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28 changes: 14 additions & 14 deletions README.md
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[![License](https://img.shields.io/github/license/KarrLab/bpforms.svg)](LICENSE)
![Analytics](https://ga-beacon.appspot.com/UA-86759801-1/bpforms/README.md?pixel)

# BpForms: concrete representation of non-canonical DNA, RNA, and proteins
# `BpForms`: toolkit for concretely representating 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` 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:
`BpForms` encompasses five tools:

* A notation for describing non-canonical biopolymers. See below and the [documentation](https://docs.karrlab.org/bpforms/) for details and examples.
* A web app, [https://bpforms.org](https://bpforms.org), for calculating properties of non-canonical biopolymers
* A [JSON REST API](https://docs.karrlab.org/bpforms/master/0.0.1/rest_api.html#rest-api) for programmatically calculating properties of non-canonical biopolymers
* A command line interface for calculating properties of non-canonical biopolymers. See the [documentation](https://docs.karrlab.org/bpforms/master/0.0.1/cli.html) for more information.
* A Python API for programmatically calculating properties of non-canonical biopolymers. See the [documentation](https://docs.karrlab.org/bpforms/master/0.0.1/python_api.html) for more information.

The BpForms notation and data model can concretely represent the structure of non-canonical forms of biopolymers. For example, the following text represents a modified DNA molecule that contains a deoxyinosine monomer at the fourth position.
* A notation 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 monomer 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 of non biopolymers enables the BpForms software to calculate the chemical formulae, molecular weights, and charges of biopolymers, as well as the major protonation and tautomerization state of biopolymers at specific pHs.
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](https://bpforms.org)
* A JSON REST API: [https://bpforms.org/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` 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.

## Installation
1. Install the third-party dependencies listed below. Detailed installation instructions are available in [An Introduction to Whole-Cell Modeling](http://docs.karrlab.org/intro_to_wc_modeling/master/0.0.1/installation.html).
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pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms
```

* To install the rest API, BpForms must be installed with the `[all]` option:
* To install the rest API, `BpForms` must be installed with the `[all]` option:
```
pip install bpforms[all]
pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[all]
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## License
The package is released under the [MIT license](LICENSE).

## Citing BpForms
## 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
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31 changes: 12 additions & 19 deletions docs/index.rst
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`BpForms` documentation
=======================

`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` is a set of tools for unambiguously representing the structures of modified forms of biopolymers such as DNA, RNA, and protein.
`BpForms` emcompasses five tools:

* The `BpForms` notation can unambiguously represent the structure of modified forms of biopolymers. For example, the following represents a modified DNA molecule that contains a deoxyinosine monomer at the fourth position::
* A notation for concretely describing the primary structures of non-canonical biopolymers. See :numref:`notation` for detailed information. For example, the following represents a modified DNA molecule that contains a deoxyinosine monomer at the fourth position:
::

ACG[
id: "dI" | structure: "O=C1NC=NC2=C1N=CN2"
]T

* This concrete representation of modified biopolymers enables the `BpForms` software tools to calculate the chemical formulae, molecular weights, and charges of biopolymers, as well as automatically calculate the major protonation and tautomerization state of biopolymers at specific pHs.

`BpForms` emcompasses five tools:

* Notation for describing biopolymers: See :numref:`notation`.
* Web-based graphical interface: See `https://bpforms.org <https://bpforms.org>`_ and :numref:`graphical_web_interface`.
* REST JSON API: See :numref:`rest_api`.
* Command line interface: See :numref:`cli`.
* Python API: See :numref:`python_api`.

`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>`_. In addition, `BpForms` are a valuable tool for experimental proteomics. In particular, we developed `BpForms` because there were no notations, schemas, data models, or file formats for concretely representing modified forms of biopolymers, despite the existence of several databases and ontologies of DNA, RNA, and protein modifications and the `ProForma Proteoform Notation <https://www.topdownproteomics.org/resources/proforma/>`_.
This concrete representation enables the `BpForms` software tools to calculate properties of non-canonical biopolymers.

The `BpForms` syntax was inspired by the ProForma Proteoform Notation. `BpForms` improves upon this syntax in several ways:
* Tools for calculating properties of non-canonical biopolymers including their chemical formulae, molecular weights, charges, and major protonation and tautomerization states.

* A web-based graphical interface: See `https://bpforms.org <https://bpforms.org>`_ and :numref:`graphical_web_interface`.
* A JSON REST API: See `https://bpforms.org/api <https://bpforms.org/api>`_ and :numref:`rest_api`.
* A command line interface: See :numref:`cli`.
* A Python API: See :numref:`python_api`.

* `BpForms` separates the representation of modified biopolymers from the chemical processes which generate them.
* `BpForms` clarifies the representation of multiply modified monomers. This is necessary to represent the combinatorial complexity of modified DNA, RNA, and proteins.
* `BpForms` can be customized to represent any modification and, therefore, is not limited to previously enumerated modifications. This is also necessary to represent the combinatorial complexity of modified DNA, RNA, and proteins.
* `BpForms` supports two additional types of uncertainty in the structures of biopolyers: uncertainty in the position of a modified nucleotide/amino acid and uncertainty in its charge.
* `BpForms` has a concrete grammar. This enables error checking, as well the calculation of chemical formulae, masses, and charges which is essential for modeling.
`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 modified 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.

Contents
--------
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