Pranav Mahableshwarkar

@pmahable

Joined on Jan 19, 2023

  • Welcome to Part 2 of ExploreInformatics! In this project, you will train and test a hidden markov model to detect motif occurrences in a sequence. Setup Before starting this portion of the assignment, enter your cs181-projects24 directory and run git pull. This will pull the necessary scripts and support files for this assignment into your directory. Then enter the cs1810 docker container by running ./run-docker. All of the packages needed for this application should already be embedded into the Docker image. All of the code for this project can be found in the motif_hmm directory in the cs181-user directory. Everything you will need to complete this assignment can be found within that folder. In particular, you will implement some minor preprocessing of the data we have given you in preprocessing.py. From here, you will implement the training and testing of your HMMs in hmm_traintest.py. Finally, you will make minor edits to explore_hmm.py and run the script to see the results of your implementations (i.e., explore_hmm.py is where you will actually call the functions in the other two files). :::danger
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  • Welcome to CS1810! In this handout, we will be setting up a container (to be explained soon) for you to use in this class. This includes all of the projects on beautiful algorithms and exploreinformatics. In exploreinformatics, we are going to explore how the alignment algorithms and HMMs from class are applied in a real-world setting. To get us started, we need to install a bunch of packages. Unfortunately, a lot of the bioinformatics packages have not adapted to the new M1/M2 Apple chips. So, instead of creating complex conda environments, we will be using Docker! This container will contain all packages (Python and R) that you might need in CS 1810. We encourage you to use the container to run your code! :::warning Note: If you run into issues with your Docker at any point during the course, please reference the Docker Debugging Guide at the bottom of this page. ::: Environment Setup Your computer is probably running Mac OS X, Windows, or Linux. These different operating systems all come with different libraries and preinstalled software. In this class, we will use a container, a technology that will allow every student to access the same environment setup and software packages. The container runs a Linux-based operating system, Ubuntu.
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