Corpus ID: 12160699

Python: a programming language for software integration and development.

@article{Sanner1999PythonAP,
  title={Python: a programming language for software integration and development.},
  author={Michel F. Sanner},
  journal={Journal of molecular graphics \& modelling},
  year={1999},
  volume={17 1},
  pages={
          57-61
        }
}
  • M. Sanner
  • Published 1999
  • Computer Science, Medicine
  • Journal of molecular graphics & modelling
One of the challenges in bio-computing is to enable the efficient use and inter-operation of a wide variety of rapidly-evolving computational methods to simulate, analyze, and understand the complex properties and interactions of molecular systems. In our laboratory we investigates several areas, including protein-ligand docking, protein-protein docking, and complex molecular assemblies. Over the years we have developed a number of computational tools such as molecular surfaces… Expand
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A component-based software environment for visualizing large macromolecular assemblies.
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References

SHOWING 1-2 OF 2 REFERENCES
Integrating Computation and Visualization for Biomolecular Analysis: An Example Using Python and AVS
TLDR
An approach based on the Python programming language is presented to achieve a high level of integration between these different computational methods and the primary visualization system AVS, removing many limitations of AVS while increasing dramatically the inter-operability of the authors' computational tools. Expand
Reuse: Been There, Done That
TLDR
Over-all, I believe the field of reuse has made considerable progress and the benefits of successful software reuse pro-grams are seen and the lessons learned from those who have been there are reviewed. Expand