diff --git a/package.json b/package.json
index f0e11d87..7246dd9a 100644
--- a/package.json
+++ b/package.json
@@ -13,6 +13,8 @@
"dayjs": "1.11.7",
"from-exponential": "^1.1.1",
"ga-gtag": "1.2.0",
+ "highcharts": "^11.4.8",
+ "highcharts-react-official": "^3.2.1",
"history": "4.10.1",
"http-proxy-middleware": "^2.0.1",
"jquery": "^3.5.1",
@@ -32,6 +34,7 @@
"react-scripts": "5.0.1",
"react-table": "^7.7.0",
"react-tooltip": "^5.11.2",
+ "react-wordcloud": "^1.2.7",
"redux": "^4.0.1",
"redux-thunk": "^2.3.0",
"tocbot": "^4.25.0",
diff --git a/src/App/App.jsx b/src/App/App.jsx
index d83cd4eb..ac2b5754 100644
--- a/src/App/App.jsx
+++ b/src/App/App.jsx
@@ -25,8 +25,12 @@ import SearchPageConnected from '../Search/searchPage';
import GeneCentricViewConnected from '../AnalysisPage/GeneCentricViewRat/geneCentricViewPage';
import GraphicalClustering from '../AnalysisPage/GraphicalClustering/graphicalClusteringPage';
import CodeRepositories from '../CodeRepoPage/codeRepoPage';
-import MainStudyConnected from '../MainStudy/mainStudy';
+import ProjectOverviewConnected from '../MainStudy/overview';
+import ExerciseBenefits from '../MainStudy/exerciseBenefits';
+import StudyAssays from '../MainStudy/studyAssays';
import Tutorials from '../Tutorials/tutorials';
+import License from '../License/licensePage';
+import DataDeposition from '../DataDeposition/dataDepositionPage';
import Publications from '../Publications/publications';
import MultiOmicsWorkingGroups from '../MultiOmicsWorkingGroups/multiOmicsWorkingGroups';
import FullTableEnduranceTraining from '../Publications/Data/Animal/Phenotype/fullTableEnduranceTraining';
@@ -134,9 +138,22 @@ function App({ history = History }) {
/>
+
+
+
+
+
-
);
}
diff --git a/src/App/__test__/App.test.jsx b/src/App/__test__/App.test.jsx
index a72acc89..9d03c89d 100644
--- a/src/App/__test__/App.test.jsx
+++ b/src/App/__test__/App.test.jsx
@@ -23,7 +23,7 @@ describe('', () => {
});
test('It should contain fifteen children', () => {
- expect(component.find('Route').length).toBe(21);
+ expect(component.find('Route').length).toBe(25);
});
test('It should contain four children', () => {
@@ -81,7 +81,7 @@ describe('Unauthenticated Application routing', () => {
test('loads the browse data page at /project-overview', () => {
history.push('/project-overview');
mountApp.update();
- testCorrectComponentInPath(mountApp, 'Route', 'MainStudy', '/project-overview', history);
+ testCorrectComponentInPath(mountApp, 'Route', 'ProjectOverview', '/project-overview', history);
});
test('loads the linkout page at /external-links', () => {
diff --git a/src/BrowseDataPage/components/dataDownloadsMain.jsx b/src/BrowseDataPage/components/dataDownloadsMain.jsx
index 3fdb2219..66e25563 100644
--- a/src/BrowseDataPage/components/dataDownloadsMain.jsx
+++ b/src/BrowseDataPage/components/dataDownloadsMain.jsx
@@ -55,8 +55,11 @@ function DataDownloadsMain({
Explore and download the MoTrPAC multi-omics datasets, which
includes quantitative results and analyses of molecular changes from
- exercise across tissues. Currently, the complete young rat endurance
- training dataset is publicly available.
+ exercise across tissues. Currently, the complete young adult rat endurance
+ training dataset is publicly available and provided under the
+ {' '}
+ CC BY 4.0 license
+ .
{' '}
{userType && userType === 'internal'
? 'The young rat acute exercise and human precovid sedentary adult datasets are currently available to consortium members only in the early preview phase. '
diff --git a/src/CodeRepoPage/codeRepoPage.jsx b/src/CodeRepoPage/codeRepoPage.jsx
index 84da7b47..bc149e52 100644
--- a/src/CodeRepoPage/codeRepoPage.jsx
+++ b/src/CodeRepoPage/codeRepoPage.jsx
@@ -1,7 +1,9 @@
import React from 'react';
+import { Link } from 'react-router-dom';
import { Helmet } from 'react-helmet';
import PageTitle from '../lib/ui/pageTitle';
import IconSet from '../lib/iconSet';
+import ExternalLink from '../lib/ui/externalLink';
const repositories = {
pipelines: [
@@ -102,10 +104,24 @@ export function CodeRepositories() {
-
+
Explore the source codes integral to the workflow of the MoTrPAC
data, from ingestion to analysis.
-
+
+
+ The MoTrPAC open source repositories are hosted on GitHub and
+ provided under the
+ {' '}
+
+ . The data available through the MoTrPAC Data Hub portal is
+ provided under the
+ {' '}
+ CC BY 4.0 license
+ .
+
{renderRepoComponent('Pipelines', repositories.pipelines)}
diff --git a/src/DataDeposition/dataDepositionPage.jsx b/src/DataDeposition/dataDepositionPage.jsx
new file mode 100644
index 00000000..12e0f7f5
--- /dev/null
+++ b/src/DataDeposition/dataDepositionPage.jsx
@@ -0,0 +1,191 @@
+import React from 'react';
+import { Helmet } from 'react-helmet';
+import PageTitle from '../lib/ui/pageTitle';
+import ExternalLink from '../lib/ui/externalLink';
+
+function DataDeposition() {
+ return (
+
+
+
+ Data Deposition at Public Repositories - MoTrPAC Data Hub
+
+
+
+
+
+ Aside from being made available through the Data Hub portal, the MoTrPAC
+ animal study data have also been submitted to a number of public
+ repositories. Below is an overview of each dataset type and the public
+ repositories to which the data have been submitted.
+
+ {/* Epigenomics and transcriptomics data deposition table */}
+
diff --git a/src/License/licensePage.jsx b/src/License/licensePage.jsx
new file mode 100644
index 00000000..e746e0a2
--- /dev/null
+++ b/src/License/licensePage.jsx
@@ -0,0 +1,40 @@
+import React from 'react';
+import { Helmet } from 'react-helmet';
+import PageTitle from '../lib/ui/pageTitle';
+import ExternalLink from '../lib/ui/externalLink';
+
+function License() {
+ return (
+
+
+
+ MoTrPAC Data License - MoTrPAC Data Hub
+
+
+
+
+
+ The data available through the MoTrPAC Data Hub portal is provided
+ under the Creative Commons Attribution 4.0 International License
+ (CC BY 4.0). This license allows users to use, share, adapt, distribute,
+ and reproduce the data in any medium or format, provided appropriate
+ credit is given to the original author(s) and the source, a link to the
+ Creative Commons license is included, and any modifications are clearly
+ indicated.
+
+
+ To view the full terms of this license, please visit Creative Commons
+ Attribution 4.0 International License (CC BY 4.0) at
+ {' '}
+
+
+
+
+
+ );
+}
+
+export default License;
diff --git a/src/MainStudy/exerciseBenefits.jsx b/src/MainStudy/exerciseBenefits.jsx
new file mode 100644
index 00000000..81c26d5f
--- /dev/null
+++ b/src/MainStudy/exerciseBenefits.jsx
@@ -0,0 +1,143 @@
+import React from 'react';
+import { Link } from 'react-router-dom';
+import { Helmet } from 'react-helmet';
+import ReactWordcloud from 'react-wordcloud';
+import PageTitle from '../lib/ui/pageTitle';
+import ExternalLink from '../lib/ui/externalLink';
+import exerciseBenefitsData from './exerciseBenefitsData';
+import exerciseBenefitsReferenceData from './exerciseBenefitsReferenceData';
+
+const exerciseBenefits = [
+ 'Improved immune system',
+ 'Younger-looking skin',
+ 'Reduced risk of cancer ',
+ 'Reduced risk of metabolic disease',
+ 'Better temperature regulation',
+ 'Better sex',
+ 'Improved sleep',
+ 'Reduced risk for depression',
+ 'Improved insulin sensitivity',
+ 'Improved blood lipid profile',
+ 'Better self-esteem',
+ 'Better oxygen transport',
+ 'More, larger, and more efficient mitochondria',
+ 'Increased reliance on lipid metabolism',
+ 'Stronger skeleton, joints and tendons',
+ 'Reduced risk of all-cause mortality',
+ 'Reduced risk of cardiovascular diseases',
+ 'Improved cognition',
+ 'Reduced stress response',
+ 'Reduced risk for dementia',
+];
+
+function ExerciseBenefits() {
+ const options = {
+ rotations: 0,
+ rotationAngles: [0],
+ fontFamily: 'sans-serif',
+ fontSizes: [20, 60],
+ fontWeight: 'bold',
+ padding: 1,
+ deterministic: false,
+ enableTooltip: false,
+ scale: 'sqrt',
+ spiral: 'archimedean',
+ transitionDuration: 1000,
+ };
+
+ function getRandomInt(min, max) {
+ return Math.floor(Math.random() * (max - min + 1)) + min;
+ }
+
+ const words = exerciseBenefits.map((benefit) => ({
+ text: benefit,
+ value: getRandomInt(100, 800),
+ }));
+
+ return (
+
+
+
+ Benefits of Exercise - MoTrPAC Data Hub
+
+
+
+
+
+
+ Regular physical activity is associated with many health benefits,
+ supported by extensive evidence in the medical literature.
+
In this intervention, we're specifically interested in the long term
@@ -176,11 +178,13 @@ function MainStudy({ profile, allFiles, handleDataFetch }) {
tissues. Rats were endurance-exercise trained on treadmills and
tissue samples were collected at either 1, 2, 4, or 8 weeks of
training, with a 48 hour rest or wash out period before samples were
- collected. See the{' '}
+ collected. See the
+ {' '}
{' '}
+ />
+ {' '}
to learn more.