@PNNL-Comp-Mass-Spec

Computational Mass Spectrometry @ Pacific Northwest National Laboratory

  • DMS Capture Task Manager

    C# BSD-2-Clause Updated Sep 22, 2018
  • DMS Analysis Tool Manager

    C# BSD-2-Clause Updated Sep 22, 2018
  • PRISM Data Management System database schema

    SQLPL 1 2 Updated Sep 22, 2018
  • Tool to merge split-fasta MS-GF+ search result mzids.

    C# Updated Sep 22, 2018
  • Merges the contents of a tab-delimited text file with peptide search results (e.g. from X!Tandem or MSGF+) with the corresponding MASIC results files, appending the relevant MASIC stats for each PSM. Also supports reporter ion abundances.

    Visual Basic Updated Sep 22, 2018
  • Used to de-isotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.

    C# 7 2 Updated Sep 22, 2018
  • The AScore program can process first-hits or synopsis files from MSGF+, SEQUEST, or X!Tandem to compute confidence scores for the position of phosphorylated residues.

    C# Updated Sep 22, 2018
  • DMS Update Manager

    C# Updated Sep 22, 2018
  • MyEMSL Reader

    C# 1 Updated Sep 21, 2018
  • MTS manager for retrieving files from MyEMSL

    C# 1 Updated Sep 21, 2018
  • Creates a new storage folder for newly created data packages

    C# Updated Sep 22, 2018
  • 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# Updated Sep 22, 2018
  • DMS Space Manager

    C# Updated Sep 22, 2018
  • Utility for generating plots of the mass measurement errors before and after processing with mzRefinery

    C# Updated Sep 22, 2018
  • Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.

    C# 1 Updated Sep 22, 2018
  • The Mage suite of tools provide access to DMS files and metadata.

    C# Updated Sep 22, 2018
  • all the materials for the publication about the Kaiko

    Jupyter Notebook Updated Sep 21, 2018
  • Instrument directory scanner

    C# Updated Sep 21, 2018
  • Reads manager status messages from an ActiveMQ server and push them into the DMS database.

    C# Updated Sep 21, 2018
  • DataPackage Archive Manager

    C# Updated Sep 21, 2018
  • DataImportManager (DIM)

    C# Updated Sep 21, 2018
  • deep learning-based de novo peptide sequencing tool

    Python Updated Sep 21, 2018
  • Exports Sql Server database objects as schema files. Exported objects include tables, views, stored procedures, and functions,plus also database properties including database roles and logins. The program can also export table data to create SQL files with an Insert Into statement for each row.

    Visual Basic 1 1 BSD-2-Clause Updated Sep 21, 2018
  • The CPULoadTester can be used to simulate varying levels of load on a computer, by estimating the value of Pi, using either a single thread or multiple threads.

    C# Updated Sep 21, 2018
  • DMS Program Runner Service

    C# Updated Sep 21, 2018
  • Organism Database (FASTA file) programs, including PRISMSeq Uploader and the FastaFileMaker console application

    Visual Basic 1 Updated Sep 21, 2018
  • DMS EMail Manager

    C# Updated Sep 21, 2018
  • The Protein Coverage Summarizer can be used to determine the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

    Visual Basic 1 BSD-2-Clause Updated Sep 21, 2018
  • The Peptide Hit Results Processor can be used to convert an X!Tandem results file (XML format), MSGF+ .tsv results file, or SEQUEST synopsis file (or first hits file) to a series of tab-delimited text files summarizing the results.

    C# Updated Sep 21, 2018
  • The File Comparison Sampler console application compares two or more files to check whether the start of the files match, the end of the files match, and selected sections inside the files also match. It is useful for comparing large files without reading the entire file. It also supports comparison of files in two directories.

    C# 1 Updated Sep 21, 2018