{"id":13680857,"url":"https://github.com/michaelmarty/MassSpecCodingClub","last_synced_at":"2025-04-30T00:31:07.102Z","repository":{"id":215316911,"uuid":"610889713","full_name":"michaelmarty/MassSpecCodingClub","owner":"michaelmarty","description":"A community dedicated to education of computer coding applied to mass spectrometry applications. 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Learning Resources - Programming"],"sub_categories":["Table of Contents"],"readme":"# Mass Spec Coding Club\nThe Mass Spec Coding Club (MSCC) is a community dedicated to education of computer coding applied to mass spectrometry applications. Our goal is to make coding accessible to mass spectrometry researchers and provide free resources and open-source examples. \n\nAs the community develops, we will continue to post more content, and we welcome contributions from anyone. \n\n# Discord Server\n\nWant to chat with community members and join meetings, join us on the [Mass Spec Coding Club Discord Server](https://discord.gg/24GupxGn3d). It's easy to set up, and you can run it from a browser if you'd like. We will pick a time soon and start hosting meetings/office hours there. \n\nIn the meantime, feel free to post questions to the text channels there, and people can answer. \n\n# Learning Modules\n\n## Module 0: Setting Up Python and Plotting A Spectrum\n\nThis series of lessons will cover how to set up Python from scratch and write a simple script to plot a mass spectrum. Skills and learning outcomes are outlined below each video\n\n* [Lesson 0.0: Setting up Python from Scratch](https://youtu.be/BLaoo1S3ImU)\n  * How to set up and run Python\n  * Setting variables\n  * Printing to the terminal\n* [Lesson 0.1: Loading Data Into Python](https://youtu.be/vpbdUQp8m0U)\n  * Importing libraries\n  * Reading from text files into NumPy arrays\n  * Intro to array slicing\n* [Lesson 0.2: Plotting a Spectrum](https://youtu.be/88m4a9CEeBY)\n  * Plotting a spectrum with MatPlotLib\n  * Normalizing the y-axis\n* [Lesson 0.3: Too Fast, Go Back - Review and Background from Module 0](https://youtu.be/V6alRhace2A)\n  * Fundamentals of how computers work\n  * Basics of code concepts\n  * Discussion of variables, functions, and classes\n  * How to define functions\n\nThe data files, Python code, and notes used in this module are available in the \"Module 0\" folder.\n\n## Module 1: Calculating Masses\n\nThe goal of module 1 is to show how Python can be used to predict masses of various molecules, starting with proteins.\n\n* [Lesson 1.0: Calculating Protein Masses](https://youtu.be/FFR1gg2cA6E)\n  * Using a Dictionary\n  * Creating a function\n  * Looping through protein sequence to calculate the protein mass\n* [Lesson 1.1: Improving Our Protein Mass Calculator](https://youtu.be/lxTrA_EPeNg)\n  * String manipulation\n  * Passing variables through functions\n  * If/then statements\n  * Monoisotopic mass calculation for protein\n* [Lesson 1.2: Calculating Masses from Glycans, SMILES, and Formulas](https://youtu.be/XSgA7SODmSg)\n  * Using Glypy to calculate masses from GlycoCT strings\n  * Using molmass to calculate masses from formulas\n  * Using RDKit to calculate masses from SMILES strings\n* [Lesson 1.3: Too Fast, Go Back - For Loops, If/Then, and Function Options](https://youtu.be/xg1QxAzznkg)\n  * Writing For loops\n  * If/Then statements and Boolean tests\n  * Passing options to functions\n* Homework 1\n  * For those who want to test their skills and calculate some RNA masses, check out homework1.py in Module 1.\n\nCheck back for more videos, and reach out if you like these [mtmarty@arizona.edu](mailto:mtmarty@arizona.edu). \n\n# Ideas for Future Tutorials\n\nHere are some ideas that users have suggested. If you have other suggestions, please enter them in the [\"What Projects Would You Like to See?\"](https://github.com/michaelmarty/MassSpecCodingClub/discussions/3) discussion. If you would like to volunteer to make a module on one of these topics, please add your name here.\n\n* Plotting multiple spectra with for loops and string parsing (Michael Marty)\n* Reading vendor files\n* Writing to different output files\n* Exploring other Python MS packages\n* How to use public databases (Ming?)\n* Applications to polymers and oligonucleotides\n* Ion mobility\n* Using Git and GitHub\n* Gasp, R!\n  * There are a lot of great R resources for MS already, so maybe we could organize and link those here too.\n\n# Funding\n\nFunding is provided by the National Science Foundation: CHE-1845230. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmichaelmarty%2FMassSpecCodingClub","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmichaelmarty%2FMassSpecCodingClub","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmichaelmarty%2FMassSpecCodingClub/lists"}