Related papers: Biospectrogram: a tool for spectral analysis of bi…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
Hyperspectral imaging is useful for applications ranging from medical diagnostics to agricultural crop monitoring; however, traditional scanning hyperspectral imagers are prohibitively slow and expensive for widespread adoption. Snapshot…
SMART is a software package written in IDL to reduce and analyze Spitzer data from all four modules of the Infrared Spectrograph, including the peak-up arrays. The software is designed to make full use of the ancillary files generated in…
Spectral line observations encode a wealth of information. A key challenge, therefore, lies in the interpretation of these observations in terms of models to derive the physical and chemical properties of the astronomical environments from…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
This paper presents NEUROSPF, a tool for the symbolic analysis of neural networks. Given a trained neural network model, the tool extracts the architecture and model parameters and translates them into a Java representation that is amenable…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
GPTIPS is a free, open source MATLAB based software platform for symbolic data mining (SDM). It uses a multigene variant of the biologically inspired machine learning method of genetic programming (MGGP) as the engine that drives the…
Satellite imagery allows a plethora of applications ranging from weather forecasting to land surveying. The rapid development of computer vision systems could open new horizons to the utilization of satellite data due to the abundance of…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
This manuscript describes the software package SCOUT, which analyzes, characterizes, and corrects one-dimensional signals. Specifically, it allows to check and correct for stationarity, detect spurious samples, check for normality, check…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
We present PlanetPack, a new software tool that we developed to facilitate and standardize the advanced analysis of radial velocity (RV) data for the goal of exoplanets detection, characterization, and basic dynamical $N$-body simulations.…
Feature selection is a pattern recognition approach to choose important variables according to some criteria to distinguish or explain certain phenomena. There are many genomic and proteomic applications which rely on feature selection to…
Live time-lapse microscopy is essential for a wide range of biological applications. Software-based automation is the gold standard for the operation of hardware accessories necessary for image acquisition. Given that current software…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
Two-dimensional (2D) materials have attracted extensive attention due to their unique characteristics and application potentials. Raman spectroscopy, as a rapid and non-destructive probe, exhibits distinct features and holds notable…
In this paper, we present a nonlinear analysis software toolkit, which can help in biomechanical gait data analysis by implementing various nonlinear statistical analysis algorithms. The toolkit is proposed to tackle the need for an…
First-principles computational spectroscopy is a critical tool for interpreting experiment, performing structure refinement, and developing new physical understanding. Systematically setting up input files for different simulation codes and…