GSoC OpenSwathWorkflow project #242
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📝 WalkthroughWalkthroughAdds a new Google Summer of Code 2026 project entry for "Accelerating OpenSwathWorkflow for Large-Scale In Silico Spectral Libraries" to the news document; the same project description is inserted twice (duplicated) within the file. Changes
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Actionable comments posted: 3
🤖 Fix all issues with AI agents
In `@content/en/news/GSoC2026.md`:
- Line 89: The sentence describing OpenSwathWorkflow ends with the fragment
"candidate selection, scoring."—update the sentence containing
"OpenSwathWorkflow" so it reads smoothly (e.g., "leading to increased memory
usage, longer runtimes, and scalability bottlenecks in candidate selection and
scoring.") or otherwise insert "and"/rewrite to remove the fragment and restore
proper flow.
- Around line 87-103: Remove the stray trailing marker "--" at the end of the
section and replace it with the repository's standard YAML/Markdown separator
'---' (or simply delete it if no separator is needed) so separators are
consistent with the rest of the document; update the block that ends after the
Tasks list (the fragment containing "**Estimated Project Length:** ..." and the
Tasks) to end with '---' instead of '--'.
- Around line 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.
content/en/news/GSoC2026.md
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| **Estimated Project Length:** 200 hours | Difficulty: Medium | ||
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| 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. | ||
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| 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. | ||
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| A key deliverable of this project is a systematic performance evaluation of OpenSwathWorkflow before and after optimization. | ||
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| 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. | ||
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| -- No newline at end of file |
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Clean up the trailing “--” and keep separators consistent.
Line 103 appears to be a stray marker; elsewhere the file uses ---. Please remove it or replace with the standard separator.
🧹 Proposed edit
---🧰 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 87 - 103, Remove the stray trailing
marker "--" at the end of the section and replace it with the repository's
standard YAML/Markdown separator '---' (or simply delete it if no separator is
needed) so separators are consistent with the rest of the document; update the
block that ends after the Tasks list (the fragment containing "**Estimated
Project Length:** ..." and the Tasks) to end with '---' instead of '--'.
Comment on lines
+95
to
+100
| 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. |
Contributor
There was a problem hiding this comment.
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.
replace , with and
Contributor
There was a problem hiding this comment.
Actionable comments posted: 1
🤖 Fix all issues with AI agents
In `@content/en/news/GSoC2026.md`:
- Around line 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.
Comment on lines
+83
to
+103
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| ### 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 | ||
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| 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. | ||
| 5. Validate that the optimized implementation provides comparable results to the original implementation and other DIA software tools. | ||
|
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||
| -- |
Contributor
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🧩 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 -50Repository: 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 -nRepository: 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.
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Add GSoC OpenSwathWorkflow proposal
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