diff --git a/pypi-readme.rst b/pypi-readme.rst new file mode 100644 index 0000000..a4b302e --- /dev/null +++ b/pypi-readme.rst @@ -0,0 +1,76 @@ +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) + +.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/bioprinter/badge.svg?branch=master + :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/bioprinter?branch=master + + +Bioprinter (webpage here_) is a Python package for producing 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 + + British flag drawn with 3 different strains of the bacterium *E. coli*. + +These bio-prints (and many others!) were presented at the University of Edinburgh's SynthSys Open days 2016 (strain selection and acoustic printing by Paulina Kanigowska). + +Bioprinter is released on Github_ under the MIT licence (Copyright 2015 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 (`project on Github `_). + +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 +----- + +The image file to be printed can have any resolution, but note that the width/height ratio of the plate the image is printed on is 1.5. Ensure 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 + +Run the following code in Python or save in ``dolly.py``: + +.. code:: python + + from bioprinter import bioprint + + bioprint( + image_filename="/path/to/image/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" + ) + +The saved script can be executed 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 Acoustic Liquid Handler `_ (tested with Labcyte Echo 555 Series). 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 diff --git a/setup.py b/setup.py index 305091c..6a69b38 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ version=__version__, author="Zulko", description="", - long_description=open("README.rst").read(), + long_description=open("pypi-readme.rst").read(), license="MIT", url="https://github.com/Edinburgh-Genome-Foundry/bioprinter", keywords="bioprinter pointillism living art",