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I need to implement a project in Python which deals with Amino Acids detection in Cryo EM electron density scan (MAP format) by means of FFT, cross-correlation, 3D harmonics, and SVM (machine learning) tools.

There are dozens of available Python packages and I didn't find comprehensive enough comparison table of them. To avoid trial each of existing ones, please tell me who ever applied such functions to let me use best fitting package to concentrate on algorithmic issues rather than on reinventing the wheel of classic functions.

Leon Kigelman
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  • -1 down vote As this calls for opinion and is very broad, it is not a good question for SO. See the section on asking questions linked here. http://stackoverflow.com/tour. I believe that the more appropriate Stack Exchange site would be programmers which is specifically for questions that require opinion.http://programmers.stackexchange.com/ – Albert Rothman Apr 27 '16 at 21:06

1 Answers1

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I would start with installing "The SciPy Stack", whose core packages include (among others):

  • NumPy, the fundamental package for numerical computation. It defines the numerical array and matrix types and basic operations on them.
  • The SciPy library, a collection of numerical algorithms and domain-specific toolboxes, including signal processing (including FFT), optimization, statistics and much more.
  • Matplotlib, a mature and popular plotting package, that provides publication-quality 2D plotting as well as rudimentary 3D plotting
  • pandas, providing high-performance, easy to use data structures.

Many other packages are built on these core packages:

  • Since you are working with biological data, I would also recommend you install BioPython
  • To work with SVM and do machine learning, install scikit-learn
  • I have never used it, but specifically for working with Cryo EM electron density scans, there exists TEMPy:

an object-oriented Python library designed to help the user in the analysis of structures of macromolecular assemblies, especially in the context of 3D electron microscopy density maps.

Also, see this related question.

BioGeek
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  • How could I integrate several environments into one, to avoid switching and debugging between different working frames? – Leon Kigelman Apr 27 '16 at 19:20
  • @LeonKigelman I think you have a fundamental misunderstanding about working with Python packages. You just install all the above packages (via e.g. `pip` and then you just `import` them in your program. No switching between frameworks or environments. If you don't want to install each package manually, then download a scientific distribution like [Anaconda](https://www.continuum.io/downloads) which comes bundled with all of the above packages (except for TEMPy). – BioGeek Apr 28 '16 at 13:55