2b:null 2c:["$","title",null,{"children":"AssemblyDB Release Monitoring | Jonathon Keeney | Observable"}] 31:T47f,historyFiles = [ { version: "baseline", attachment: FileAttachment(".tsv") }, { version: "1.1", attachment: FileAttachment("v-1.1.tsv") }, { version: "1.15", attachment: FileAttachment("v-1.5.tsv") }, { version: "1.2", attachment: FileAttachment("v-1.20.tsv") }, { version: "1.2.5", attachment: FileAttachment("v-1.25.tsv") }, { version: "1.3", attachment: FileAttachment("v-1.30.tsv") }, { version: "1.3.5", attachment: FileAttachment("v-1.35.tsv") }, { version: "1.3.8", attachment: FileAttachment("v-1.38.tsv") }, { version: "1.4", attachment: FileAttachment("v-1.4.tsv") }, { version: "1.5", attachment: FileAttachment("v-1.5.tsv") }, { version: "1.6", attachment: FileAttachment("v-1.6.tsv") }, { version: "1.7", attachment: FileAttachment("v-1.7.tsv") }, { version: "1.8", attachment: FileAttachment("v-1.8.tsv") }, { version: "1.8.3", attachment: FileAttachment("assemblyQC_ARGOS_extended1.83.tsv") }, { version: "1.9", attachment: FileAttachment("v-1.9.tsv") }, ]32:Tbe1,makeHistoryTable = data => { const columns = [ "genome_assembly_id", "biosample", "taxonomy_id", "n50", "length", "rpkm" ]; // If a column is missing data, use empty values const normalizedData = data.map(row => Object.fromEntries( columns.map(column => [ column, Object.hasOwn(row, column) ? row[column] : "" ]) ) ); const hasNumber = value => value !== null && value !== undefined && value !== "" && Number.isFinite(Number(value)); const sparkbar = (column, exponent = 1) => { const values = normalizedData .map(row => row[column]) .filter(hasNumber) .map(Number); const maximum = d3.max(values); if (!(maximum > 0)) { return value => hasNumber(value) ? Number(value).toLocaleString("en-US") : ""; } const scale = d3.scalePow() .exponent(exponent) .domain([0, maximum]) .range([0, 100]) .clamp(true); return value => { if (!hasNumber(value)) return ""; const number = Number(value); const width = number === 0 ? 0 : Math.max(2, scale(number)); return html`

${number.toLocaleString("en-US")}

`; }; }; const table = Inputs.table(normalizedData, { columns, format: { n50: sparkbar("n50"), length: sparkbar("length", 3), rpkm: sparkbar("rpkm") }, sort: "length", reverse: true }); // Use the same proportional widths in every table (the percentages total 100%) const columnWidths = [ "24%", // genome_assembly_id "18%", // biosample "14%", // taxonomy_id "14%", // n50 "16%", // length "14%" // rpkm ]; const renderedTable = table.querySelector("table"); if (renderedTable) { renderedTable.style.width = "100%"; renderedTable.style.tableLayout = "fixed"; // Define row width and alignment for (const row of renderedTable.querySelectorAll("tr")) { [...row.children].forEach((cell, index) => { if (columnWidths[index]) { cell.style.width = columnWidths[index]; cell.style.maxWidth = columnWidths[index]; } // Value alignment cell.style.textAlign = index < 2 ? 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2f:{"id":"f776dfba96b806ad","slug":"assemblydb-release-monitoring","title":"AssemblyDB Release Monitoring","thumbnail":"15ff1fcf5e2cb3e36bf93681c24aba0420ed755e207e0bb4507b0c634a3e2036","access_level":"public","create_time":"$D2026-08-03T13:54:59.511Z","update_time":"$D2026-08-03T14:25:56.990Z","view_time":null,"first_public_time":"$D2026-08-03T13:54:59.511Z","fork":{"id":"cbb3abf51ab977ee","slug":null,"title":"History of AssemblyDB","owner":{"id":"a497d1ef2ce28acc","login":"neurogenomics","name":"Jonathon Keeney"}},"stars":0,"starred":false,"owner":{"type":"team","id":"a497d1ef2ce28acc","login":"neurogenomics","name":"Jonathon Keeney","avatar_url":null,"tier":"starter_2024"},"version":229,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"9d5322b35a731b90","login":"neurogenomics","name":"Jonathon Keeney","avatar_url":"https://avatars-next.observableusercontent.com/0b97a1e0fdca2e9eb5d751c94674364f41b99edb7e767c78c0e366f8c4e754e4","tier":null}],"members":[{"type":"individual","id":"9d5322b35a731b90","login":"neurogenomics","name":"Jonathon Keeney","avatar_url":"https://avatars-next.observableusercontent.com/0b97a1e0fdca2e9eb5d751c94674364f41b99edb7e767c78c0e366f8c4e754e4","tier":null,"role":"editor"},{"type":"team","id":"a497d1ef2ce28acc","login":"neurogenomics","name":"Jonathon Keeney","avatar_url":null,"tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":0,"collection":{"id":"8ec415297241bbcf","slug":"argos","title":"Argos","owner":{"id":"a497d1ef2ce28acc","login":"neurogenomics","name":"Jonathon Keeney"}},"type":"notebook","body":{"title":"AssemblyDB Release Monitoring","cells":[{"id":0,"value":"# AssemblyDB Release Monitoring","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":156,"value":"The [Argos](https://data.argosdb.org/) project is an FDA-sponsored knowledgebase of high quality infectious disease genomes used by the FDA and BARDA. This page monitored the genome assembly database for consistency across releases. It has since been discontinued (monitoring is now carried out internally in [HIVE](https://hive.biochemistry.gwu.edu/)).","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":145,"value":"#### Sample approx.~ every 5 releases initially, then every 10","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":191,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":182,"value":"historyData = Promise.all(\n historyFiles.map(async ({version, attachment}) => ({\n version,\n data: await attachment.tsv({typed: true})\n }))\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":184,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":187,"value":"html`

\n ${historyData.map(({version, data}) => html`\n

Version ${version}

\n ${makeHistoryTable(data)}\n

\n `)}\n

`","pinned":false,"hidden":false,"mode":"html","author":"$undefined","summary":"$undefined"},{"id":88,"value":"function sparkbar(max) {\n return x => htl.html`

${x.toLocaleString(\"en\")}`\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":4,"value":"//fileTable = d3.tsvParse(await FileAttachment('.tsv').tsv(), d3.autoType)\nfileTable = FileAttachment(\".tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":8,"value":"fileTable1_1 = FileAttachment(\"v-1.1.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":12,"value":"fileTable1_2 = FileAttachment(\"v-1.2.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":14,"value":"fileTable1_3 = FileAttachment(\"v-1.3.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":16,"value":"fileTable1_4 = FileAttachment(\"v-1.4.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":18,"value":"fileTable1_5 = FileAttachment(\"v-1.5.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":20,"value":"fileTable1_6 = FileAttachment(\"v-1.6.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":22,"value":"fileTable1_7 = FileAttachment(\"v-1.7.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":24,"value":"fileTable1_8 = FileAttachment(\"v-1.8.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":26,"value":"fileTable1_9 = FileAttachment(\"v-1.9.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":103,"value":"fileTable1_15 = FileAttachment(\"v-1.15.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":108,"value":"fileTable1_20 = FileAttachment(\"v-1.20.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":110,"value":"fileTable1_25 = FileAttachment(\"v-1.25.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":112,"value":"fileTable1_30 = FileAttachment(\"v-1.30.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":114,"value":"fileTable1_35 = FileAttachment(\"v-1.35.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":116,"value":"fileTable1_38 = FileAttachment(\"v-1.38.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":169,"value":"fileTable1_39 = FileAttachment(\"assemblyQC_ARGOS_extended1.83.tsv\").tsv({typed: true})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":31,"value":"mySample = fileTable.columns[\"genome_assembly\"]","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":37,"value":"count = d3.count(fileTable)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":46,"value":"viewof name = htl.html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"}],"files":"$W33","stdlib":"1","titling":"auto"}} 30:"$2f:body"