Related papers: Biospectrogram: a tool for spectral analysis of bi…
Providing high-quality electron images and hyperspectral X-ray maps is a focus of many modern electron microscopy laboratories. Nevertheless, further image processing and annotations are often needed to prepare them for publications and…
Spectrograph is an optical device that is used to disperse photons of different energies $E$ into distinct directions and space locations, and to take a snapshot of the whole spectrum of photon energies with a spatially sensitive photon…
LineStacker is a new open access and open source tool for stacking of spectral lines in interferometric data. LineStacker is an ensemble of CASA tasks, and can stack both 3D cubes or already extracted spectra. The algorithm is tested on…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
Machine learning is an important tool for analyzing high-dimension hyperspectral data; however, existing software solutions are either closed-source or inextensible research products. In this paper, we present cuvis.ai, an open-source and…
Addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological…
Shotgun proteomics is a high-throughput technology used to identify unknown proteins in a complex mixture. At the heart of this process is a prediction task, the spectrum identification problem, in which each fragmentation spectrum produced…
Biological neural networks are often modeled as systems of coupled, nonlinear, ordinary or partial differential equations. The number of differential equations used to model a network increases with the size of the network and the level of…
We describe v02 of igmspec, a database of publically available ultraviolet, optical, and near-infrared spectra that probe the intergalactic medium (IGM). This database, a child of the specdb repository in the specdb github organization,…
Major advancements in fields as diverse as biology and quantum computing have relied on a multitude of microscopic techniques. All optical, electron and scanning probe microscopy advanced with new detector technologies and integration of…
RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like…
The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle…
We introduce HAMscope, a compact, snapshot hyperspectral autofluorescence miniscope that enables real-time, label-free molecular imaging in a wide range of biological systems. By integrating a thin polymer diffuser into a widefield…
Background: Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Life science is entering a new era of petabyte-level sequencing data. Converting such big data to biological insights represents a huge challenge for computational analysis. To this end, we developed DeepMetabolism, a biology-guided deep…
BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these…
Many materials have distinct spectral profiles. This facilitates estimation of the material composition of a scene at each pixel by first acquiring its hyperspectral image, and subsequently filtering it using a bank of spectral profiles.…
DNA origami is an interdisciplinary area where DNA can be used as a building block for making useful stuff at nanoscale. This work presents an open source software DNA pen (based on the recent work of Peng Yin and his group) which can be…
We introduce a Genetic Algorithm (GA) based, open-source project to solve multi-objective optimization problems of materials characterization data analysis including EXAFS, XPS and nanoindentation. The modular design and multiple crossover…