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.

GitHub

Several high-quality, well-maintained software packages developed by the lab are available under the MoseleyBioinformaticsLab 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

We put certain production-level R packages on BioConductor 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

nmrstarlib

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

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.

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.

SSNMR Assignment Software Suite (SASS)

Proof of concept software demonstrating automated protein resonance assignment of magic angle spinning solid-state protein NMR peaklists.

PyNAC

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.

Son of Bayesian Model Optimized Reference Correction (SoBaMORC)

Web service and software that performs chemical shift reference correction for unassigned NMR peak lists.
  • Link to web service coming soon.
  • Link to FigShare repo coming soon.
Topic revision: r24 - 20 Sep 2017, AndreySmelter
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