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Fran McDadeFran McDade
Fran McDade
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feat: add about page (#19)
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‎app/components/About/components/Section/components/SectionRoadmap/components/MDX/comprehensiveComparitiveGenomics.mdx

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In coordination with UCSC Genome Browser and NCBI we will begin
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work on creating a comprehensive comparative genomics resource by
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creating genome alignments and synteny maps within key clades.
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This data will provide information on evolutionary dynamics of
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pathogens and vectors.

‎app/components/About/components/Section/components/SectionRoadmap/components/MDX/genomicDataReviewAndValidation.mdx

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Review all genomic data and associated annotations currently
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available from VeuPathDb. During this stage all genome builds will
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be validated against data currently available from GenBank and
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RefSeq at NCBI. This will ensure that all data is current and is
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in sync with official public builds.

‎app/components/About/components/Section/components/SectionRoadmap/components/MDX/howToAnalyzeYourData.mdx

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In combination with the Galaxy Training Network (GTN) we will
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begin developing tutorials highlighting various aspects of our new
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system and explaining how to analyze your data using these tools.

‎app/components/About/components/Section/components/SectionRoadmap/components/MDX/index.tsx

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export { default as ComprenhensiveComparitiveGenomics } from "./comprehensiveComparitiveGenomics.mdx";
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export { default as GenomicDataReviewAndValidation } from "./genomicDataReviewAndValidation.mdx";
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export { default as HowToAnalyzeYourData } from "./howToAnalyzeYourData.mdx";
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export { default as LaunchGalaxyInstance } from "./launchGalaxyInstance.mdx";
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export { default as LaunchGenomeBrowsers } from "./launchGenomeBrowsers.mdx";

‎app/components/About/components/Section/components/SectionRoadmap/components/MDX/launchGalaxyInstance.mdx

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Launch a Galaxy instance specifically configured for the needs of
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eukaryotic pathogen and vector community. Carry-over and update
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existing workflows from VeuPathDb Galaxy instance. In combination
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with existing Galaxy best practices this will allow us to provide
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users with the most up-to-date version of most common analyses
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including transcriptomics (bulk and single cell RNA-seq), variant
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discovery, assembly, annotation, and many other applications.

‎app/components/About/components/Section/components/SectionRoadmap/components/MDX/launchGenomeBrowsers.mdx

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This will involve ingesting data and annotation tracks into UCSC
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Genome Browser infrastructure. In coordination with the VeuPathDb
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team we will make the best effort to carry over existing JBrowse
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tracks and custom annotations.

‎app/components/About/components/Section/components/SectionRoadmap/sectionRoadmap.styles.ts

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import {
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inkLight,
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smokeMain,
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} from "@databiosphere/findable-ui/lib/styles/common/mixins/colors";
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import {
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textBodyLarge4002Lines,
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textBodyLarge500,
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} from "@databiosphere/findable-ui/lib/styles/common/mixins/fonts";
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import styled from "@emotion/styled";
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import { Section, SectionLayout } from "../../section.styles";
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export const StyledSection = styled(Section)`
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border-top: 1px solid ${smokeMain};
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`;
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export const StyledSectionLayout = styled(SectionLayout)`
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padding: 96px 16px 98px;
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`;
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export const Category = styled.div`
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margin: 40px 0;
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&:first-of-type {
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margin-top: 0;
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}
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&:last-of-type {
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margin-bottom: 0;
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}
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`;
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export const CategoryTitle = styled.h4`
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${textBodyLarge500};
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margin: 4px 0 16px;
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`;
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export const CategoryText = styled.div`
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${textBodyLarge4002Lines};
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color: ${inkLight};
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margin: 0;
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`;

‎app/components/About/components/Section/components/SectionRoadmap/sectionRoadmap.tsx

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import { Chip } from "@mui/material";
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import {
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SectionContent,
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Subhead,
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SubHeadline,
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SubheadText,
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} from "../../section.styles";
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import {
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ComprenhensiveComparitiveGenomics,
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GenomicDataReviewAndValidation,
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HowToAnalyzeYourData,
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LaunchGalaxyInstance,
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LaunchGenomeBrowsers,
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} from "./components/MDX";
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import {
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Category,
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CategoryText,
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CategoryTitle,
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StyledSection,
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StyledSectionLayout,
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} from "./sectionRoadmap.styles";
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export const SectionRoadmap = (): JSX.Element => {
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return (
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<StyledSection>
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<StyledSectionLayout>
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<SubHeadline>
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<Subhead>Roadmap</Subhead>
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<SubheadText>The high level roadmap for the Fall 24 is:</SubheadText>
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</SubHeadline>
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<SectionContent>
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<Category>
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<Chip label="Q1, 2024" />
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<CategoryTitle>Genomic Data Review & Validation</CategoryTitle>
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<CategoryText>
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<GenomicDataReviewAndValidation />
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</CategoryText>
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</Category>
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<Category>
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<Chip label="Q2, 2024" />
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<CategoryTitle>
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Launch genome browsers for all VeuPathDb species
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</CategoryTitle>
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<CategoryText>
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<LaunchGenomeBrowsers />
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</CategoryText>
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</Category>
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<Category>
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<Chip label="Q2, 2024" />
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<CategoryTitle>Launch a Galaxy instance</CategoryTitle>
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<CategoryText>
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<LaunchGalaxyInstance />
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</CategoryText>
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</Category>
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<Category>
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<Chip label="Q3, 2024" />
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<CategoryTitle>
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How to analyze your data using these tools
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</CategoryTitle>
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<CategoryText>
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<HowToAnalyzeYourData />
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</CategoryText>
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</Category>
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<Category>
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<Chip label="Q3, 2024" />
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<CategoryTitle>
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Comprehensive comparative genomics resource
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</CategoryTitle>
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<CategoryText>
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<ComprenhensiveComparitiveGenomics />
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</CategoryText>
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</Category>
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</SectionContent>
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</StyledSectionLayout>
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</StyledSection>
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);
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};

‎app/components/About/components/Section/components/SectionWhatToExpect/components/MDX/expectations.mdx

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- Dataset explorer providing access to genomic data and annotations for all 785 species currently accessible on VeuPathDb
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- Launch of a dedicated Galaxy instance at [https://brc.usegalaxy.org](https://brc.usegalaxy.org) that will provide access to key workflows and will be tightly integrated with the Dataset Explorer
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- Launch of a documentation and support site for brc-analytics users and developers

‎app/components/About/components/Section/components/SectionWhatToExpect/components/MDX/index.tsx

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export { default as Expectations } from "./expectations.mdx";

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