Metadata-Version: 1.0
Name: bioprinter
Version: 0.1.1
Summary: UNKNOWN
Home-page: https://github.com/Edinburgh-Genome-Foundry/bioprinter
Author: Zulko
Author-email: UNKNOWN
License: MIT
Description: BioPrinter
        ===========
        .. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/bioprinter.svg?branch=master
           :target: https://travis-ci.org/Edinburgh-Genome-Foundry/bioprinter
           :alt: Travis CI build status (Python 3)
        
        Bioprinter (webpage here_ ) is a Python module to produce living art. It transforms an image into files that a liquid dispenser can use to *print* the image to a plate using pigmented yeast or bacteria.
        
        Here are two examples of bio-art:
        
        .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_dolly.jpeg
            :align: center
        
            Dolly drawn with baker yeast (white), violacein-producing yeast (black), and carotene-producing yeast (orange)
        
        
        .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_england.jpeg
            :align: center
        
            England flag drawn with 3 different strains of the bacterium *E. coli*.
        
        Bioprinter is released on Github_ under the MIT licence (¢ Edinburgh Genome Foundry), everyone is welcome to contribute !
        
        Bioprinter was written at the Edinburgh Genome Foundry by Zulko_ after an original idea and Matlab code by Mike Shen (`Mike's project on Github <https://github.com/mshen5/BioPointillism>`_).
        
        Installation
        --------------
        
        
        If you have PIP installed: ::
        
            (sudo) pip install ez_setup bioprinter
        
        Or unzip the source code in a directory and type in a terminal: ::
        
            sudo python setup.py install
        
        
        Usage
        --------
        
        In the same folder as your code, place an image. It can have any resolution, but keep in mind that the width/height ratio of the plate it is printed on is 1.5. Make sure that a specific color is used to mark the un-pigmented background of the image, here we use blue:
        
        .. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/dolly.jpeg
            :align: center
        
        Then write the following code in ``dolly.py``:
        
        .. code:: python
        
            from bioprinter import bioprint
        
            bioprint(
                image_filename="../docs/_static/images/dolly.jpeg",
                output_filename="dolly.csv",
                bg_color=[0, 0, 255], # blue background represents empty wells
                pigments_wells={"A1": [0, 0, 0],  # black yeast in source well A1
                                "A2": [250, 120, 10],  # orange yeast in well A2
                                "A3": [255, 255, 255]},  # white yeast in well A3
                quantified_image_filename="dolly_preview.jpeg"
            )
        
        Execute in a terminal with ``python dolly.py``. This will produce a ``dolly.csv`` file as well as a preview image of the final printing (so that you can check if the image looks good at this low resolution).
        
        Prepare a source plate with the right pigmented yeasts in wells A1, A2, A3, use an agar plate as the destination plate, and feed ``dolly.csv`` to the `Labcyte Echo <http://www.labcyte.com/products/liquidhandling/echo-555-liquid-handler>`_. Once the printing is finished, incubate 2 days at 30C (it would be one day at 37C for bacteria). Enjoy the result !
        
        
        .. _here: http://edinburgh-genome-foundry.github.io/bioprinter/
        .. _Zulko: https://github.com/Zulko/
        .. _Github: https://github.com/Edinburgh-Genome-Foundry/bioprinter
        
Keywords: bioprinter pointillism living art
Platform: UNKNOWN
