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bpforms-0.0.9
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مشاهده بیشترتوضیحات
Unambiguous representation of modified DNA, RNA, and proteins
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bpforms-0.0.9 |
| نام | bpforms |
| نسخه کتابخانه | 0.0.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Karr Lab |
| ایمیل نویسنده | info@karrlab.org |
| آدرس صفحه اصلی | https://www.bpforms.org |
| آدرس اینترنتی | https://pypi.org/project/bpforms/ |
| مجوز | MIT |
|PyPI package| |Documentation| |Test results| |Test coverage| |Code
analysis| |License| |Analytics|
``BpForms``: toolkit for concretely describing non-canonical DNA, RNA, and proteins
===================================================================================
``BpForms`` is a set of tools for concretely representing the primary
structures of non-canonical forms of biopolymers, such as oxidized DNA,
methylated RNA, and acetylated proteins, and calculating properties of
non-canonical biopolymers.
``BpForms`` encompasses five tools:
- A grammar for concretely describing the primary structures of
non-canonical biopolymers. See the
`documentation <https://docs.karrlab.org/bpforms/>`__ for more
information. For example, the following text represents a modified
DNA molecule that contains a deoxyinosine monomeric form at the
fourth position.
``ACG[id: "dI" | structure: "[H][C@]1(O)C[C@@]([H])(O[C@]1([H])CO)N1C=NC2=C1N=CN=C2O"]T``
This concrete representation enables the ``BpForms`` software tools to
calculate properties of non-canonical biopolymers.
- Tools for calculating properties of non-canonical biopolymers
including their chemical formulae, molecular weights, charges, and
major protonation and tautomerization states.
- A web app: https://bpforms.org
- A JSON REST API: https://bpforms.org/api
- A command line interface. See the
`documentation <https://docs.karrlab.org/bpforms/master/0.0.1/cli.html>`__
for more information.
- A Python API. See the
`documentation <https://docs.karrlab.org/bpforms/master/0.0.1/python_api.html>`__
for more information.
``BpForms`` was motivated by the need to concretely represent the
biochemistry of DNA modification, DNA repair, post-transcriptional
processing, and post-translational processing in `whole-cell
computational models <https://www.wholecell.org>`__. ``BpForms`` is also
a valuable tool for experimental proteomics and synthetic biology. In
particular, we developed ``BpForms`` because there were no notations,
schemas, data models, or file formats for concretely representing
non-canonical forms of biopolymers, despite the existence of several
databases and ontologies of DNA, RNA, and protein modifications, the
`ProForma Proteoform
Notation <https://www.topdownproteomics.org/resources/proforma/>`__, and
the `MOMODICS <http://modomics.genesilico.pl/>`__ codes for modified RNA
bases.
*BpForms* can be combined with `*BcForms* <https://www.bcforms.org>`__
to concretely describe the primary structure of complexes.
Installation
------------
The following is a brief guide to installing ``BpForms``. The
`Dockerfile <Dockerfile>`__ in the repository contains detailed
instructions for how to install ``BpForms`` in Ubuntu Linux.
1. Install the third-party dependencies listed below.
- `ChemAxon Marvin <https://chemaxon.com/products/marvin>`__:
optional to calculate major protonation and tautomerization states
and draw molecules
- `Java <https://www.java.com>`__ >= 1.8
- `Open Babel <http://openbabel.org>`__
- `Pip <https://pip.pypa.io>`__ >= 19.0
- `Python <https://www.python.org>`__ >= 3.6
2. To use Marvin to calculate major protonation and tautomerization
states, set ``JAVA_HOME`` to the path to your Java virtual machine
(JVM) ``export JAVA_HOME=/usr/lib/jvm/default-java``
3. To use Marvin to calculate major protonation and tautomerization
states, add Marvin to the Java class path
``export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar``
4. Install this package
- Install the latest release from PyPI: ``pip install bpforms``
- Install the latest revision from GitHub:
``pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[chem] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms``
- To calculate major protonation and tautomerization states,
``BpForms`` must be installed with the ``[protontation]`` option:
``pip install bpforms[protontation] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[protontation]``
- To draw molecules, ``BpForms`` must be installed with the
``[draw]`` option:
``pip install bpforms[draw] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[draw]``
- To export the alphabets in OBO format, ``BpForms`` must be
installed with the ``[onto_export]`` option:
``pip install bpforms[onto_export] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[onto_export]``
- To install the rest API, ``BpForms`` must be installed with the
``[rest_api]`` option:
``pip install bpforms[rest_api] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[rest_api]``
Examples, tutorial, and documentation
-------------------------------------
Please see the `documentation <https://docs.karrlab.org/bpforms>`__. An
`interactive
tutorial <https://sandbox.karrlab.org/notebooks/bpforms/Tutorial.ipynb>`__
is also available in the whole-cell modeling sandbox.
License
-------
The package is released under the `MIT license <LICENSE>`__.
Citing ``BpForms``
------------------
Lang PF, Chebaro Y & Jonathan R. Karr. BpForms: a toolkit for concretely
describing modified DNA, RNA and proteins. arXiv:1903.10042.
`:link: <https://arxiv.org/abs/1903.10042>`__
Development team
----------------
This package was developed by the `Karr Lab <https://www.karrlab.org>`__
at the Icahn School of Medicine at Mount Sinai in New York, USA.
- `Jonathan Karr <https://www.karrlab.org>`__
- `Yassmine
Chebaro <https://www.linkedin.com/in/yassmine-chebaro-6bb8a05/>`__
- `Paul Lang <http://www.dtc.ox.ac.uk/people/17/langp/>`__
Questions and comments
----------------------
Please contact the `Karr Lab <mailto:info@karrlab.org>`__ with any
questions or comments.
.. |PyPI package| image:: https://img.shields.io/pypi/v/bpforms.svg
:target: https://pypi.python.org/pypi/bpforms
.. |Documentation| image:: https://readthedocs.org/projects/bpforms/badge/?version=latest
:target: https://docs.karrlab.org/bpforms
.. |Test results| image:: https://circleci.com/gh/KarrLab/bpforms.svg?style=shield
:target: https://circleci.com/gh/KarrLab/bpforms
.. |Test coverage| image:: https://coveralls.io/repos/github/KarrLab/bpforms/badge.svg
:target: https://coveralls.io/github/KarrLab/bpforms
.. |Code analysis| image:: https://api.codeclimate.com/v1/badges/e35081f676dfbb5ac46f/maintainability
:target: https://codeclimate.com/github/KarrLab/bpforms
.. |License| image:: https://img.shields.io/github/license/KarrLab/bpforms.svg
:target: LICENSE
.. |Analytics| image:: https://ga-beacon.appspot.com/UA-86759801-1/bpforms/README.md?pixel
نیازمندی
| مقدار | نام |
|---|---|
| - | attrdict |
| - | beautifulsoup4 |
| - | biopython |
| >=3.0.0 | cement |
| - | configobj |
| - | jinja2 |
| >=0.6.6 | lark-parser |
| - | mendeleev |
| <3 | openbabel |
| - | pandas |
| - | requests |
| - | requests-cache |
| >=0.15 | ruamel.yaml |
| - | setuptools |
| - | sqlalchemy |
| >=0.0.14 | wc-utils[chem] |
| - | capturer |
| - | flask |
| - | flask-restplus |
| - | hurry.filesize |
| - | jupyter |
| - | lxml |
| - | matplotlib |
| - | mock |
| - | numpy |
| - | plyplus |
| >=1 | pronto |
| - | psutil |
| - | pyjnius |
| >=1.8 | sphinx |
| - | sphinx-fontawesome |
| >=0.4.2 | sphinx-rtd-theme |
| >=0.1.1 | sphinxcontrib-addmetahtml |
| - | sphinxcontrib-bibtex |
| >=0.1.1 | sphinxcontrib-googleanalytics |
| - | sphinxcontrib-spelling |
| - | sphinxprettysearchresults |
| >=0.0.14 | wc-utils[protonation] |
| >=1.8 | sphinx |
| - | sphinx-fontawesome |
| >=0.4.2 | sphinx-rtd-theme |
| >=0.1.1 | sphinxcontrib-addmetahtml |
| - | sphinxcontrib-bibtex |
| >=0.1.1 | sphinxcontrib-googleanalytics |
| - | sphinxcontrib-spelling |
| - | sphinxprettysearchresults |
| >=0.0.14 | wc-utils[protonation] |
| >=1 | pronto |
| - | pyjnius |
| >=0.0.14 | wc-utils[protonation] |
| - | flask |
| - | flask-restplus |
| - | capturer |
| - | hurry.filesize |
| - | jupyter |
| - | lxml |
| - | matplotlib |
| - | mock |
| - | numpy |
| - | plyplus |
| - | psutil |
نحوه نصب
نصب پکیج whl bpforms-0.0.9:
pip install bpforms-0.0.9.whl
نصب پکیج tar.gz bpforms-0.0.9:
pip install bpforms-0.0.9.tar.gz