From 687716f4bb7b0be0e5ba9dfb325d808109595de1 Mon Sep 17 00:00:00 2001
From: Joshua Charkow <joshuacharkow@gmail.com>
Date: Thu, 29 Jan 2026 11:44:46 -0500
Subject: [PATCH 1/4] GSoC OpenSwathWorkflow project

---
 content/en/news/GSoC2026.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/content/en/news/GSoC2026.md b/content/en/news/GSoC2026.md
index fa483e6..6d70035 100644
--- a/content/en/news/GSoC2026.md
+++ b/content/en/news/GSoC2026.md
@@ -80,3 +80,24 @@ Tasks:
 7. Provide a recommendation report for future binding strategy based on findings.
 
 ---
+
+### 3) Accelerating OpenSwathWorkflow for Large-Scale In Silico Spectral Libraries
+**Proposed Mentors:** Joshua Charkow
+**Skills:** C++, Algorithm Optimization, Profiling
+**Estimated Project Length:** 200 hours | Difficulty: Medium
+
+OpenSwathWorkflow is a central component of OpenMS for Data Independent Acquisition (DIA) analysis, enabling targeted extraction and scoring of chromatographic signals using spectral libraries. While OpenSwathWorkflow performs well for conventional experimental libraries, the increasing adoption of large in silico–generated spectral libraries presents substantial computational challenges. Such libraries can contain millions of precursors, leading to increased memory usage, longer runtimes, and scalability bottlenecks in candidate selection, scoring.
+
+This project aims to analyze and improve the computational performance and scalability of OpenSwathWorkflow, with a particular focus on workflows using very large in silico spectral libraries. The goal is to identify bottlenecks, redesign performance-critical components where necessary, and introduce optimizations that enable efficient processing without compromising identification quality.
+
+A key deliverable of this project is a systematic performance evaluation of OpenSwathWorkflow before and after optimization.
+
+Tasks:
+1. Develop a comprehensive understanding for the OpenSwathWorkflow algorithm
+1. Develop a benchmarking dataset for profiling. 
+2. Profile OpenSwathWorkflow to identify computational bottlenecks.
+3. Identify algorithmic bottlenecks and propose changes. 
+4. Experiment with different algorithms using inspiration from other open source DIA projects.  
+5. Validate that the optimized implementation provides comparable results to the original implementation and other DIA software tools.
+
+--
\ No newline at end of file

From d3585d3420d821a941e8ff2611fff797c9a60e39 Mon Sep 17 00:00:00 2001
From: Joshua Charkow <joshuacharkow@gmail.com>
Date: Mon, 23 Mar 2026 19:24:43 -0400
Subject: [PATCH 2/4] feature: add tally survey to OpenMS website

---
 layouts/index.html          |  2 ++
 layouts/partials/tally.html | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+)
 create mode 100644 layouts/partials/tally.html

diff --git a/layouts/index.html b/layouts/index.html
index 0a8571d..01136f5 100644
--- a/layouts/index.html
+++ b/layouts/index.html
@@ -38,4 +38,6 @@
     {{ if .Site.Params.casestudies }}
     {{ partial "casestudies.html" . }}
     {{ end }}
+
+    {{ partial "tally.html" . }}
 {{ end }}
\ No newline at end of file
diff --git a/layouts/partials/tally.html b/layouts/partials/tally.html
new file mode 100644
index 0000000..db04440
--- /dev/null
+++ b/layouts/partials/tally.html
@@ -0,0 +1,19 @@
+<script>
+window.TallyConfig = {
+  "formId": "pbV6Qq",
+  "popup": {
+    "emoji": {
+      "text": "👋",
+      "animation": "wave"
+    },
+    "autoClose": 0,
+    "open": {
+      "trigger": "scroll"
+    },
+    "showOnce": true,
+    "doNotShowAfterSubmit": true
+  }
+};
+</script>
+
+<script async src="https://tally.so/widgets/embed.js"></script>
\ No newline at end of file

From 4cfad548011d6a60dabdcdf8d48f8230579e6a5b Mon Sep 17 00:00:00 2001
From: Matteo Pilz <matteo.pilz@uni-tuebingen.de>
Date: Wed, 25 Mar 2026 16:05:23 +0100
Subject: [PATCH 3/4] Apply suggestion from @coderabbitai[bot]

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
---
 layouts/partials/tally.html | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/layouts/partials/tally.html b/layouts/partials/tally.html
index db04440..7e80c11 100644
--- a/layouts/partials/tally.html
+++ b/layouts/partials/tally.html
@@ -16,4 +16,12 @@
 };
 </script>
 
-<script async src="https://tally.so/widgets/embed.js"></script>
\ No newline at end of file
+<script>
+  // Replace with your existing consent signal / CMP API
+  if (window.userHasConsentedToExternalEmbeds === true) {
+    const s = document.createElement("script");
+    s.async = true;
+    s.src = "https://tally.so/widgets/embed.js";
+    document.head.appendChild(s);
+  }
+</script>
\ No newline at end of file

From 5af83caaf76b14bae6280b9aa5ce9726b0c4b178 Mon Sep 17 00:00:00 2001
From: Matteo Pilz <matteo.pilz@uni-tuebingen.de>
Date: Wed, 25 Mar 2026 16:28:15 +0100
Subject: [PATCH 4/4] Simplify Tally widget script inclusion

Replaced consent-based script loading with a direct async script tag for Tally widget.
---
 layouts/partials/tally.html | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/layouts/partials/tally.html b/layouts/partials/tally.html
index 7e80c11..4bb1879 100644
--- a/layouts/partials/tally.html
+++ b/layouts/partials/tally.html
@@ -16,12 +16,4 @@
 };
 </script>
 
-<script>
-  // Replace with your existing consent signal / CMP API
-  if (window.userHasConsentedToExternalEmbeds === true) {
-    const s = document.createElement("script");
-    s.async = true;
-    s.src = "https://tally.so/widgets/embed.js";
-    document.head.appendChild(s);
-  }
-</script>
\ No newline at end of file
+<script async src="https://tally.so/widgets/embed.js"></script>