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