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cameo-0.9.0b1
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مشاهده بیشترتوضیحات
cameo - computer aided metabolic engineering & optimization
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cameo-0.9.0b1 |
| نام | cameo |
| نسخه کتابخانه | 0.9.0b1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Nikolaus Sonnenschein, Joao Cardoso, Emre Özdemir, Kristian Jensen |
| ایمیل نویسنده | niko.sonnenschein@gmail.com |
| آدرس صفحه اصلی | http://cameo.bio |
| آدرس اینترنتی | https://pypi.org/project/cameo/ |
| مجوز | Apache License Version 2.0 |
Cameo—Computer Aided Metabolic Engineering and Optimization
-----------------------------------------------------------
.. summary-start
|Join the chat at https://gitter.im/biosustain/cameo| |PyPI| |License|
|Build Status| |Coverage Status| |DOI| |zenhub| |binder|
What is cameo?
~~~~~~~~~~~~~~
**Cameo** is a high-level python library developed to aid the strain
design process in metabolic engineering projects. The library provides a
modular framework of simulation and strain design methods that targets
developers that want to develop new design algorithms and custom analysis workflows.
Furthermore, it exposes a high-level API to users that just want to
compute promising strain designs.
Curious? Head over to `try.cameo.bio <http://try.cameo.bio>`__
and give it a try.
Please cite https://doi.org/10.1021/acssynbio.7b00423 if you've used cameo in a scientific publication.
.. summary-end
Installation
~~~~~~~~~~~~
.. installation-start
Use pip to install cameo from `PyPI <https://pypi.python.org/pypi/cameo>`__.
::
$ pip install cameo
In case you downloaded or cloned the source code from `GitHub <https://github.com/biosustain/cameo>`__
or your own fork, you can run the following to install cameo for development.
::
$ pip install -e <path-to-cameo-repo> # recommended
You might need to run these commands with administrative
privileges if you're not using a virtual environment (using ``sudo`` for example).
Please check the `documentation <http://cameo.bio/installation.html>`__
for further details.
.. installation-end
Documentation and Examples
~~~~~~~~~~~~~~~~~~~~~~~~~~
Documentation is available on `cameo.bio <http://cameo.bio>`__. Numerous `Jupyter notebooks <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/tree/master/>`__
provide examples and tutorials and also form part of the documentation. They are also availabe in executable form on (`try.cameo.bio <http://try.cameo.bio>`__).
Furthermore, course materials for a two day cell factory engineering course are available `here <https://biosustain.github.io/cell-factory-design-course/>`__.
.. showcase-start
High-level API (for users)
^^^^^^^^^^^^^^^^^^^^^^^^^^
Compute strain engineering strategies for a desired product in a number
of host organisms using the high-level interface (runtime is on the order of hours).
::
from cameo.api import design
design(product='L-Serine')
`Output <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/08-high-level-API.ipynb>`__
The high-level API can also be called from the command line.
::
$ cameo design vanillin
For more information run
::
$ cameo --help
Low-level API (for developers)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Find gene knockout targets using evolutionary computation.
::
from cameo import models
from cameo.strain_design.heuristic import GeneKnockoutOptimization
from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield
model = models.bigg.e_coli_core
obj = biomass_product_coupled_yield(
model.reactions.Biomass_Ecoli_core_w_GAM,
model.reactions.EX_succ_e,
model.reactions.EX_glc_e)
ko = GeneKnockoutOptimization(model=model, objective_function=obj)
ko.run(max_evaluations=50000, n=1, mutation_rate=0.15, indel_rate=0.185)
`Output <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/05-predict-gene-knockout-strategies.ipynb>`__
Predict heterologous pathways for a desired chemical.
::
from cameo.strain_design import pathway_prediction
predictor = pathway_prediction.PathwayPredictor(model)
pathways = predictor.run(product="vanillin")
`Output <http://nbviewer.ipython.org/github/biosustain/cameo-notebooks/blob/master/07-predict-heterologous-pathways.ipynb>`__
.. showcase-end
Contributions
~~~~~~~~~~~~~
... are very welcome! Please read the `guideline <CONTRIBUTING.rst>`__ for instructions how to contribute.
.. url-marker
.. |Join the chat at https://gitter.im/biosustain/cameo| image:: https://badges.gitter.im/biosustain/cameo.svg
:target: https://gitter.im/biosustain/cameo?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
.. |PyPI| image:: https://img.shields.io/pypi/v/cameo.svg
:target: https://pypi.python.org/pypi/cameo
.. |License| image:: http://img.shields.io/badge/license-APACHE2-blue.svg
:target: http://img.shields.io/badge/license-APACHE2-blue.svg
.. |Build Status| image:: https://travis-ci.org/biosustain/cameo.svg?branch=master
:target: https://travis-ci.org/biosustain/cameo
.. |Coverage Status| image:: https://coveralls.io/repos/biosustain/cameo/badge.svg?branch=devel
:target: https://coveralls.io/r/biosustain/cameo?branch=devel
.. |DOI| image:: https://zenodo.org/badge/5031/biosustain/cameo.svg
:target: https://zenodo.org/badge/latestdoi/5031/biosustain/cameo
.. |zenhub| image:: https://img.shields.io/badge/Shipping_faster_with-ZenHub-5e60ba.svg?style=flat-square
:target: https://zenhub.com
.. |binder| image:: https://mybinder.org/badge_logo.svg
:target: https://mybinder.org/v2/gh/biosustain/cameo-notebooks/binder?urlpath=lab/tree/index.ipynb
نیازمندی
| مقدار | نام |
|---|---|
| >=1.9.1 | numpy |
| >=0.14.0 | scipy |
| >=1.5.1 | blessings |
| >=1.1.3 | pandas |
| >=1.2 | ordered-set |
| >=0.11.1 | cobra |
| >=0.15.2 | future |
| >=1.4.2 | optlang |
| >=2.4 | numexpr |
| >=2.10.0 | requests |
| >=2.4 | networkx |
| >=1.1.2 | escher |
| >=0.4 | IProgress |
| >=1.0 | inspyred |
| >=1.2.0 | lazy-object-proxy |
| >=2.1.1 | palettable |
| ==1.0.1 | gnomic |
| >=2.4.5 | openpyxl |
| >=6.7 | click |
| <=0.12.1 | bokeh |
| >=4.1.1 | ipywidgets |
| - | pytest-benchmark |
| >=3.6.0 | lxml |
| >=5.13.0 | python-libsbml |
| >=2.10.5 | redis |
| >=4.12.0 | plotly |
| >=1.0.0 | jupyter |
| >=0.5 | numpydoc |
| >=1.3.5 | Sphinx |
| - | pytest-cov |
| >=5.0.1 | ipyparallel |
| - | pytest |
| <=0.12.1 | bokeh |
| >=1.3.5 | Sphinx |
| >=0.5 | numpydoc |
| >=1.0.0 | jupyter |
| >=4.1.1 | ipywidgets |
| >=2.10.5 | redis |
| >=5.0.1 | ipyparallel |
| >=4.12.0 | plotly |
| >=5.13.0 | python-libsbml |
| >=3.6.0 | lxml |
| - | pytest |
| - | pytest-cov |
| - | pytest-benchmark |
نحوه نصب
نصب پکیج whl cameo-0.9.0b1:
pip install cameo-0.9.0b1.whl
نصب پکیج tar.gz cameo-0.9.0b1:
pip install cameo-0.9.0b1.tar.gz