{"id":19162972,"url":"https://github.com/hernanmd/covid-2019","last_synced_at":"2025-05-07T11:21:30.727Z","repository":{"id":71140938,"uuid":"237383627","full_name":"hernanmd/COVID-2019","owner":"hernanmd","description":"Analysis of Coronavirus outbreak data with Pharo","archived":false,"fork":false,"pushed_at":"2023-08-16T14:50:16.000Z","size":46,"stargazers_count":7,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-19T21:25:35.984Z","etag":null,"topics":["analysis","bioinformatics","coronavirus","coronavirus-analysis","coronavirus-tracking","covid-19","covid-virus","ncov-2019","pharo","smalltalk"],"latest_commit_sha":null,"homepage":"","language":"Smalltalk","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/hernanmd.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,"zenodo":null}},"created_at":"2020-01-31T07:49:11.000Z","updated_at":"2023-08-14T19:45:23.000Z","dependencies_parsed_at":null,"dependency_job_id":"35ec185b-db68-4338-a841-d0bd7d3d4151","html_url":"https://github.com/hernanmd/COVID-2019","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hernanmd%2FCOVID-2019","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hernanmd%2FCOVID-2019/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hernanmd%2FCOVID-2019/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hernanmd%2FCOVID-2019/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/hernanmd","download_url":"https://codeload.github.com/hernanmd/COVID-2019/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252866122,"owners_count":21816397,"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":["analysis","bioinformatics","coronavirus","coronavirus-analysis","coronavirus-tracking","covid-19","covid-virus","ncov-2019","pharo","smalltalk"],"created_at":"2024-11-09T09:13:44.430Z","updated_at":"2025-05-07T11:21:30.713Z","avatar_url":"https://github.com/hernanmd.png","language":"Smalltalk","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n[![license-badge](https://img.shields.io/badge/license-MIT-blue.svg)](https://img.shields.io/badge/license-MIT-blue.svg)\n[![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n[![Build Status](https://travis-ci.org/hernanmd/COVID-2019.svg?branch=master)](https://travis-ci.org/hernanmd/COVID-2019)\n\n# Introduction\n\nAnalysis of Coronavirus outbreak data with [Pharo](https://www.pharo.org) 8.x\n\n# Installation\n\n```smalltalk\nMetacello new\n   baseline: 'COVID19';\n   repository: 'github://hernanmd/COVID-2019/src';\n   load.\n```\n\n# Usage\n\n## Data Visualization\n\nFor visualization of cases as provided by CSSEGISandData, evaluate in Pharo 8:\n\n```smalltalk\nBioCOVID19Viz exampleLiveData\n```\n\n## Alignment\n\nFor genomic analysis install [BioSmalltalk](https://github.com/hernanmd/BioSmalltalk) and evaluate the following one-liner to align the sequences with MAFFT:\n\n```smalltalk\nBioCOVID19GenomicAnalysis alignSeqs.\n```\n\nTo add accession numbers as they appear in the NCBI GenBank repository, edit the class side methods matching the sequencing location:\n\n  - seqsFromChina\n  - seqsFromItaly\n  - seqsFromUSA\n  - ...\n\nThe resulting alignment is written in 'mafft_output.align' in the Pharo image directory.\n\nAccessions are retrieved from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide\u0026VirusLineage_ss=Wuhan%20seafood%20market%20pneumonia%20virus,%20taxid:2697049\n\n## Reference Genome download\n\nTo download the latest build of the reference genome (as of 01/02/2020) from NCBI:\n\n```smalltalk\nBionCoV2019GD new download.\n```\n\nDownloaded files are located into the Pharo image directory.\n\n# Misc\n\nTo create a GitHub Pharo project with Continuous Integration support from scrath follow [this video](https://www.youtube.com/watch?v=Wnt3OBhR18I).\n\n# ToDo\n\n  - Download accessions from here: https://dev.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml (currently restricted access?)\n  - Add sequences from GISAID\n  - Evaluate MAFFT alignment quality.\n\n# Sample output\n\n![](https://user-images.githubusercontent.com/4825959/75620782-ec299d80-5b6b-11ea-918a-8cee8d3aa419.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhernanmd%2Fcovid-2019","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhernanmd%2Fcovid-2019","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhernanmd%2Fcovid-2019/lists"}