Holli Brown

CILI-CURE 21

04/05/2019

Objectives:

The overall objective for today’s lab was for students to understand the components of Quantitative Insights into Microbial Ecology, or QIIME, and develop knowledge in using the application. Students will also work with Terminal, an application on MacBooks, in order to download and update the MiniConda, which will serve as the environment to run QIIME. Students will also run programs in order to set up and update MiniConda, as well as opening new folders, and testing the QIIME system. Although this lab was computer heavy, students should pick up on this information for future labs.

Procedure:

1. Students will open the terminal help page in order to grasp what terminal does and how to work it.
2. After getting oriented with terminal, students will move on to downloading MiniConda from the internet.
3. MiniCOnda was installed and updated through the ‘box’ format found on the website. Once the conda application has been established, students can now enter into the QIIME server.
4. In the terminal, we will recall the conda environment by pasting this into the terminal:wget https://data.qiime2.org/distro/core/qiime2-2019.1-py36-osx-conda.ymlconda env create -n qiime2-2019.1 –file qiime2-2019.1-py36-osx-conda.yml
5. This will recall the conda environment. Next we will activate the conda environment by typing this into the terminal:

   activate qiime2-2019.1

6. This will activate QIIME, and students can now explore QIIME by usingqiime –help 
7. QIIME is now ready to use.
8. Students will finish QTM’s and turn them in online.

Results:

As a result, students learned many controls, such as Ls; which means to list contents. Students can also create folders that will appear on their computers. Students also had a laugh by typing say “ “ and the computer will read what you typed. Miniconda by downloading it through the web, and updated and installed it using terminal app found under utilities. With this, QIIME was activated, and students learned about the steps involved in QIIME itself, as a useful tool for next generation sequencing later on in research.

Future Steps:

In the future, I wish we had time to actually use QIIME, as we set it up but it feels like we didn’t use it. Overall, I feel like this information is pertinent to future studies.