docs/index.rst
``datanator``
=====================
``datanator`` is a software tool for finding experimental data for building and calibrating dynamical models of cellular biochemistry such as metabolite, RNA, and protein abundances; protein complex compositions; transcription factor binding motifs; and kinetic parameters. ``datanator`` is particularly useful for building large models, such as whole-cell models, that require large amounts of data to constrain large numbers of parameters. ``datanator`` was motivated by the need for large amounts of data to constrain whole-cell models and the fact that this data is hard to utilize because it is scattered across numerous siloed repositories.
``datanator`` currently supports the following data types and data sources:
* Metabolite concentrations: `ECMDB <http://www.ecmdb.ca>`_ and `YMBD <http://www.ymdb.ca>`_
* RNA abundance: `ArrayExpress <https://www.ebi.ac.uk/arrayexpress>`_
* Protein abundance: `PaxDb <http://pax-db.org>`_
* Protein complex composition: `CORUM <http://mips.helmholtz-muenchen.de/corum>`_
* Transcription factor binding motifs: `JASPAR <http://jaspar.genereg.net>`_
* Reaction kinetics: `SABIO-RK <http://sabio.h-its.org>`_
* Taxonomy: `NCBI Taxonomy <https://www.ncbi.nlm.nih.gov/taxonomy>`_
``datanator`` (1) downloads these repositories; (2) normalizes their data to a common ontology and units; (3) stores their data to a local SQLite database; and (4) provides a Python API for (a) finding relevant data to model a specific organism and environmental condition from similar species, reactions, genotypes (taxon, variant), and environments (temperature, pH, media), and (b) reducing multiple relevant observations to a single consensus recommended parameter value, and (c) exporting these consensus recommendations and their provenance to an Excel workbook. To make ``datanator`` easier to use, we plan to develop user-friendly command line and web-based interfaces for finding data for SBML-encoded models.
``datanator`` is under active development and is not yet ready for end users. Please check back soon for updates.
This website contains detailed documentation of the ``datanator`` source code. Going forward, this website will also contain detailed instructions and tutorials on how to use ``datanator``.
Contents
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.. toctree::
:maxdepth: 3
:numbered:
intro
installation
tutorial
API documentation <source/modules.rst>
about
references.rst