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Python Resources

We use Python for almost all our projects. It is a very powerful yet easy to learn language that both software developers and scientists enjoy using. See python.org for more details about the language.

Software for computational chemistry and biology

  • PyDaylight - A rapid application development library for Python based on the Daylight chemical informatics toolkits. Researchers enjoy it because it lets them implement and test new chemical algorithms in less than half the time of traditional methods.
  • Biopython - Biopython is an international collaboration to collect and produce open source bioinformatics tools written in the Python programming language.
  • Martel - Martel lets you work with existing flat-file bioinformatics formats as if they are already in XML. It is the core parsing framework for our products and for Biopython because it simplifies and standardizes how to access all the data in a file.
  • EUtils - A library which uses NCBI's EUtils network interface to query GenBank, PubMed and other databases.
  • Mindy - The Biopython flat-file indexing system

Other libraries and scripts

  • ReseekFile - Seek to the start of a file stream even when the underlying file does not support reseeking.
  • MultiDict - Dictionary-like objects where the keys may have multiple values.
  • sre_dump - Make a mapping from sre's parse tree back to the original regular expression
  • PyRSS2Gen - A Python library for generating RSS 2.0 feeds.
  • PyJudy - A Python wrapper to the Judy sparse dynamic array library.
  • python4ply - a grammar for the Python language written in Python for PLY

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