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Reads our code, interprets what to do and executes it.
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When we write and execute code we are telling the computer to do something. Structure and Interpretation of Computer Programs, 1985 WHAT IS COMMENTING?
“Programs must be written for people to read, and only incidentally for machines to execute.” We can see the exact directory structure of MSI using FileZilla. Follow the instructions onĭocs.microsoft/en-us/windows/wsl/install-win10 For newer versions of Windows,Įvery Other time: Open your Linux terminal and type (test): Initialize the distribution and set up a new user. If unsure which distribution to choose, Ubuntu usually works well.
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It will not show up as you typeįirst Time : (If not previously done) Activate “Windows Subsystem for Linux” and install a Linuxĭistribution. Ssh will then ask for your password, which is your x500 password. This way we can get to our results Logging In: We can break up our problem into smaller chunksĪnd run them at the same time on multiple processors. Takes a really long time if we want to do it accurately.īelow is an example of parallel computation. To a reference, also known as OTU picking (we will talk about what this is later in the course), it For example, if we want to align millions of DNA sequences The instructions have to be done in a certain order and only one can be done at a time. When run a command on MSI we are taking a big dataset and executing a bunch of instructions.
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Below is an example of serial computation. We can do the same type of thing with computers. Set up in series (bulbs one after another), on the right the circuit is set up in parallel (electricity Look at the example below with light bulbs. When we use MSI we can complete our tasks faster if we run them in parallel. Resource of many large computers that we can use to perform our computational tasks. For the context of this course, you can think of MSI as a
They offer numerous services, such a batch high performance computing (HPC), MSI stands for the Minnesota Supercomputing Institute. To download it go to this linkĪnd choose the right installer for your operating system: It works as a wrapper for R to create somewhat of a personalized console with different panesĬontaining different information about what you are working on. Instead we will be installing an Integrated Development Environment (IDE) for R called RStudio. We will never be using these because it is kind of a clunky way to use R. Choose your appropriateĪfter this downloads, you will probably get two R icons which open a dialogue which looks R, we will need to download it for your particular operating system. R can do everything we would need to do in Excel and a lot more. R is the programming language we will use to analyze and plot our data. This is a point and click (and type) program with a visual user interface. For the ease of troubleshooting, everyone is required to Modifications into the files they create. We cannot use something like Word, or Notepad because they embed special We need a special text editor because theĬomputer will be reading in and processing our files directly, so they must be formatted Word for writing our papers and assignments, we need a text editor to write the type of textįiles we use in computational microbiology. Sublime Text is a text editor sublimetext/3. We will set up the MSI-specifics later when we first log in to MSI. This is a point and click program with a visual user interface. The course hasįileZilla will let you connect your computer to the supercomputers at MSI project. Lastly, students mayĬheck out a MacBook laptop from McGrath library to use for the semester.
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Windows can also use Putty to access MSI: putty/ Students may also purchaseĪ Windows 10 upgrade at a significant discount through the University. As an alternative, students running older versions of Currently WSL is only availableįor the Windows 10 operating system. Need to this, and will access MSI using their terminal instead. PLOT SPECIFIC TAXA.Īpplication included in Linux that we will use specifically for MSI.REDIRECTING COMMAND OUTPUT (TO ANOTHER COMMAND).GETTING LINES FROM A FILE (BEGINNING OR END).OVERVIEW OF COMPUTATIONAL MICROBIOLOGY WORKFLOW.Teshera-Levye, Rachel Soble, & Maxwell Kramer Tonya Ward Contributions by: Elise Morton, Gabe Al-Ghalith, Joseph Guhlin, Andrew Honsey, Jen
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Computational Microbiology Lab Manual (Biology 3004 ) VERSION 3.