Publicly Available Software and Related Published Results

Utilized Data and Code Sharing Repositories

GitHub

• These packages are well-documented and designed for high reusability by other computational scientists.

Python Package Index (PyPI)

• PyPI makes packages much easier to install and reuse, allowing access to scientists with a wide range of computational competence.

BioConductor and CRAN

FigShare

• FigShare has integration with GitHub; however, we typically create a FigShare repository that includes both results and the code used to generate the results in a manner organized to facilitate scientific reproducibility.

Software Projects

nmrstarlib

• Repo on GitHub
• Package on PyPI
• Documentation on ReadTheDocs
• Related Publications:
  • Andrey Smelter, Morgan Astra, Hunter N.B. Moseley. "A Fast and Efficient Python Library for Interfacing with the Biological Magnetic Resonance Data Bank" BMC Bioinformatics 18, 175 (2017).
  • Andrey Smelter, Eric C. Rouchka, and Hunter N.B. Moseley. "Detecting and accounting for multiple sources of positional variance in peak list registration analysis and spin system grouping" J Biomol NMR DOI 10.1007/s10858-017-0126-5 (2017).
    • ssc software - https://doi.org/10.6084/m9.figshare.4814605
    • ssc documentation - https://doi.org/10.6084/m9.figshare.4816441
    • experimental peak lists - https://doi.org/10.6084/m9.figshare.4815163
    • simulated peak lists - https://doi.org/10.6084/m9.figshare.5260660
    • results of grouping algorithm - https://doi.org/10.6084/m9.figshare.4815160

GOcats

• Repo on GitHub
• Package on PyPI
• Documentation on ReadTheDocs

mwtab

• Repo on GitHub
• Package on PyPI
• Documentation on ReadTheDocs

jpredapi

• Repo on GitHub
• Package on PyPI
• Documentation on ReadTheDocs

Data Visualization and Quality Control Library

• Repo on GitHub

Bayesian Model Optimized Reference Correction (BaMORC)

• Xi Chen, Andrey Smelter, and Hunter N.B. Moseley. "Automatic 13C Chemical Shift Reference Correction for Unassigned Protein NMR Spectra" J Biomol NMR 72,11 (2018)
• Repo on GitHub
• Repo on CRAN
• FigShare repo

Academic Tracker

• Repo on GitHub
• Package on PyPI
• Documentation on GitHub

Minimum Information About Geospatial Information System (MIAGIS)

• Repo on GitHub
• Package on PyPI
• Documentation on GitHub

Older Software Projects (not on GitHub)

SSNMR Assignment Software Suite (SASS)

• Related Publications:
  • Hunter N.B. Moseley, Lindsay J. Sperling, and Chad M. Rienstra. "Automated Protein Resonance Assignments of Magic Angle Spinning Solid-State NMR Spectra of β1 Immunoglobulin Binding Domain of Protein G (GB1)" J Biomol NMR 48, 123-128 (2010).
    • https://doi.org/10.6084/m9.figshare.31808020

PyNAC

• Related Publications:
  • Hunter N.B. Moseley. "Correcting for the Effects of Natural Abundance in Stable Isotope Resolved Metabolomics Experiments Involving Ultra-High Resolution Mass Spectrometry." BMC Bioinformatics 11, 139-144 (2010).
  • William J. Carreer, Robert M. Flight, and Hunter N.B. Moseley. "A computational framework for high-throughput isotopic natural abundance correction of omics-level ultra-high resolution FT-MS datasets" Metabolites, 3, 853-866 (2013).
    • https://doi.org/10.6084/m9.figshare.31807723

Chemically Aware Substructure Search (CASS)

• Related Publications:
  • Joshua M. Mitchell, Teresa, W-M. Fan, Andrew N. Lane, Hunter N.B. Moseley. "Development and In silico Evaluation of Large-Scale Metabolite Identification Methods using Functional Group Detection for Metabolomics" Frontiers in Genetics - Systems Biology 5, 237 (2014).
    • https://doi.org/10.6084/m9.figshare.31807993

Metal Ion Coordination Analysis Software

• Related Publications:
  • Sen Yao, Robert M. Flight, Eric C. Rouchka, and Hunter N.B. Moseley. "A less biased analysis of metalloproteins reveals novel zinc coordination geometries" Proteins: Structure, Function, and Bioinformatics 83, 1470 (2015).
    • Full results on FigShare - https://dx.doi.org/10.6084/m9.figshare.4229333
  • Sen Yao, Robert M. Flight, Eric C. Rouchka, Hunter N.B. Moseley. "Aberrant coordination geometries discovered in the most abundant metalloproteins" Proteins: Structure, Function, and Bioinformatics 85, 885 (2017).
    • Full results on FigShare - https://doi.org/10.6084/m9.figshare.4229297
  • Sen Yao, Robert M. Flight, Eric C. Rouchka, Hunter N.B. Moseley. "Perspectives and Expectations in Structural Bioinformatics of Metalloproteins" Proteins: Structure, Function, and Bioinformatics 85, 938 (2017).