Repositories list

• DBSchema_PgSQL_DMS

  Public
  PRISM Data Management System PostgreSQL database schema

  PLpgSQL

  •0•3•0•0•Updated Oct 30, 2024Oct 30, 2024

• DMS-Website

  Public
  DMS Website

  PHP

  •0•1•0•1•Updated Oct 29, 2024Oct 29, 2024

• proteomics_therapy

  Public
  Collection of lessons from IO group's data analysis workshops (i.e. TheRa.py Sessions)

  TeX

  •1•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• PHRP

  Public
  Converts a MS-GF+ .tsv search result file or an X!Tandem results file (XML format) into a series of tab-delimited text files, summarizing the results. It also supports results files from MaxQuant, MSAlign, TopPIC, MODa, MODPlus, and MSPathFinder, along with SEQUEST Synopsis/First Hits files.

  mass-spectrometry

  C#

  •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

• DMS-Analysis-Manager

  Public
  DMS Analysis Tool Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•3•0•0•Updated Oct 23, 2024Oct 23, 2024

• PNNL.DIA.utils

  Public
  **WORK IN PROGRESS** misc. functions for DIA proteomics data analysis and parsing to MSnSet objects

  R

  •

  Other

  •1•0•0•0•Updated Oct 22, 2024Oct 22, 2024

• DMS-Capture-Task-Manager

  Public
  DMS Capture Task Manager

  C#

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Oct 18, 2024Oct 18, 2024

• PRISM-Class-Library

  Public
  The PRISM Class Library is a collection of routines used by many of the software tools that support the Data Management System at PNNL.

  C#

  •2•2•0•0•Updated Oct 16, 2024Oct 16, 2024

• DBSchema_DMS

  Public
  PRISM Data Management System database schema

  TSQL

  •3•3•0•0•Updated Oct 12, 2024Oct 12, 2024

• DMS-Organism-Database-Handler

  Public
  Organism Database (FASTA file) programs, including PRISMSeq Uploader and the FastaFileMaker console application

  C#

  •1•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• Parameter-File-Editor

  Public
  DLL for retrieving parameter files from DMS

  Visual Basic .NET

  •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

• MS-File-Info-Scanner

  Public
  Examines a series of MS data files (or data directories) and extracts the acquisition start and end times, number of spectra, and the total size of the data. In addition, it can create 2D-plot graphics of the m/z values vs. time for QA purposes.

  mass-spectrometryms-spectrum

  C#

  •3•8•1•0•Updated Oct 1, 2024Oct 1, 2024

• VSProj-NuGet-Version-Updater

  Public
  Searches for Visual Studio project files (.csproj and.vsproj) that reference a specific NuGet package and updates the referenced version to a newer version if necessary.

  C#

  •0•0•0•0•Updated Sep 26, 2024Sep 26, 2024

• MASIC

  Public
  MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis, characterizing the peak(s) in each SIC, computing peak statistics including elution time of the peak apex, peak area, and peak signal/noise. It can also extract reporter ion abundances (e.g. iTRAQ or TMT).

  mass-spectrometryms-spectrum

  C#

  •4•15•3•0•Updated Sep 24, 2024Sep 24, 2024

• DMS-Space-Manager

  Public
  DMS Space Manager

  C#

  •0•0•0•0•Updated Sep 22, 2024Sep 22, 2024

• DataPackage-Archive-Manager

  Public
  DataPackage Archive Manager

  C#

  •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

• DeconTools

  Public
  Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.

  mass-spectrometryms-spectrum

  C#

  •4•17•1•0•Updated Sep 20, 2024Sep 20, 2024

• MyEMSL-Reader

  Public
  MyEMSL Reader

  C#

  •0•2•0•0•Updated Sep 20, 2024Sep 20, 2024

• AScore

  Public
  The AScore program can process first-hits or synopsis files from MS-GF+, SEQUEST, or X!Tandem to compute confidence scores for the position of phosphorylated residues.

  mass-spectrometry

  C#

  •1•3•0•0•Updated Sep 18, 2024Sep 18, 2024

• Interference-Detection

  Public
  Algorithm for quantifying the homogeneity of species isolated for fragmentation in LC-MS/MS analyses using data directed acquisition (DDA).

  mass-spectrometry

  C#

  •0•0•0•0•Updated Sep 18, 2024Sep 18, 2024

• Mage

  Public
  The Mage suite of tools provide access to DMS files and metadata.

  C#

  •0•0•0•0•Updated Sep 18, 2024Sep 18, 2024

• Cyclops

  Public
  The Cyclops library can be used to apply a workflow of data analysis steps to data stored in a SQLite database

  C#

  •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

• Buzzard

  Public
  Utility for manually and automatically adding datasets to DMS

  C#

  •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

• DMS-Update-Manager

  Public
  DMS Update Manager

  C#

  •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

• Package_Folder_Create_Manager

  Public
  Creates a new storage folder for newly created data packages

  C#

  •0•0•0•0•Updated Sep 14, 2024Sep 14, 2024

• Data-Import-Manager

  Public
  DataImportManager (DIM)

  C#

  •0•0•0•0•Updated Sep 14, 2024Sep 14, 2024

• DMS-Instrument-Directory-Scanner

  Public
  Instrument directory scanner

  C#

  •0•0•0•0•Updated Sep 14, 2024Sep 14, 2024

• Thermo-Raw-File-Reader

  Public
  .NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific

  mass-spectrometryms-spectrum

  C#

  •12•38•1•0•Updated Sep 9, 2024Sep 9, 2024

• UIMF-Library

  Public
  Used to create, modify and extract data from UIMF files, which are SQLite databases of mass spectrometry data acquired at Pacific Northwest National Laboratory (PNNL)

  C#

  •

  Other

  •4•1•0•0•Updated Sep 9, 2024Sep 9, 2024

• DLL-Version-Inspector

  Public
  This program inspects a .NET DLL or .Exe to determine the version. This allows a 32-bit .NET application to call this program via the command prompt to determine the version of a 64-bit DLL or Exe.

  C#

  •0•0•0•0•Updated Sep 8, 2024Sep 8, 2024