Release history

Main improvements in the past releases:

0.1.0

  • First release of pypath, for initial testing.

0.2.0

  • Lots of small improvements in almost every module

  • Networks can be read from local files, remote files, lists or provided by any function

  • Almost all redistributed data have been removed, every source downloaded from the original provider.

0.3.0

  • First version with partial Python 3 support.

0.4.0

  • pyreact module with BioPaxReader and PyReact classes added

  • Process description databases, BioPax and PathwayCommons SIF conversion rules are supported

  • Format definitions for 6 process description databases included.

0.5.0

  • Many classes have been added to the plot module

  • All figures and tables in the manuscript can be generated automatically

  • This is supported by a new module, analysis, which implements a generic workflow in its Workflow class.

0.7.74

  • homology module: finds the homologs of proteins using the NCBI Homologene database and the homologs of PTM sites using UniProt sequences and PhosphoSitePlus homology table

  • ptm module: fully integrated way of processing enzyme-substrate interactions from many databases and their translation by homology to other species

  • export module: creates pandas.DataFrame or exports the network into tabular file

  • New webservice

  • TF Regulons database included and provides much more comprehensive transcriptional regulation resources, including literature curated, in silico predicted, ChIP-Seq and expression pattern based approaches

  • Many network resources added, including miRNA-mRNA and TF-miRNA interactions

Upcoming

  • New, more flexible network reader class

  • Full support for multi-species molecular interaction networks (e.g. pathogene-host)

  • Better support for not protein only molecular interaction networks (metabolites, drug compounds, RNA)

  • ChEMBL webservice interface, interface for PubChem and eventually forDrugBank

  • Silent mode: a way to suppress messages and progress bars