======================
Scientific Programming
======================

This course is brought to you by:

- `Stefano Teso <http://disi.unitn.it/~teso/>`_

  **e-mail**: teso _AT_ disi _DOT_ unitn _DOT_ it

  **Office hours**: Tuesday, 14:00-15:00, Room 143 Povo 2.

- `Toma Tebaldi <https://github.com/tomateba>`_

  **e-mail**: t _DOT_ tebaldi _AT_ unitn _DOT_ it

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    https://drive.google.com/open?id=0B0wILN942aEVOEN5VnBhSWdnWHM

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Remaining classes:

- 21/11/2016

- 5/12/2016

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Finals will be on:

- 24/1/2017, 9:00-11:00

- 8/2/2017, 14:00-16:00

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Data
----

The sample data can be downloaded `this link <http://disi.unitn.it/~teso/courses/sciprog/data.zip>`_.

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Syllabus
--------

The course will offer a (rather thorough) introduction to the **Python**
language, as well as to Python packages relevant to biological and scientific
applications.

We will work with the following Python packages:

#. `biopython <http://biopython.org/>`_, for managing biological resources

#. `pandas <http://pandas.pydata.org/>`_, for dealing with tabular data, statistics and visualization

#. `numpy <http://www.numpy.org/>`_, for general-purpose numerical manipulation

.. note::
    There are many more Python packages out there!

    Feel free to browse through
    `PyPI - the Python Package Index <https://pypi.python.org/pypi>`_ for a
    wide selection of packages. At the time of writing, it hosts 89422 distinct
    packages!

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Bibliography
------------

Books:

.. [book1] M. Lutz, *Learning Python* (5th edition), O'REILLY, 2013.
.. [book2] A. Via, K. Rother, A. Tramontano, *Managing Your Biological Data with Python*, CRC Press, 2014.

Other useful material:

- The `Python for Biologists <http://pythonforbiologists.com/>`_ website is tailored for biologists.
- S. Bassi, *A Primer on Python for Life Science Researchers*, PLoS Computational Biology, 2007.
- The official Python website can be found `here <https://www.python.org/>`_.
  There is also a `Getting Started <https://www.python.org/about/gettingstarted/>`_
  section you may want to peruse.
- A few `slides <http://disi.unitn.it/~teso/courses/sciprog/intro.pdf>`_ on programming languages and the basics of Python.

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Evaluation
----------

There will be two midterms, consisting of *practical* programming tests on the
two halves of the program, roughly corresponding to the Python language *sans*
external libraries, and the usage of scientific libraries.

There will be an (alternative) final exam, consisting of a *practical*
programming test.

In both the midterms and the final, the sudent will be asked to write a (short)
Python program making use of the technologies presented during the course. The
score will depend on the student's proficiency in Python programming.

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.. include:: shell_basics.rst

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.. include:: python_basics.rst

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.. include:: python_numbers.rst

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.. include:: python_numbers_solutions.rst

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.. include:: python_strings.rst

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.. include:: python_strings_solutions.rst

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.. include:: python_lists.rst

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.. include:: python_lists_solutions.rst

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.. include:: python_tuples.rst
.. include:: python_tuples_exercises.rst

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.. include:: python_tuples_solutions.rst

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.. include:: python_dictionaries.rst
.. include:: python_dictionaries_exercises.rst

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.. include:: python_dictionaries_solutions.rst

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.. include:: python_io.rst
.. include:: python_io_exercises.rst

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.. include:: python_io_solutions.rst

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.. include:: python_complex_statements.rst
.. include:: python_complex_statements_exercises.rst

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.. include:: python_complex_statements_solutions.rst

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.. include:: python_functions.rst
.. include:: python_functions_exercises.rst

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.. include:: python_functions_solutions.rst

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.. include:: python_programs.rst
.. include:: python_programs_solutions.rst

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.. include:: python_packages.rst

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.. include:: python_biopython.rst
.. include:: python_biopython_exercises.rst
.. include:: python_biopython_solutions.rst

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.. include:: python_pandas.rst
.. include:: python_pandas_exercises.rst
.. include:: python_pandas_solutions.rst

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.. include:: python_appendices.rst
.. include:: python_appendices_exercises.rst

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.. toctree::
    :maxdepth: 2

    shell_basics
    python_basics
    python_numbers
    python_numbers_solutions
    python_strings
    python_strings_solutions
    python_lists
    python_lists_solutions
    python_tuples
    python_tuples_exercises
    python_tuples_solutions
    python_dictionaries
    python_dictionaries_exercises
    python_dictionaries_solutions
    python_io
    python_io_exercises
    python_io_solutions
    python_complex_statements
    python_complex_statements_exercises
    python_complex_statements_solutions
    python_functions
    python_functions_exercises
    python_functions_solutions
    python_programs
    python_programs_solutions
    python_packages
    python_biopython
    python_biopython_exercises
    python_biopython_solutions
    python_pandas
    python_pandas_exercises
    python_pandas_solutions
    python_appendices
    python_appendices_exercises