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    • PRISM Data Management System PostgreSQL database schema
      PLpgSQL
      0300Updated Oct 30, 2024Oct 30, 2024
    • DMS Website
      PHP
      0101Updated Oct 29, 2024Oct 29, 2024
    • Collection of lessons from IO group's data analysis workshops (i.e. TheRa.py Sessions)
      TeX
      1000Updated 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.
      C#
      0000Updated Oct 23, 2024Oct 23, 2024
    • DMS Analysis Tool Manager
      C#
      BSD 2-Clause "Simplified" License
      0300Updated Oct 23, 2024Oct 23, 2024
    • **WORK IN PROGRESS** misc. functions for DIA proteomics data analysis and parsing to MSnSet objects
      R
      Other
      1000Updated Oct 22, 2024Oct 22, 2024
    • DMS Capture Task Manager
      C#
      BSD 2-Clause "Simplified" License
      0100Updated Oct 18, 2024Oct 18, 2024
    • 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#
      2200Updated Oct 16, 2024Oct 16, 2024
    • PRISM Data Management System database schema
      TSQL
      3300Updated Oct 12, 2024Oct 12, 2024
    • Organism Database (FASTA file) programs, including PRISMSeq Uploader and the FastaFileMaker console application
      C#
      1000Updated Oct 7, 2024Oct 7, 2024
    • DLL for retrieving parameter files from DMS
      Visual Basic .NET
      0000Updated Oct 2, 2024Oct 2, 2024
    • 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.
      C#
      3810Updated Oct 1, 2024Oct 1, 2024
    • 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#
      0000Updated 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).
      C#
      41530Updated Sep 24, 2024Sep 24, 2024
    • DMS Space Manager
      C#
      0000Updated Sep 22, 2024Sep 22, 2024
    • DataPackage Archive Manager
      C#
      0000Updated Sep 20, 2024Sep 20, 2024
    • Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.
      C#
      41710Updated Sep 20, 2024Sep 20, 2024
    • MyEMSL Reader
      C#
      0200Updated 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.
      C#
      1300Updated Sep 18, 2024Sep 18, 2024
    • Algorithm for quantifying the homogeneity of species isolated for fragmentation in LC-MS/MS analyses using data directed acquisition (DDA).
      C#
      0000Updated Sep 18, 2024Sep 18, 2024
    • Mage

      Public
      The Mage suite of tools provide access to DMS files and metadata.
      C#
      0000Updated 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#
      0000Updated Sep 17, 2024Sep 17, 2024
    • Buzzard

      Public
      Utility for manually and automatically adding datasets to DMS
      C#
      0000Updated Sep 16, 2024Sep 16, 2024
    • DMS Update Manager
      C#
      0000Updated Sep 16, 2024Sep 16, 2024
    • Creates a new storage folder for newly created data packages
      C#
      0000Updated Sep 14, 2024Sep 14, 2024
    • DataImportManager (DIM)
      C#
      0000Updated Sep 14, 2024Sep 14, 2024
    • Instrument directory scanner
      C#
      0000Updated Sep 14, 2024Sep 14, 2024
    • .NET DLL wrapper for reading Thermo .Raw files. Uses ThermoFisher.CommonCore NuGet packages provided by Thermo Fisher Scientific
      C#
      123810Updated Sep 9, 2024Sep 9, 2024
    • 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
      4100Updated Sep 9, 2024Sep 9, 2024
    • 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#
      0000Updated Sep 8, 2024Sep 8, 2024