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GSoC OpenSwathWorkflow project #242

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GSoC OpenSwathWorkflow project
jcharkow Jan 29, 2026
62d19e1
minor: fix typo
jcharkow Jan 29, 2026
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21 changes: 21 additions & 0 deletions content/en/news/GSoC2026.md
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Expand Up @@ -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 and 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.
Comment on lines +95 to +100
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⚠️ Potential issue | 🟡 Minor

Fix task list numbering and wording.

There’s a duplicated “1.” and a couple of phrasing issues that make the task list harder to follow. Suggest renumbering and tightening the wording.

🛠️ Proposed edit 
 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.
+1. Develop a comprehensive understanding of the OpenSwathWorkflow algorithm.
+2. Develop a benchmarking dataset for profiling.
+3. Profile OpenSwathWorkflow to identify computational bottlenecks.
+4. Identify algorithmic bottlenecks and propose changes.
+5. Experiment with different algorithms using inspiration from other open-source DIA projects.
+6. Validate that the optimized implementation provides comparable results to the original implementation and other DIA software tools.
🧰 Tools
🪛 LanguageTool

[grammar] ~100-~100: Use a hyphen to join words.
Context: ...rithms using inspiration from other open source DIA projects. 5. Validate that ...

(QB_NEW_EN_HYPHEN)

🤖 Prompt for AI Agents 
In `@content/en/news/GSoC2026.md` around lines 95 - 100, Fix the duplicated "1."
and tighten wording under the "Tasks:" list: renumber the items sequentially
1–5, change the first item to "Develop a comprehensive understanding of the
OpenSwathWorkflow algorithm", the second to "Create a benchmarking dataset for
profiling", the third to "Profile OpenSwathWorkflow to identify computational
bottlenecks", the fourth to "Propose algorithmic changes to address identified
bottlenecks", and the fifth to "Experiment with alternative algorithms inspired
by other open‑source DIA projects"; ensure consistent punctuation and remove
extra spaces.

5. Validate that the optimized implementation provides comparable results to the original implementation and other DIA software tools.

--
Comment on lines +83 to +103
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⚠️ Potential issue | 🟠 Major

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Search for the project title in the file
echo "=== Searching for project title ==="
rg -n "Accelerating OpenSwathWorkflow for Large-Scale In Silico Spectral Libraries" content/en/news/GSoC2026.md

echo ""
echo "=== Searching for mentor name ==="
rg -n "Joshua Charkow" content/en/news/GSoC2026.md

echo ""
echo "=== Full file structure for context ==="
rg -n "^###|^--" content/en/news/GSoC2026.md | head -50

Repository: OpenMS/OpenMS-website

Length of output: 521

🏁 Script executed:

#!/bin/bash
# Read the specific lines to verify task numbering and other issues
sed -n '83,103p' content/en/news/GSoC2026.md | cat -n

Repository: OpenMS/OpenMS-website

Length of output: 2022

Fix task numbering, grammar, and formatting issues.

The project description does not contain duplicates. However, there are real issues to address:

  • Task numbering (lines 96-97): First two tasks are both numbered "1." — renumber to "1." and "2."
  • Grammar (line 96): Change "understanding for the" to "understanding of the"
  • Hyphenation (line 100): Change "open source" to "open-source"
  • Separator (line 103): Change -- to ---
🧰 Tools
🪛 LanguageTool

[style] ~91-~91: As an alternative to the over-used intensifier ‘very’, consider replacing this phrase.
Context: ...h a particular focus on workflows using very large in silico spectral libraries. The goal ...

(EN_WEAK_ADJECTIVE)

[grammar] ~100-~100: Use a hyphen to join words.
Context: ...rithms using inspiration from other open source DIA projects. 5. Validate that ...

(QB_NEW_EN_HYPHEN)

🤖 Prompt for AI Agents 
In `@content/en/news/GSoC2026.md` around lines 83 - 103, Fix the issues in the
"Tasks:" list and nearby text: renumber the first two task items under "Tasks:"
so they are "1." and "2." (currently both "1."), change the phrase
"understanding for the OpenSwathWorkflow algorithm" to "understanding of the
OpenSwathWorkflow algorithm", replace "open source" with "open-source" in the
line referencing other DIA projects, and replace the trailing separator `--`
with an em-dash `---`; locate these edits around the "Tasks:" block and the
sentence mentioning "OpenSwathWorkflow" and "open source" to apply the fixes.