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Publicly Available Software and Related Published Results

Utilized Data and Code Sharing Repositories


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.


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.


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:

Specific example projects are below.


Python library for reading, writing, and accessing BMRB entries in NMR-STAR and JSONized NMR-STAR formats.


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.


Python library for reading, writing, and accessing entries in mwTab and JSONized mwTab formats from Metabolomics Workbench Data Repository.


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.

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.


High-throughput natural abundance correction software for stable isotope resolved metabolomics (SIRM) experiments

Chemically Aware Substructure Search (CASS)

Software for building and searching functional group annotated metabolite databases.

Metal Ion Coordination Analysis Software

Software for analyzing metal ion coordination in PDB entries.
Topic revision: r30 - 31 Aug 2022, TravisThompson
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