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Updating "Getting Started" information #61

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67150bc
Updating to include data model information
guittari Sep 10, 2025
4562aff
Adding outlines for each new page
guittari Sep 10, 2025
e0297fe
Update DocumentationPage.vue
guittari Sep 10, 2025
da210af
Update DocumentationPage.vue
guittari Sep 10, 2025
4a9e3b5
Updating standards pages
guittari Oct 14, 2025
4519ce7
Update frontend/src/pages/WorkflowGuidancePage.vue
guittari Oct 21, 2025
c7eba0a
Merge branch 'main' into 50-data-model-tab
guittari Oct 23, 2025
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6 changes: 5 additions & 1 deletion frontend/src/constants/mainLayout.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,11 @@ export const defaultTabs: Tab[] = [
external: false,
dropdown: {
show: false,
children: [{ name: 'Documentation', route: '/documentation', external: false }],
children: [
{ name: 'Documentation', route: '/documentation', external: false },
{ name: 'Data Standards Overview', route: '/standards', external: false },
{ name: 'Workflow Guidance', route: '/guidance', external: false },
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@erikjohnson24 erikjohnson24 Sep 11, 2025

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Is "Data Ingest Guidnace" or "Data Upload Guidance" more accessible to users? I wonder if that will be easier for the non-expert user to quickly understand.

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@CodyCBakerPhD CodyCBakerPhD Oct 22, 2025

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+1 to adding extra words to describe which type of workflow this documentation is about (sometimes people have a lot of 'workflows' floating around for all kinds of things)

],
},
},
{ name: 'Tools', route: '/tools', external: false },
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266 changes: 266 additions & 0 deletions frontend/src/pages/OverviewStandardsPage.vue
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@@ -0,0 +1,266 @@
<template>
<q-page class="column items-center">
<PageTitle title="Data Standards" subtitle="EMBER interoperability & reproducibility" />

<div class="q-mx-xl full-width max-w-screen-lg">
<!-- Overview -->
<q-card flat class="q-mt-lg">
<q-card-section>
<div class="text-h2 scrollable">Overview</div>
<p>
EMBER follows widely adopted, community-driven data standards to promote interoperability and reproducibility across multimodal neuroscience datasets.
The framework currently supports
<a href="https://bids.neuroimaging.io/index.html" target="_blank" rel="noopener" class="link">BIDS</a>
and
<a href="https://nwb.org/about-nwb/" target="_blank" rel="noopener" class="link">NWB</a>
formats, along with hybrid layouts that combine both where appropriate, and anticipate accepting new standards.
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@CodyCBakerPhD CodyCBakerPhD Oct 22, 2025

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Suggested change
formats, along with hybrid layouts that combine both where appropriate, and anticipate accepting new standards.
formats, along with hybrid layouts that combine both where appropriate.

I'd suggest not planting abstract seeds of 'expectations' since 'who knows what will happen' in the future

Can (and should) always come back and modify the line if something changes later down the road

These standards ensure datasets remain consistent, shareable, and aligned with best practices in the BBQS and DCAIC communities.
</p>

<q-banner inline-actions class="q-mt-sm bg-grey-2 q-pa-md rounded-xl">
<template #avatar>
<q-icon name="rule" />
</template>
<div class="text-body1">
As outlined on the
<router-link to="/documentation" class="link">Documentation</router-link>
page, all data must be converted to BIDS and/or NWB before upload.
<div>
Uploading raw, non-standardized folders is not supported by the EMBER–DANDI CLI, though, we also encourage community members to reach out for assistance with data formatting or validator setup.
</div>
</div>
</q-banner>
</q-card-section>
</q-card>

<!-- BIDS Essentials (uniform subsections) -->
<q-card flat class="q-mt-lg">
<q-card-section>
<div class="text-h2 scrollable">BIDS Essentials</div>
<q-list>
<q-item>
<q-item-section>
<q-item-label overline>Scope</q-item-label>
<q-item-label>
MRI, EEG/MEG/iEEG, diffusion, functional, microscopy, behavioral logs, and derivatives.
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@CodyCBakerPhD CodyCBakerPhD Oct 22, 2025

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Suggested change
MRI, EEG/MEG/iEEG, diffusion, functional, microscopy, behavioral logs, and derivatives.
MRI/fMRI, EEG/MEG/iEEG, diffusion, microscopy, behavioral logs, and derivatives.

Is this clearer?

Also is 'diffusion' clear enough on its own?

</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>Core files</q-item-label>
<q-item-label>
<ul class="q-ml-lg q-mt-sm">
<li><code>dataset_description.json</code> with <i>Name</i>, <i>BIDSVersion</i>, <i>Contributors</i></li>
<li><code>participants.tsv</code> plus <code>participants.json</code> for column metadata</li>
<li><code>README</code> and <code>CHANGES</code> for human-readable context</li>
</ul>
</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>Organization</q-item-label>
<q-item-label>
<ul class="q-ml-lg q-mt-sm">
<li>Subject/session hierarchy (<code>sub-</code>, optional <code>ses-</code>)</li>
<li>Modality folders (e.g., <code>anat</code>, <code>func</code>, <code>dwi</code>, <code>eeg</code>, <code>ieeg</code>, <code>meg</code>, <code>micr</code>, <code>beh</code>, <code>derivatives</code>)</li>
<li>Sidecar JSONs define acquisition parameters</li>
</ul>
</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>Naming & metadata</q-item-label>
<q-item-label>
<ul class="q-ml-lg q-mt-sm">
<li>Key–value filename entities (<code>sub</code>, <code>ses</code>, <code>task</code>, <code>run</code>, <code>acq</code>)</li>
<li>Modality-specific suffixes (e.g., <code>_bold</code>, <code>_T1w</code>, <code>_ieeg</code>)</li>
</ul>
</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label>
Learn more: <a href="https://bids.neuroimaging.io/index.html" target="_blank" rel="noopener" class="link">BIDS</a>
</q-item-label>
</q-item-section>
</q-item>
</q-list>
</q-card-section>
</q-card>

<!-- NWB Essentials (mirrors BIDS layout) -->
<q-card flat class="q-mt-lg">
<q-card-section>
<div class="text-h2 scrollable">NWB Essentials</div>
<q-list>
<q-item>
<q-item-section>
<q-item-label overline>Scope</q-item-label>
<q-item-label>
Neurophysiology including ephys, behavior, optical physiology, and multimodal time series.
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@CodyCBakerPhD CodyCBakerPhD Oct 22, 2025

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Suggested change
Neurophysiology including ephys, behavior, optical physiology, and multimodal time series.
Neurophysiology data, such as extracellular or intracellular electrophysiology (including EEG/iEEG), optical physiology, together with behavior, other multimodal time series, metadata tables, and annotated events.

</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>Core files</q-item-label>
<q-item-label>
<ul class="q-ml-lg q-mt-sm">
<li>HDF5-based <code>.nwb</code> file per session capturing acquisition, processing, and analysis</li>
<li>Schema-validated containers for data, metadata, and results</li>
</ul>
</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>Organization</q-item-label>
<q-item-label>
<ul class="q-ml-lg q-mt-sm">
<li>Subject, devices, electrodes/units, intervals, and processing modules</li>
<li>Raw under <code>acquisition</code>; derived under <code>processing</code></li>
</ul>
</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>Naming & metadata</q-item-label>
<q-item-label>
<ul class="q-ml-lg q-mt-sm">
<li>Use object types/names from PyNWB/MatNWB</li>
<li>Record units, sampling rates, and reference time consistently</li>
<li>Leverage NDX extensions when needed</li>
</ul>
</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label>
Learn more: <a href="https://nwb.org/about-nwb/" target="_blank" rel="noopener" class="link">NWB</a>
</q-item-label>
</q-item-section>
</q-item>
</q-list>
</q-card-section>
</q-card>

<!-- Hybrid Layout Example -->
<q-card flat class="q-mt-lg">
<q-card-section>
<div class="text-h2 scrollable">Hybrid Layout Example</div>
<q-list>
<q-item>
<q-item-section>
<q-item-label overline>BIDS + NWB</q-item-label>
<q-item-label>
Store <code>.nwb</code> files within a BIDS directory structure (e.g., iEEG or behavior):
</q-item-label>
<q-item-label>
<code class="q-pa-xs bg-grey-2">sub-01/ses-01/ieeg/sub-01_ses-01_task-rest_run-01_ieeg.nwb</code>
</q-item-label>
</q-item-section>
</q-item>
</q-list>
</q-card-section>
</q-card>

<!-- Validation Tools & Services (uniform presentation) -->
<q-card flat class="q-mt-lg">
<q-card-section>
<div class="text-h2 scrollable">Validation Tools & Services</div>
<q-list>
<q-item>
<q-item-section>
<q-item-label overline>BIDS Validator</q-item-label>
<q-item-label>
Check directory layout, filenames, and sidecars, then iterate until clean.
</q-item-label>
<q-item-label>
<a href="https://bids-standard.github.io/bids-validator/" target="_blank" rel="noopener" class="link">Open BIDS Validator</a>
</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>NWB Validation</q-item-label>
<q-item-label>
Validate with <code>pynwb validate</code> or NWBInspector for schema compliance and metadata completeness.
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@CodyCBakerPhD CodyCBakerPhD Oct 22, 2025

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Suggested change
Validate with <code>pynwb validate</code> or NWBInspector for schema compliance and metadata completeness.
Validate with <a href="https://nwbinspector.readthedocs.io/en/dev/index.html" target="_blank" rel="noopener" class="link">NWB Inspector</a> for schema compliance and metadata completeness.

To have one fewer thing to 'need to know'

FYI the NWB Inspector also runs and reports pynwb validate

</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>EMBER–DANDI</q-item-label>
<q-item-label>
Server-side checks run during upload; retain validation logs with the dataset for traceability.
</q-item-label>
</q-item-section>
</q-item>
</q-list>
</q-card-section>
</q-card>

<!-- Metadata Standards -->
<q-card flat class="q-mt-lg">
<q-card-section>
<div class="text-h2 scrollable">Metadata Standards</div>
<q-list>
<q-item>
<q-item-section>
<q-item-label overline>Required fields</q-item-label>
<q-item-label>
Project, subject or session identifiers, modality, acquisition date.
</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>Controlled vocabularies</q-item-label>
<q-item-label>
Species, anatomy, and device names using stable terms where available.
</q-item-label>
</q-item-section>
</q-item>
<q-item>
<q-item-section>
<q-item-label overline>Ontologies</q-item-label>
<q-item-label>
Uberon (anatomy), NCBI Taxonomy (species), and behavior/task ontologies as appropriate.
</q-item-label>
</q-item-section>
</q-item>
</q-list>
<p class="q-px-md q-pt-sm">
EMBER enforces core metadata fields and encourages controlled vocabularies and ontologies.
</p>
</q-card-section>
</q-card>


</div>
</q-page>
</template>

<script setup lang="ts">
import PageTitle from 'src/components/PageTitle.vue'
</script>

<style scoped>
.q-item__section > .text-overline {
font-size: 1rem;
}
.scrollable {
scroll-margin-top: 100px;
}
code {
font-family: ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, 'Liberation Mono', 'Courier New', monospace;
font-size: 0.9em;
}
.rounded-xl { border-radius: 1rem; }
</style>
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