{"id":16619353,"url":"https://github.com/tomwhite/misp-2017","last_synced_at":"2026-04-18T21:04:18.605Z","repository":{"id":66918160,"uuid":"112766292","full_name":"tomwhite/misp-2017","owner":"tomwhite","description":"MISP camp 2017 materials and code","archived":false,"fork":false,"pushed_at":"2017-12-20T15:32:32.000Z","size":656,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-01-17T21:43:52.246Z","etag":null,"topics":["bioinformatics","data","data-visualization","hackathon"],"latest_commit_sha":null,"homepage":"","language":"Python","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/tomwhite.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":"2017-12-01T17:14:10.000Z","updated_at":"2018-06-17T19:16:18.000Z","dependencies_parsed_at":"2023-05-14T01:00:27.648Z","dependency_job_id":null,"html_url":"https://github.com/tomwhite/misp-2017","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/tomwhite%2Fmisp-2017","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomwhite%2Fmisp-2017/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomwhite%2Fmisp-2017/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tomwhite%2Fmisp-2017/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tomwhite","download_url":"https://codeload.github.com/tomwhite/misp-2017/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242988047,"owners_count":20217539,"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":["bioinformatics","data","data-visualization","hackathon"],"created_at":"2024-10-12T02:25:03.670Z","updated_at":"2026-04-18T21:04:13.582Z","avatar_url":"https://github.com/tomwhite.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MISP Camp 2017\n\nThis repo contains some of the code developed by Group A during MISP Camp 2017 in Denmark.\n\n## Getting Started with Spark\n\nThis project has a few examples of how to use [Apache Spark](https://spark.apache.org/).\nIt is designed to be used with [Cloudera Data Science Workbench](https://www.cloudera.com/documentation/data-science-workbench/latest/topics/cdsw_overview.html).\n\nSee _word_count.py_ and _tips.r_ for examples.\n\n## Data analysis of Chikungunya Defective Genomes\n\nSee _del.py_ and _entropy.py_. Also, _norm.sh_ for producing rough normalization read counts.\n\nThe following two images show the distribution of deletion start position across the genome. Note that for passage 2 deletions start in all gene regions, while by passage 12 deletions are not found in structural genes.\n\n![Passage 2](images/passage2.png)\n\n![Passage 12](images/passage12.png)\n\nThe following shows the distribution of GC bases across the genome.\n\n![GC distribution](images/gc.png)\n\nFinally, this diagram shows how normalized Shannon entropy varies by passage and replicate. There is a general downward trend to lower entroy states (more ordered), with some oscillation.\n\n![Entropy](images/entropy.png)","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftomwhite%2Fmisp-2017","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftomwhite%2Fmisp-2017","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftomwhite%2Fmisp-2017/lists"}