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You are here: Moseley Bioinformatics Lab>Main Web>SoftwareDevelopment (31 Aug 2022, TravisThompson)
Publicly Available Software and Related Published Results
Utilized Data and Code Sharing Repositories
FigShare
We use FigShare repositories to disseminate our complete published results in order to facilitate full reproducibility.
- 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.
GitHub
Several high-quality, well-maintained software packages developed by the lab are available under the MoseleyBioinformaticsLab organizational account on GitHub.
- These packages are well-documented and designed for high reusability by other computational scientists.
Python Package Index (PyPI )
We put certain production-level Python packages on PyPI to facilitate easy reusability by other scientists.
- PyPI makes packages much easier to install and reuse, allowing access to scientists with a wide range of computational competence.
BioConductor and CRAN
We put certain production-level R packages on BioConductor or CRAN to facilitate high and easier reusability by other computational scientists.
Lab HTTP/FTP
Older packages developed by the lab and/or published results are distributed from our lab http/ftp server in order to maintain results for scientific reproducibility.
- We are in the process of migrating some of these published results onto FigShare.
Software Projects
Most of our software projects are available on GitHub: https://github.com/MoseleyBioinformaticsLab Specific example projects are below.nmrstarlib
Python library for reading, writing, and accessing BMRB entries in NMR-STAR and JSONized NMR-STAR formats.
- 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
GOcats is an Open Biomedical Ontology (OBO) parser and categorizing utility, currently specialized for the Gene Ontology (GO), which can help scientists interpret large-scale experimental results by organizing redundant and highly- specific annotations into customizable, biologically-relevant concept categories.
Concept subgraphs are defined by lists of keywords created by the user.
Concept subgraphs are defined by lists of keywords created by the user.
mwtab
Python library for reading, writing, and accessing entries in
mwTab and JSONized mwTab formats from Metabolomics Workbench Data Repository. jpredapi
jpredapi is a Python library for submitting jobs to JPRED - A Protein Secondary Structure Prediction Server.
Data Visualization and Quality Control Library
Set of useful R functions for calculating various measures from data and visualizing them.
Bayesian Model Optimized Reference Correction (BaMORC )
Software package that performs chemical shift reference correction for unassigned NMR peak lists.
- 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
Academic Tracker was created to automate the process of making sure that federally funded publications get listed on PubMed and that the grant funding source for them is cited.
Minimum Information About Geospatial Information System (MIAGIS)
MIAGIS was created to help automate the process of creating a metadata file for GIS data depositions.
Older Software Projects (not on GitHub )
SSNMR Assignment Software Suite (SASS)
Proof of concept software demonstrating automated protein resonance assignment of magic angle spinning solid-state protein NMR peaklists.
- Related Publications:
PyNAC
High-throughput natural abundance correction software for stable isotope resolved metabolomics (SIRM) experiments
- 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).
Chemically Aware Substructure Search (CASS)
Software for building and searching functional group annotated metabolite databases.
- Related Publications:
Metal Ion Coordination Analysis Software
Software for analyzing metal ion coordination in PDB entries.
- 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
- Original tarball on FTP site - http://files.cesb.uky.edu/software/Metal/zinc_analysis_v2.tar.gz
- Tarball was updated Dec 15, 2015 to correct accidental revisions that did not reflect the results from the paper.
- 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
- Full results on FTP site - http://files.cesb.uky.edu/software/Metal/fiveMetalManuscript.tar.gz
- 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).
- 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).
- FTP Site
Topic revision: r30 - 31 Aug 2022, TravisThompson
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