harvard.edu

Installation

For now all you can grab is the source. This will change as updates proceed. Eventually, a full installer should be available. The dependencies are:

1. SWIG, license, whatever license you like for redistribution
2. Python 2.X, v2.5 or greater
3. Perl
4. Numpy, license, BSD
5. Open source Phoenix drivers v5.59 for the Phoenix frame grabber from Active Silicon
6. Java, and even Netbeans for reviewing the old GUI

To build:

1. git clone the repository to a directory, such as /usr/local to create the directory such as /usr/local/Polonator

    cd /usr/local
    git clone git@github.com:grinner/Polonator.git
   

2. set the POLONATOR_PATH environment variable to the above directory in your .profile, .bash_profile, or .bashrc. For instance add or run in bash depending on use case:

    export POLONATOR_PATH = /usr/local/Polonator
   

3. change directories to the:

    cd $POLONATOR_PATH
   

4. run:

    sh build_main.sh
   

Usage

Polonator will be an installable python module. You might find it most useful for tasks involving DNA sequencing. Typical usage often looks like this:

#!/usr/bin/env python

from polonator import maestro
from polonator import camera

if camera.isReady():
    print "Taking another photo:", maestro.snap()

Links

• Image ingestion simulator - a hack of the G.007 image ingestion system to create a standalone simulator for developing new image processing and basecalling algorithms for DNA sequencing