3e:null 3f:["$","title",null,{"children":"SEA-PHAGES Template | Bioinformatics_2023 | Observable"}] 45:[] 43:{"id":"6c6e970ab645b8e9","slug":null,"title":"SEA-PHAGES Template","thumbnail":"479ded046c755d1037b5cc22e0bf87a0740b6753dd3e0cc126ef33641413bafe","access_level":"public","create_time":"$D2023-12-06T01:06:58.629Z","update_time":"$D2023-12-06T01:06:58.629Z","view_time":null,"first_public_time":"$D2023-12-06T01:06:58.629Z","has_unpublished_edits":null,"fork":true,"stars":0,"starred":false,"owner":{"type":"team","id":"51977d5a29ffae7e","login":"wcu","name":"Bioinformatics_2023","avatar_url":"https://avatars-next.observableusercontent.com/9fdaa12d9dbcff744a9af6f26b531f21ea83c083793a977cd6ded1a871f562dc","tier":"starter_2024","bio":"","following":false},"version":522,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"933f977041fbae63","login":"mdgainey","name":"Maria Gainey","avatar_url":"https://avatars-next.observableusercontent.com/4dd2f66b14faff6df731b1ed5613c54674a46163082f5ce8920fd6b1d8819f0b","tier":null,"bio":"","following":false}],"members":[{"type":"individual","id":"933f977041fbae63","login":"mdgainey","name":"Maria Gainey","avatar_url":"https://avatars-next.observableusercontent.com/4dd2f66b14faff6df731b1ed5613c54674a46163082f5ce8920fd6b1d8819f0b","tier":null,"role":"editor"},{"type":"team","id":"51977d5a29ffae7e","login":"wcu","name":"Bioinformatics_2023","avatar_url":"https://avatars-next.observableusercontent.com/9fdaa12d9dbcff744a9af6f26b531f21ea83c083793a977cd6ded1a871f562dc","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"titling":"auto","title":"SEA-PHAGES Template","cells":[{"id":0,"value":"# SEA-PHAGES Template\n\nWe hope that this notebook will help you get started accessing SEA-PHAGES data in a data science context. What you choose to do with that is up to you, but it's at least a good starting point for building tools for data export, sequence analysis, annotation, and visualization. By using the notebook as a template, you will start with the following:\n- a working mechanism for signing in to Phamerator.org\n- a demonstration of how to retrieve data\n- menus that allow you and your users to make selections\n- a table with controls for filtering, sorting, and slicing data\n- a few examples of data visualization using the _Plot_ library\n\nTo get started, _**fork this notebook**_ by using the _Fork button_ or _Fork menu item_ at the top of this notebook.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":33,"value":"terms","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":353,"value":"md`### *Welcome${user.name ? \", \" + user.name.split(\" \")[0] : \"\"}!* :)`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":18,"value":"viewof formData = {\n let formData = \"Signed In\";\n formData = formWithSubmit(html`\n \n`);\n return formData;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":43,"value":"viewof dataset = Inputs.select(user.datasets.sort(), {\n label: \"Select a data set\",\n value: \"Actino_Draft\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":519,"value":"**Table 1.** The basics on every phage in this data set.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":514,"value":"genomes_table = genomes","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"genomes_table","database":"$undefined"},{"id":46,"value":"viewof selectedCluster = Inputs.select(\n clusters.map((c) => c.name),\n {\n label: \"Select a cluster\"\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":47,"value":"viewof selectedPhage = Inputs.select(phages.map((p) => p.phagename).sort(), {\n label: \"Select a phage\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":75,"value":"genes_table = genes","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"genes_table","database":"$undefined"},{"id":479,"value":"clusters_table = clusters","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"clusters_table","database":"$undefined"},{"id":482,"value":"phages_table = phages","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"phages_table","database":"$undefined"},{"id":486,"value":"phamilies_table = phamilies","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"phamilies_table","database":"$undefined"},{"id":264,"value":"---\n## Data\n\nThe data in the cells below were downloaded using the Phamerator.org API based on what you have selected in the menus above.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":52,"value":"clusters = getPhameratorData(dataset, \"/clusters\", user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":512,"value":"genomes = getPhameratorData(dataset, \"/genomes\", user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":62,"value":"phages = getPhameratorData(dataset, `/phagesbycluster/${selectedCluster}`, user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":71,"value":"genes = getPhameratorData(\n dataset,\n `/genes/${selectedPhage}`,\n user.email,\n user.password\n).then((value) =>\n value.map((v) => {\n v.genefunction = v.genefunction === \"\" ? null : v.genefunction;\n return v;\n })\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":79,"value":"phamilies = getPhameratorData(dataset, \"/phamilies\", user.email, user.password)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":183,"value":"genomeLength = getPhameratorData(\n dataset,\n `/genome/${selectedPhage}`,\n user.email,\n user.password\n).then((v) => v.genomelength)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":38,"value":"---\n\n## Appendix\n\nThe cells below are required.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"","database":"$undefined"},{"id":5,"value":"import {\n terms,\n getPhameratorData,\n user,\n formWithSubmit,\n styles\n} with { formData } from \"@scresawn/phamerator-api-utilities\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":204,"value":"import { Plot } from \"@mkfreeman/plot-tooltip\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":21,"value":"styles","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W45","stdlib":"1"}} 44:"$43:body"

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