31:[] 2f:{"title":"RNA Structure Visualization","cells":[{"id":0,"value":"md`# RNA Structure Visualization`","pinned":false,"hidden":false,"mode":"ojs"},{"id":132,"value":"md`The RNA is defined by a sequence of different nucleobases: adenine (A), cytosine (C), guanine (G), or uracil (U) which are then folded into the actual RNA molecule (https://en.wikipedia.org/wiki/RNA). The structure defines how the RNA molecule is actually folded. See also http://eternagame.org/ to learn more about RNA and how it's being used. This notebooks uses the following library to visualize RNAs: https://github.com/ViennaRNA/fornac. The RNA below comes from the OpenVaccine: COVID-19 mRNA Vaccine Degradation Prediction Competition: https://www.kaggle.com/c/stanford-covid-vaccine/.`","pinned":false,"hidden":false,"mode":"ojs"},{"id":12,"value":"html`

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":89,"value":"viewof parameters = form(html``)","pinned":false,"hidden":false,"mode":"ojs"},{"id":71,"value":"md`#### Source code using Forna, a visualization library based on d3`","pinned":false,"hidden":false,"mode":"ojs"},{"id":14,"value":"container = {\n var container = new forna.FornaContainer(\"#rna_ss\", {'applyForce': true});\n\n var options = {\n 'sequence': parameters.sequence,\n 'structure': parameters.structure,\n };\n\n container.addRNA(options.structure, options);\n \n container.changeColorScheme(parameters.color);\n \n return container\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":5,"value":"require('jquery')","pinned":false,"hidden":false,"mode":"ojs"},{"id":99,"value":"import {form, formValue} from '@mbostock/form-input'","pinned":false,"hidden":false,"mode":"ojs"},{"id":8,"value":"d3 = require('d3')","pinned":false,"hidden":false,"mode":"ojs"},{"id":10,"value":"forna = require('fornac')","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W31","stdlib":"1","titling":"auto"}