Learn Python for Science – NumPy, SciPy and Matplotlib




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This workshop was given as an introduction to using python for scientific and other data intensive purposes. The examples are related to bench top laboratory data analysis. The speaker is Shane Neeley, a bioengineering masters student at Rice University and it was hosted by Brightwork CoResearch, an independent research and entrepreneurship facility in Houston, Texas.

Comment your e-mail and I will add you to a dropbox folder with the code.
Or go to this link: https://github.com/Shane-Neeley/Brightwork

Visit the blog at https://www.ShaneNeeley.com

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Comment List

  • Shane Neeley
    January 4, 2021

    though i can't python a lot but I love so so much to python

  • Shane Neeley
    January 4, 2021

    Saurabhsharma8689@gmail.com

  • Shane Neeley
    January 4, 2021

    Dear Shane, if you are reading this: thank you. You can't even imagine how great it was following this tutorial and instead of doing initial research on my own (which would take a lot) I simply watched this short 1+ hour lecture and had basics covered.

    I hope you're doing well!

  • Shane Neeley
    January 4, 2021

    @Shane – The demonstration is good, but wanted to point one factual error in your commentary. The function time.time() gives time in seconds since year 1970, which comes close to 15 billion seconds in year 2018. But I heard you saying it gives out seconds since the beginning of mankind, like hundreds of thousands of years ago. That's not quite true. Hope you take it easy as its not a huge blunder considering your knowledge of the area

  • Shane Neeley
    January 4, 2021

    Shane thanks for the video, just one correction, the time() function returns the number of seconds from the epoch (Jan 1, 1970) not from the dawn of man. See https://wiki.python.org/moin/WorkingWithTime

  • Shane Neeley
    January 4, 2021

    In case you have your dataset and you wants to import it via pandas or numpy using import function, do you need to save your data into numpy library or? If yes how do you do this?

    I have a dataset from internet Im trying to practice to manipulate the data using numpy import function, but it tells me file error. Im suggesting that maybe i need to save the file in the desktop and if i go to python and use import function it doesn't work.. Please i need explanation how to solve this…
    You may reach me via email kamasbah@gmail.com

    Your aid is highly needed thank you.

    Im thinking how do i need to save the file for it to be recognise as by numpy import function.

  • Shane Neeley
    January 4, 2021

    just to clarify, @5:14, you said it's three columns and four rows. Shouldn't it be the other way around? like three rows and four columns?

  • Shane Neeley
    January 4, 2021

    Good Job Shane, very good material for scientist to start with Python in their work!!

  • Shane Neeley
    January 4, 2021

    very good tutorial.. good job

  • Shane Neeley
    January 4, 2021

    I do not recommend this video for learning NumPy. I would find something more professional.

  • Shane Neeley
    January 4, 2021

    Do not use `os` for working with files. Use pathlib – it is new to Python 3. Also look at the glob module.

  • Shane Neeley
    January 4, 2021

    which compiler you used to excute code

  • Shane Neeley
    January 4, 2021

    His presenting is fine. Actually it's preferable. I don't understand the hate in this comment section.

  • Shane Neeley
    January 4, 2021

    You can also learn julia programming for data science
    https://www.udemy.com/learning-path-julia-explore-data-science-with-julia/

  • Shane Neeley
    January 4, 2021

    Thanks for uploading this. Good introduction.

  • Shane Neeley
    January 4, 2021

    Please don't upload this kind of shitty videos. please do improve your presentation skills. it looks like as if your talking to your self.

  • Shane Neeley
    January 4, 2021

    This is python2 not python3. People still use python2 and it is still updated even though python3 is available – this is confusing to newbies. Some of the commands in the script he uses https://github.com/Shane-Neeley/Brightwork/blob/master/fundamentals_08032013.py will not work in python3. Thanks for the video! Appreciate it! 🙂

  • Shane Neeley
    January 4, 2021

    Please help me: I am unable to install scipy in my windows using pip

    This is the error I am facing, which I never faced before. Here I go with my console output:

    C:UsersPrakhar Dev Gupta>pip install scipy
    Collecting scipy
    Using cached scipy-0.19.0.zip
    Installing collected packages: scipy
    Running setup.py install for scipy … error
    Complete output from command f:python.exe -u -c "import setuptools, tokenize;__file__='C:\Users\PRAKHA~1\AppData\Local\Temp\pip-build-sszq6d8s\scipy\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('rn', 'n');f.close();exec(compile(code, file, 'exec'))" install –record C:UsersPRAKHA~1AppDataLocalTemppip-18kpwh14-recordinstall-record.txt –single-version-externally-managed –compile:

    Note: if you need reliable uninstall behavior, then install
    with pip instead of using `setup.py install`:

    – `pip install .` (from a git repo or downloaded source
    release)
    – `pip install scipy` (last SciPy release on PyPI)

    lapack_opt_info:
    lapack_mkl_info:
    libraries mkl_rt not found in ['f:lib', 'C:\', 'f:libs']
    NOT AVAILABLE

    openblas_lapack_info:
    libraries openblas not found in ['f:lib', 'C:\', 'f:libs']
    NOT AVAILABLE

    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    F:libsite-packagesnumpydistutilssystem_info.py:1051: UserWarning: Specified path C:projectsnumpy-wheelswindows-wheel-builderatlas-buildsatlas-3.10.1-sse2-32lib is invalid.
    pre_dirs = system_info.get_paths(self, section, key)
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
    NOT AVAILABLE

    atlas_3_10_info:
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
    NOT AVAILABLE

    atlas_threads_info:
    Setting PTATLAS=ATLAS
    <class 'numpy.distutils.system_info.atlas_threads_info'>
    NOT AVAILABLE

    atlas_info:
    <class 'numpy.distutils.system_info.atlas_info'>
    NOT AVAILABLE

    F:libsite-packagesnumpydistutilssystem_info.py:572: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
    self.calc_info()
    lapack_info:
    libraries lapack not found in ['f:lib', 'C:\', 'f:libs']
    NOT AVAILABLE

    F:libsite-packagesnumpydistutilssystem_info.py:572: UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
    self.calc_info()
    lapack_src_info:
    NOT AVAILABLE

    F:libsite-packagesnumpydistutilssystem_info.py:572: UserWarning:
    Lapack (http://www.netlib.org/lapack/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
    the LAPACK_SRC environment variable.
    self.calc_info()
    NOT AVAILABLE

    Running from scipy source directory.
    non-existing path in 'scipy\integrate': 'quadpack.h'
    Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "C:UsersPRAKHA~1AppDataLocalTemppip-build-sszq6d8sscipysetup.py", line 416, in <module>
    setup_package()
    File "C:UsersPRAKHA~1AppDataLocalTemppip-build-sszq6d8sscipysetup.py", line 412, in setup_package
    setup(**metadata)
    File "F:libsite-packagesnumpydistutilscore.py", line 135, in setup
    config = configuration()
    File "C:UsersPRAKHA~1AppDataLocalTemppip-build-sszq6d8sscipysetup.py", line 336, in configuration
    config.add_subpackage('scipy')
    File "F:libsite-packagesnumpydistutilsmisc_util.py", line 1001, in add_subpackage
    caller_level = 2)
    File "F:libsite-packagesnumpydistutilsmisc_util.py", line 970, in get_subpackage
    caller_level = caller_level + 1)
    File "F:libsite-packagesnumpydistutilsmisc_util.py", line 907, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
    File "scipysetup.py", line 15, in configuration
    config.add_subpackage('linalg')
    File "F:libsite-packagesnumpydistutilsmisc_util.py", line 1001, in add_subpackage
    caller_level = 2)
    File "F:libsite-packagesnumpydistutilsmisc_util.py", line 970, in get_subpackage
    caller_level = caller_level + 1)
    File "F:libsite-packagesnumpydistutilsmisc_util.py", line 907, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
    File "scipylinalgsetup.py", line 20, in configuration
    raise NotFoundError('no lapack/blas resources found')
    numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

    —————————————-
    Command "f:python.exe -u -c "import setuptools, tokenize;__file__='C:\Users\PRAKHA~1\AppData\Local\Temp\pip-build-sszq6d8s\scipy\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('rn', 'n');f.close();exec(compile(code, file, 'exec'))" install –record C:UsersPRAKHA~1AppDataLocalTemppip-18kpwh14-recordinstall-record.txt –single-version-externally-managed –compile" failed with error code 1 in C:UsersPRAKHA~1AppDataLocalTemppip-build-sszq6d8sscipy

    C:UsersPrakhar Dev Gupta>

  • Shane Neeley
    January 4, 2021

    He is just mellow, get off his back!

  • Shane Neeley
    January 4, 2021
  • Shane Neeley
    January 4, 2021

    Are there any other good materials like this? (my area of interest is Machine Learning using python)
    especially in NLP, nltk and sklearn

  • Shane Neeley
    January 4, 2021

    this guy's codes are very efficient thanks for the upload.I will use these for further tips in my code.

  • Shane Neeley
    January 4, 2021

    Everybody commenting like they want to be wined and dined by a numpy pres. Thanks man good job.

  • Shane Neeley
    January 4, 2021

    This was incredibly helpful. Thank you for putting it together!

  • Shane Neeley
    January 4, 2021

    Thanks a loooooooooooot 😀 !!!

  • Shane Neeley
    January 4, 2021

    Nice job but your presenting skills need some TLC buddy

  • Shane Neeley
    January 4, 2021

    This guy seems to love his job …

  • Shane Neeley
    January 4, 2021

    Hi, what is the software you presented all the pics in animate_fig part? It looks great.

  • Shane Neeley
    January 4, 2021

    Thanks Shane, great video! really helpful! could i please have the code/examples? Thanks

  • Shane Neeley
    January 4, 2021

    theneermal@gmail.com. Thank You Very Much.

  • Shane Neeley
    January 4, 2021

    good workshop!

  • Shane Neeley
    January 4, 2021

    There's some good info here but you sound so fed up I could not bring myself to watch the whole presentation.

  • Shane Neeley
    January 4, 2021

    Thanks, I found it really helpful. gagagugu130ex@gmail.com

  • Shane Neeley
    January 4, 2021

    Thanks!!

  • Shane Neeley
    January 4, 2021
  • Shane Neeley
    January 4, 2021

    Thanks,man. Really appreciate it! Nice work.

  • Shane Neeley
    January 4, 2021

    Hi, I found this video really helpful. Could you share the dropbox link to me? yzong@ualberta.ca

  • Shane Neeley
    January 4, 2021

    Thanks Shane for putting this together – it was very informative. You did a great job.

  • Shane Neeley
    January 4, 2021

    In 31:00, you can iterate over a string, so no need for list(sequence).

  • Shane Neeley
    January 4, 2021

    The code please cboohas@gmail.com

  • Shane Neeley
    January 4, 2021

    Is it possible to enable higher speeds for the video?

  • Shane Neeley
    January 4, 2021

    very helpful – thanks!

  • Shane Neeley
    January 4, 2021

    Realy helpfull video. Could you  please add me to the dropbox folder. email: cosmovr@hotmail.com

  • Shane Neeley
    January 4, 2021

    numpy sucks

  • Shane Neeley
    January 4, 2021

    Could you  please add me to the dropbox folder. email: supri29@gmail.com

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