bpforms

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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:[e-mail]>__ with any questions or comments.

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