Grow your team on GitHub
GitHub is home to over 28 million developers working together. Join them to grow your own development teams, manage permissions, and collaborate on projects.Sign up
PRISM Data Management System database schema
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.
DMS Analysis Tool Manager
DMS Capture Task Manager
The FASTA File Splitter program can be used to split apart a protein FASTA file into a number of sections. Although the splitting is random, each section will have a nearly identical number of residues.
The PRISM Class Library is a collection of routines used by many of the software tools that support the Data Management System at PNNL.
DataPackage Archive Manager
Converts an mzIdentML created by MS-GF+ to a tab-delimited text file.
Utility for generating plots of the mass measurement errors before and after processing with mzRefinery
Tool to merge split-fasta MS-GF+ search result mzids.
C# reader/writer for mzIdentML files (.mzID). Also supports reading mzML files.
This program pings computers on Bionet to see which respond. It then optionally contacts DMS with the list of active hosts.
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.
Instrument directory scanner
DMS EMail Manager
MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis. The SICs are generated using the LC-MS data, then each SIC is processed using a peak finding algorithm to characterize the chromatographic peaks, providing peak statistics including elution time of the peak apex, peak ar…
The Cyclops library can be used to apply a workflow of data analysis steps to data stored in a SQLite database
The Mage suite of tools provide access to DMS files and metadata.
Algorithm for quantifying the homogeneity of species isolated for fragmentation in LC-MS/MS analyses using data directed acquisition (DDA).
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.
Parses a FASTA file (with protein name and sequence information) to check for valid text. Also returns protein and residue stats.
Class for reading Protein files, specifically .fasta files and certain tab-delimited formats
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.
.NET DLL wrapper for Thermo's MS File Reader, which is accessible by creating an account at https://thermo.flexnetoperations.com/control/thmo/login then logging in and choosing "Utility Software"
Program that implements a protein parsimony algorithm for grouping proteins with similar peptides.
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.
DMS Update Manager
The MS File Info Scanner can be used to scan a series of MS data files (or data folders) and extract 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.
LCMSNet software for instrument control
Most used topics