Installing Software for PHRM 8010

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Lecture 1- Introduction to Lead Drug Discovery

Anaconda

Anaconda is a software package that will be used throughout the PHRM 8010 course. The software functions as a simple way to install various software scientific software packages with particular emphasis on the Python and R programming languages. The advantage of this approach is that you have all your scientific software packages in a central location. Most software used in this course will be installed using Anaconda.
  1. Please download install Anaconda on a user account on your computer. This will install in your user account. Preferably, do not install the software in a root or administrator account.
  2. Open Anaconda
    1. It should look like: Soft001.pngClick to enlarge
    2. In the right section of the software is Home, Environments, Learning, and Community. Click the various sections.
      • Home: When you are on the Home screen, you will see an array of squares that show you the software than can theoretically be installed or is installed. I am talking about this Soft002.png (Click to enlarge). At the bottom of the each square is an install or launch button. Depending on how a particular environment is set up, you can launch that software. On the top of the screen is a pulldown, that shows the environment that you are in. It is this Soft003.png. What is an environment? You can think of an environment as a separate location for the installation of your software. The advantage of installing software in an environment is that it reduces the risk To the right of it is the Soft004.png. If you click on this button, it will list the "channels" that are available to you. You can think of it like television content, except it reflects a software channel.
      • Environments: You can think of environments as being a computer within a computer. The advantage of this approach is that you do not corrupt your computer and different approaches will not corrupt each other. We will be using environments a lot to protect your computer. In the middle, are a list of environments that are available for you. Depending on how many environments that you have, it might look like this: Soft005.png (Click to enlarge). At the bottom will be the following buttons: Soft006.png. The only ones that you might use are the Soft007.png or Soft008.png.
      • Learning: This section provides documentation and resources for learning about software that is installed within anaconda. I am very impressed by the quality of the tutorials that they have in this section.
      • Community: This section provides ways to ask questions to the software community. However, I would be happy to answer questions for you. I typically do a Google search to get answers to my questions.

Install Python and Spyder in Anaconda

  • Spyder is an interactive data environment or IDE for the Python Programming languages. In other words, it makes your life a lot easier and helps you with programming syntax.
  1. Open Anaconda if it is not already open.
  2. Go to environment tab and click Soft007.png.
  3. In Anaconda, name your environment PHRM_8010-Python and check the Python box. Your dialog box should look like this: Py001.png (Click to make larger)
    1. This will take a few minutes.
  4. Select the environment PHRM_8010-Python.
  5. Click Home.
    1. If you did it correctly, the screen will look like this: Py002.png (Click to make larger)
  6. Under Spyder 5.2.1, click Install.
    1. This will take a little while. Once it is finished, it will say launch underneath it.
  7. Click the launch button underneath it.
    1. If you did it correctly, it should look something like this: Py03.png
  8. MacOS only: In the lower right hand part of the screen, type: !pip install matplotlib

Other Software to Install