From baf71c08472db7759d55bdc792fd12cf151d69b3 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 31 Dec 2025 19:41:59 +0000 Subject: [PATCH 1/6] Initial plan From 21fe61940a6aed567dcf4903625d8b1fb31556a6 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 31 Dec 2025 19:48:47 +0000 Subject: [PATCH 2/6] Add peer review section to Barad Lab website Co-authored-by: bbarad <5542351+bbarad@users.noreply.github.com> --- _config.yml | 4 ++ _data/navigation.yml | 6 +-- _reviews/_template.md.txt | 22 +++++++++++ reviews/index.html | 81 +++++++++++++++++++++++++++++++++++++++ 4 files changed, 110 insertions(+), 3 deletions(-) create mode 100644 _reviews/_template.md.txt create mode 100644 reviews/index.html diff --git a/_config.yml b/_config.yml index 227c625..d0899e2 100644 --- a/_config.yml +++ b/_config.yml @@ -24,5 +24,9 @@ collections: group: publications layout: default output: True + reviews: + group: reviews + layout: default + output: True diff --git a/_data/navigation.yml b/_data/navigation.yml index 75b40ee..b730c15 100644 --- a/_data/navigation.yml +++ b/_data/navigation.yml @@ -10,9 +10,9 @@ link: "/publications" group: publications -# - name: reviews -# link: "/reviews" -# group: reviews +- name: reviews + link: "/reviews" + group: reviews - name: members link: "/members" diff --git a/_reviews/_template.md.txt b/_reviews/_template.md.txt new file mode 100644 index 0000000..76d0d71 --- /dev/null +++ b/_reviews/_template.md.txt @@ -0,0 +1,22 @@ +--- +title: "Title of Manuscript Reviewed" +date: "YYYY-MM-DD" # Date of Public Review, then update to Date of Publication +authors: "Author1 A, Author2 B, **Barad BA**" # Bold name of lab members by wrapping with ** ** +reviewers: "Reviewer1, Reviewer2" # Lab members who reviewed the manuscript +image: "img/reviews/YYYY_author.webp" # Use CDN! Optional image +abstract: "optional one-sentence abstract" + +peer-review: +- biorxiv: "" # biorxiv ID, example "2024.01.01.123456" or versioned "2024.01.01.123456v1" + pubpeer: "" # PubPeer link ID, the part after pubpeer.com/publications/ + preprint_journal: "" # Name of preprint server if not biorxiv (e.g., "arXiv", "ChemRxiv") + preprint_url: "" # Full URL to preprint if not biorxiv + pdf: "" # Full CDN link to PDF of review + +published: +- pmid: "" # PubMed ID of final published version + pdf: "" # Full CDN link to PDF of published version + +--- + +# Optional: Paste review summary or highlights here diff --git a/reviews/index.html b/reviews/index.html new file mode 100644 index 0000000..d0b200a --- /dev/null +++ b/reviews/index.html @@ -0,0 +1,81 @@ +--- +title: Peer Reviews from the Barad Lab +layout: parallax +group: reviews +banner: img/site/banners/square_tomo.webp +--- +

Peer Reviews

+
+

+Peer review of scientific manuscripts is essential for scientific communication and plays an important role in refining the body of work prior to final publication. We believe that transparency in peer review can improve the speed, quality, and collegiality of the publication process. Peer review is also an important training opportunity for lab members in scientific thinking and writing. As such, we only review manuscripts that have been posted on preprint servers and we post our peer review comments publicly. +

+ +{% assign sorted = site.reviews | sort: "date" | reverse %} +{% for review in sorted %} + +
+
+
+
{{ review.title | markdownify | remove: '

' | remove: '

' | strip }}
+
{{ review.authors | markdownify | remove: '

' | remove: '

' | strip }}
+ {% if review.reviewers %} + Reviewed by: {{ review.reviewers | markdownify | remove: '

' | remove: '

' | strip }} + {% if review.date %} - {{ review.date | date: "%B %Y" }}{% endif %} + {% endif %} +
+ {% if review.abstract %} +

{{ review.abstract | markdownify | remove: '

' | remove: '

' }}

+ {% endif %} +
+
+ +
+
+ {% if review.image %} + Key Figure + {% endif %} +
+ +
+
+{% endfor %} +
From c197c5ec34728ab8cd651975df1e23b0b5e7f0f6 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 31 Dec 2025 19:50:14 +0000 Subject: [PATCH 3/6] Improve accessibility of review images with descriptive alt text Co-authored-by: bbarad <5542351+bbarad@users.noreply.github.com> --- reviews/index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/reviews/index.html b/reviews/index.html index d0b200a..51d7455 100644 --- a/reviews/index.html +++ b/reviews/index.html @@ -32,7 +32,7 @@
{{ review.authors | markdownify | remove: '

' | remove: '

' | strip }}<
{% if review.image %} - Key Figure + Representative figure for {{review.title | strip_html | strip}} {% endif %}
-
+
{% if review.image %} - Representative figure for {{review.title | strip_html | strip}} + Representative figure for {{review.title | strip_html | strip}} {% endif %}
-
    -
    -
    Access the Review
    +
      +
      Peer Review
      {% for record in review.peer-review %} @@ -51,24 +50,29 @@
      Access the Review
    • Public Review: Link
      • {% endif %} - - {% if record.pdf %} -
    • Review PDF
      • - {% endif %} - {% endfor %} - - +
    +
      + {% if review.published %} +
      Post-Review
      +
      Access the paper
      {% for pub in review.published %} {% if pub.pmid %} -
      -
      Published Version
    • PMID: {{pub.pmid}}
      • - {% if pub.pdf %} -
    • Published PDF
      • {% endif %} + {% if pub.pdf %} +
    • Full Text
      • {% endif %} {% endfor %} + + {% if review.links %} +
      +
      Additional Link{% if review.links.size > 1 %}s{% endif %}
      + {% for link in review.links %} +
    • {{link.name}}
      • + {% endfor %} + {% endif %} + {% endif %}

From 1df9b26b4ba312103ab29f336b745a6c84e75014 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Wed, 31 Dec 2025 20:35:06 +0000 Subject: [PATCH 6/6] Replace PDF link with journal URL and label as "Journal Version" Co-authored-by: bbarad <5542351+bbarad@users.noreply.github.com> --- _reviews/_template.md.txt | 2 +- reviews/index.html | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/_reviews/_template.md.txt b/_reviews/_template.md.txt index f19dc6a..92b973e 100644 --- a/_reviews/_template.md.txt +++ b/_reviews/_template.md.txt @@ -12,7 +12,7 @@ peer-review: published: - pmid: "" # PubMed ID of final published version - pdf: "" # Full CDN link to PDF of published version + journal_url: "" # Full URL to the journal version # Optional additional links in post-review section links: diff --git a/reviews/index.html b/reviews/index.html index 3447e4b..9573a20 100644 --- a/reviews/index.html +++ b/reviews/index.html @@ -60,8 +60,8 @@
Access the paper
{% if pub.pmid %}
  • PMID: {{pub.pmid}}
    • {% endif %} - {% if pub.pdf %} -
  • Full Text
    • + {% if pub.journal_url %} +
  • Journal Version
    • {% endif %} {% endfor %}