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GSR: Simulator - MaSS-Simulator
| Attribute | Value |
|---|---|
| Title | MaSS-Simulator |
| Short Description | MaSS-Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms |
| Long Description | MaSS-Simulator offers many configuration options to allow the user a great degree of control over the test datasets, which can enable rigorous and large- scale testing of any proteomics algorithm. MaSS-Simulator is assessed by comparing its performance against experimentally generated spectra and spectra obtained from NIST collections of spectral library. The results show that MaSS-Simulator generated spectra match closely with real-spectra and have a relative-error distribution centered around 25%. In contrast, the theoretical spectra for same peptides have relative-error distribution centered around 150%. MaSS-Simulator will enable developers to specifically highlight the capabilities of their algorithms and provide a strong proof of any pitfalls they might face. Source code, executables, and a user manual for MaSS-Simulator can be downloaded from https://github.com/pcdslab/MaSS-Simulator. |
| Keywords | benchmarking; big data; mass spectrometry; simulator |
| Version | 1.0 |
| Project Started | 2018 |
| Last Release | 5 years, 1 month ago |
| Homepage | https://github.com/pcdslab/MaSS-Simulator |
| Citations | Awan MG, Saeed F, MaSS-Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms., Proteomics, Oct. 1, 2018 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | Sept. 28, 2022 (1082 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Proteomics, |
| Variations | Ionization, |
| Simulation Method | |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, Graphical User Interface, |
| Development | |
| Tested Platforms | |
| Language | Java, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using MaSS-Simulator has been provided.
Please propose new citations if you are aware of publications that use this software.