Find open-source science resources

The MRS4Brain Toolbox is an open-source, MATLAB-based platform for analyzing preclinical MR spectroscopic imaging data (proton and deuterium). It provides integrated workflows for preprocessing, quantification, and metabolic map analysis using a GUI.

Extending the AtomDB Atomic Database to Model New Plasma Processes and Uncertainties. This code is designed to interact with the AtomDB database. It is in active development but is now approaching feature complete for creating spectra and interacting with fitting codes like XSPEC and Sherpa.

MultiNMRFit is an open-source software designed for high-throughput analysis of one-dimensional NMR spectra, offering flexibility and reproducible results through fitting experimental spectra using built-in or user-defined signal models. It's accessible as a Python library and via a graphical user interface, supporting both novice and experienced users.

MRspecLAB is an open-access, user-friendly software platform for MRS and MRSI data analysis designed to bridge the gap between technical experts and practitioners. It provides a graphical pipeline editor for both predefined and customizable workflows, facilitating data processing and analysis.

Analysis Tool for Multi-Process, Multi-State Single-Molecule Data. KERA (Kinetic Event Resolving Algorithm) is a tool for analyzing data which consists of time-series of data at discrete states.

An end-to-end spectroscopy analysis package for FMRI, MRI and DTI brain imaging data.

DEER-PREdict is a package for double electron-electron resonance (DEER) and paramagnetic relaxation enhancement (PRE) predictions from molecular dynamics ensembles.

Prediction of Secondary Structure from Backbone Chemical Shifts and Sequence. Uses Bidirectional Long Short Term Memory and NMR Chemical Shifts.

ChiraKit is an online, open-source tool for analyzing circular dichroism (CD) spectroscopy data. It provides functionality for calculating protein secondary structure, estimating peptide helicity, fitting unfolding models, and decomposing spectra.

A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data. Open Chemometrics Toolkit for Analysis and Visualization of Vibrational Spectroscopy data. OCTAVVS: Open Chemometrics Toolbox for Analysis and Visualization of Vibrational Spectroscopy data. OCTAVVS is a set of graphical tools for high-throughput preprocessing and analysis of vibrational spectroscopy data. Currently, the preprocessing is primarily geared towards images from infrared absorption spectroscopy with focal plane array detectors

CheSPI (Chemical shift Secondary structure Population Inference) is a tool for a simple and efficient method that provides unbiased and sensitive aggregate measures of local structure and disorder.

Robust Moiety Model Selection Using Mass Spectrometry Measured Isotopologues.

Efficient Ensemble Refinement by Reweighting. BioEn - Bayesian Inference Of ENsembles. BioEn integrates a broad range of experimental data to refine ensembles of structures. For a detailed description of the procedures and the algorithm, we refer to [Hummer2015]

De Novo Molecule Identification from NMR Spectra. Molecule identification from NMR spectrum using de novo molecule generator. This code is for reference only as it requires MPI and Gaussian environment which is hard to ensure among different clusters. Also, for the NMR spectrum prediction part, we have used a Gaussain encapsulation package which we can not make public for now. Replacing this part by a traditional Gaussian code or other NMR spectrum prediction method would solve the problem.