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BioNetFit is a software tool designed for solving parameter identification problems that arise in the development of rule-based models. It solves these problems through curve fitting (i.e., nonlinear regression). BioNetFit is compatible…
GAMMA_FLOW is an open-source Python package for real-time analysis of spectral data. It supports classification, denoising, decomposition, and outlier detection of both single- and multi-component spectra. Instead of relying on large,…
Binospec is a high-throughput, 370 to 1000 nm, imaging spectrograph that addresses two adjacent 8' by 15' fields of view. Binospec was commissioned in late 2017 at the f/5 focus of the 6.5m MMT and is now available to all MMT observers.…
One of the decisions that arise when designing a neural network for any application is how the data should be represented in order to be presented to, and possibly generated by, a neural network. For audio, the choice is less obvious than…
High-resolution solar spectroscopy provides a wealth of information from photospheric and chromospheric spectral lines. However, the volume of data easily exceeds hundreds of millions of spectra on a single observation day. Therefore,…
ESPSim is an open source JAVA program that enables the comparisons of protein electrostatic potential maps via the computation of an electrostatic similarity measure. This program has been utilized to demonstrate a high degree of…
We describe a computer application designed to analyze hyperspectral data collected by the Compact Infrared Spectrometer for Mars (CRISM). The application links the spectral, imaging and mapping perspectives on the eventual CRISM dataset by…
Power-spectrum analysis is an important tool providing critical information about a signal. The range of applications includes communication-systems to DNA-sequencing. If there is interference present on a transmitted signal, it could be…
With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
The software approach to developing Digital Signal Processing (DSP) applications brings some great features such as flexibility, re-usability of resources and easy upgrading of applications. However, it requires long and tedious tests and…
We present here the tool "Virtual Spectro", a post-processor for spectroscopics analysis of hydrodynamic codes. We describe purpose and method of this tool, and the first application to analysis of high energy laser driven radiative shocks.
Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since,…
AtomAI is an open-source software package bridging instrument-specific Python libraries, deep learning, and simulation tools into a single ecosystem. AtomAI allows direct applications of the deep convolutional neural networks for atomic and…
BioSig is an open source software library for biomedical signal processing. Most users in the field are using Matlab; however, significant effort was undertaken to provide compatibility to Octave, too. This effort has been widely…
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…
Artificial intelligence (AI) tools are gaining more and more ground each year in bioinformatics. Learning algorithms can be taught easily by using the existing enormous biological databases, and the resulting models can be used for the…
In modern-day astronomy, near-infrared, optical, and ultraviolet spectroscopy are indispensable for studying a wide range of phenomena, from measuring black hole masses to analyzing chemical abundances in stellar atmospheres. However,…
The Triander program is an interactive software package for nucleotide sequence visualization. The program was developed using the freeware Pascal RAD IDE Lazarus, and its source code and binaries compiled for Windows are freely accessible…
ECGSYN, a dynamical model that faithfully reproduces the main features of the human electrocardiogram (ECG), including heart rate variability, RR intervals and QT intervals is presented. Details of the underlying algorithm and an…