Add r34 ember#62
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Summary of ChangesHello @yibeichan, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed! This pull request introduces content for two new initiatives: the EMBER project and an R34 grant. It adds a new 'About' page for EMBER, and integrates a new R34 project ('The International Development Project' by Linda E. Wilbrecht) into the 'Projects' section, including a summary on the index page, a dedicated project page, and associated team data. Highlights
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Pull Request Overview
This PR adds documentation for the EMBER (Ecosystem for Multi-modal Brain-behavior Experimentation and Research) data archive and introduces a new R34 research project grant (R34DA062119) led by Linda E. Wilbrecht at UC Berkeley. The PR creates new content pages and team data files to document the International Development Project (IDP) focusing on standardized study of experience-dependent brain and behavioral development.
Key changes:
- Addition of EMBER documentation page explaining the NIH data archive
- Creation of new R34 project entry and detailed project page
- Team data file for the R34 project principal investigator
Reviewed Changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| content/about/EMBER.md | New documentation page explaining EMBER data archive capabilities and contact information |
| content/projects/r34_14.md | Detailed project page for the International Development Project R34 grant |
| content/projects/_index.md | Added project summary entry in the main projects listing |
| data/team-r34_14.yaml | Team data file containing PI information for the R34 project |
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Code Review
This pull request adds new content for the EMBER archive and a new R34 project. The changes are mostly in markdown files. I've identified a few areas for improvement, mainly related to content consistency, maintainability, and markdown/HTML best practices. Please see my detailed comments below.
| **_Institution(s)_** - University of California, Berkeley | ||
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| It is increasingly clear that experience of adversity including poverty, trauma, and other stressors during childhood can enhance risk for mental and physical health problems later in life. These adverse experiences can be highly varied and include elements such as food insecurity, family and community violence, and multiple forms of neglect. To efficiently target interventions and to build resilience, it is imperative to understand which forms of adversity have which effects on behavior, and to determine what timing and combination of adversities puts an individual most at risk. We also need to recognize that these questions have a deep biological history. Experience in different domains likely acts on a developing organism’s developmental programming where it adjusts gene expression to adapt an individual’s phenotype in response to the environment. This adaptation may differ depending on the type of experience (for example, threat, deprivation or scarcity and other forms of uncertainty may drive different outcomes). To study these important epidemiological and biological questions in a controlled fashion we can turn to the study of the effects of developmental experience on mice whose genetics, rearing and testing conditions can be carefully controlled. However, to get a big picture view of how different forms of experience compare to one another in the field of neuroscience and behavior, we need to adopt better scientific methods that use richer, more ethologically informed behavioral tasks and rigorously standardize our protocols across sites, share data in readily comparable formats. Here we propose to initiate a team science effort, the Adversity and Resilience Consortium (ARC), to address these challenges. We will begin by comparing our existing data sets from control mice and mice that experienced adversity in development to assess how they might be combined across sites. Based on the interests of our initial team these data will focus on adolescent experience and adult learning and decision making, but can later be expanded. Next, we will develop 1) a standardized set of methods and protocols to assess behavior and 2) a public forum for sharing protocols, resources, and data that also facilitates exploration and analysis based on Open Source Brain as a model. In future work supported by larger grant mechanisms, we will work as a team using our newly standardized methods to vary exposure to deprivation, threat, and unpredictability and study behavior and brain development along with neural recordings. We predict that dimensionality reduction methods and computational models of latent processes will reveal distinct effects of different forms of adversity on mouse behavior that can be mapped back to distinct contrasts in cellular and circuit function. |
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The project summary text is duplicated in this file and in content/projects/r34_14.md. This creates a significant maintainability issue, as any future updates to the summary must be made in two places, increasing the risk of inconsistencies. To improve maintainability, this content should be sourced from a single location. Consider using a Hugo shortcode or leveraging Hugo's content management features to pull the summary from the dedicated project page (r34_14.md) instead of duplicating it here.
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| title: Meet the EMBER Team | |||
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The title "Meet the EMBER Team" seems inconsistent with the page content, which describes the EMBER project and archive rather than the team members. A more accurate title, such as "About EMBER" or "EMBER Archive", would better reflect the content and align with the linkTitle.
| title: Meet the EMBER Team | |
| title: About EMBER |
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| ### About | ||
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| The Ecosystem for Multi-modal Brain-behavior Experimentation and Research (EMBER, http://emberarchive.org/) is NIH’s data archive for brain and behavior data collected from multiple animal species, including humans. EMBER supports the BRAIN Initiative’s Brain Behavior Quantification and Synchronization (BBQS) program by enabling the storage, processing, and curation of multimodal datasets, including neural, behavioral, physiological, and environmental recordings. EMBER will accelerate discovery and foster collaboration across the BBQS consortium and the broader neuroscience community through data harmonization and synchronization capabilities, as well as metadata support and scalable queries across modalities. |
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The URL for the EMBER archive is currently plain text and not clickable. To improve usability for readers, it should be formatted as a proper markdown link.
| The Ecosystem for Multi-modal Brain-behavior Experimentation and Research (EMBER, http://emberarchive.org/) is NIH’s data archive for brain and behavior data collected from multiple animal species, including humans. EMBER supports the BRAIN Initiative’s Brain Behavior Quantification and Synchronization (BBQS) program by enabling the storage, processing, and curation of multimodal datasets, including neural, behavioral, physiological, and environmental recordings. EMBER will accelerate discovery and foster collaboration across the BBQS consortium and the broader neuroscience community through data harmonization and synchronization capabilities, as well as metadata support and scalable queries across modalities. | |
| The Ecosystem for Multi-modal Brain-behavior Experimentation and Research ([EMBER](http://emberarchive.org/)) is NIH’s data archive for brain and behavior data collected from multiple animal species, including humans. EMBER supports the BRAIN Initiative’s Brain Behavior Quantification and Synchronization (BBQS) program by enabling the storage, processing, and curation of multimodal datasets, including neural, behavioral, physiological, and environmental recordings. EMBER will accelerate discovery and foster collaboration across the BBQS consortium and the broader neuroscience community through data harmonization and synchronization capabilities, as well as metadata support and scalable queries across modalities. |
| - EMBERvault, a HIPAA-compliant storage for PII/PHI (including video and audio) from human participants; | ||
| - Temporary sandboxes for preliminary analysis and data ingest preparation. | ||
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| Visit our "Getting started" page to set up an account and see guides on data access and upload: https://emberarchive.org/getting-started |
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The link to the "Getting started" page is not clickable. It should be formatted as a markdown link to improve user experience and make navigation easier.
| Visit our "Getting started" page to set up an account and see guides on data access and upload: https://emberarchive.org/getting-started | |
| Visit our ["Getting started" page](https://emberarchive.org/getting-started) to set up an account and see guides on data access and upload. |
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| **_R34DA062119_** - [The International Development Project (IDP): An international collaboration for the standardized study of experience-dependent brain and behavioral development](https://reporter.nih.gov/search/Rzi0zieKH0GZuG8lIsQy7Q/project-details/11045432) \ | ||
| **_PI(s)_** - [Wilbrecht, Linda E.](mailto:wilbrecht@berkeley.edu)\*, |
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There's a trailing comma after the PI's name, which is inconsistent with the formatting of other single-PI projects in this file. Typically, commas are used only to separate multiple PIs. Additionally, other single-PI entries end with a backslash \, which appears to be missing here. Adjusting this will improve consistency across the project listings.
| **_PI(s)_** - [Wilbrecht, Linda E.](mailto:wilbrecht@berkeley.edu)\*, | |
| **_PI(s)_** - [Wilbrecht, Linda E.](mailto:wilbrecht@berkeley.edu)\* \ |
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| **_Project Summary_** | ||
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Using inline CSS (style="text-align: justify") mixes content with presentation, which can make the site harder to maintain and update consistently. It's a better practice to use a CSS class for styling. You could define a class like text-justify in a shared stylesheet and apply it here. This separates concerns and makes future style changes much easier.
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add ember to about
add WILBRECHT r34