{"id":16325469,"url":"https://github.com/tynes/plate-reader","last_synced_at":"2025-11-01T01:30:22.979Z","repository":{"id":104848525,"uuid":"89317899","full_name":"tynes/plate-reader","owner":"tynes","description":null,"archived":false,"fork":false,"pushed_at":"2017-05-03T01:13:46.000Z","size":149,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-26T01:26:38.029Z","etag":null,"topics":["biology"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tynes.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-04-25T04:35:45.000Z","updated_at":"2017-05-03T01:14:55.000Z","dependencies_parsed_at":"2023-07-04T22:48:25.795Z","dependency_job_id":null,"html_url":"https://github.com/tynes/plate-reader","commit_stats":{"total_commits":10,"total_committers":1,"mean_commits":10.0,"dds":0.0,"last_synced_commit":"09e178a6a94b3e2a3f86bdffe3aa9a5e212faddb"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tynes%2Fplate-reader","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tynes%2Fplate-reader/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tynes%2Fplate-reader/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tynes%2Fplate-reader/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tynes","download_url":"https://codeload.github.com/tynes/plate-reader/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239242800,"owners_count":19606100,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biology"],"created_at":"2024-10-10T23:05:07.011Z","updated_at":"2025-11-01T01:30:22.947Z","avatar_url":"https://github.com/tynes.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 96 Well Plate Analysis\n\nGenerate some graphs using Python!\n\n## Requirements\n\nMake sure that these are downloaded before starting:\n\n- [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)\n- Docker for [Mac](https://www.docker.com/docker-mac) or [Windows](https://www.docker.com/docker-windows)\n\n## Usage\n\n1. Open up your terminal of choice\n   - Try using the `ls` and `pwd` commands\n1. If you would like to download the repository to another directory, use the `cd` command and pass it the name of the directory\n   - ie `$ cd Documents`\n   - **Note: the $ indicates that it is something that you are typing on the command line, you do not need to include the $ when typing a command**\n1. Download or clone the repository by using the command `$ git clone https://github.com/Tynes/plate-reader`\n1. **C**hange **D**irectories into the newly cloned repository with the command `$ cd plate-reader`\n1. Build the Docker image with the command `$ ./build.sh`\n   - **Note: you only need to do this once**\n1. Start a Docker container (using the image we just built) by running the command `$ ./start.sh`\n   - This starts a Jupyter Notebook Server on your machine\n1. Using an internet browser, navigate to `localhost:8888` to view the Jupyter Notebook webpage\n1. There are 2 directories that correspond with each other inside of the container and outside of the container\n   - data\n   - Notebooks\n     - **Any files you add to these directories will appear in Jupyter Notebook**\n1. Add the appropriate files to the data directory on your local machine, ie drag \u0026 drop using something like Finder or Windows Explorer\n1. Looking at Jupyter Notebook in the web browser, navigate to the Notebooks directory and then click on `reader.ipynb`\n   - This will start an interactive Python session\n1. Click on the Run Cell button, it looks like a play button (or press shift+enter to speed things up) to run a cell\n1. Run each of the cells to generate the graph!\n   - Advanced users can scroll down to the bottom, select a cell and then click on the menu item Cell -\u003e Run All Above\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftynes%2Fplate-reader","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftynes%2Fplate-reader","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftynes%2Fplate-reader/lists"}