Related papers: Mass spectrometry analysis using MALDIquant
Inspection of tissues using a light microscope is the primary method of diagnosing many diseases, notably cancer. Highly multiplexed tissue imaging builds on this foundation, enabling the collection of up to 60 channels of molecular…
In this paper we explore the challenges of automating experiments in data science. We propose an extensible experiment model as a foundation for integration of different open source tools for running research experiments. We implement our…
Cancer pathology is unique to a given individual, and developing personalized diagnostic and treatment protocols are a primary concern. Mathematical modeling and simulation is a promising approach to personalized cancer medicine. Yet, the…
Mass spectrometry (MS) is used widely in biomolecular structural analysis and is particularly dominant in the study of proteins. Despite its considerable power, state-of-the-art protein MS frequently suffers from limited reliability of…
This article presents a high-throughput computer program, called EasyDD, for batch processing, analyzing and visualizing of spectral data; particularly those related to the new generation of synchrotron detectors and X-ray powder…
Mammographic mass detection and segmentation are usually performed as serial and separate tasks, with segmentation often only performed on manually confirmed true positive detections in previous studies. We propose a fully-integrated…
Markov random fields on two-dimensional lattices are behind many image analysis methodologies. mrf2d provides tools for statistical inference on a class of discrete stationary Markov random field models with pairwise interaction, which…
MATI (Microstructural Analysis Toolbox for Imaging) is a versatile MATLAB-based toolbox that combines both simulation and data fitting capabilities for microstructural dMRI research. It provides a user-friendly, GUI-driven interface that…
We introduce a data reduction package written in Interactive Data Language (IDL) for the Magellan Echellete Spectrograph (MAGE). MAGE is a medium-resolution (R ~4100), cross-dispersed, optical spectrograph, with coverage from ~3000-10000…
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…
Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and…
Mass Spectrometry (MS) is a largely used analytical technique in biology with applications such as the determination of molecule masses or the elucidation of structural data. Fourier Transform Ion Cyclotron Resonance MS is one…
Computational modeling of cancer can help unveil dynamics and interactions that are hard to replicate experimentally. Thanks to the advancement in cancer databases and data analysis technologies, these models have become more robust than…
MeerKATHI is the current development name for a radio-interferometric data reduction pipeline, assembled by an international collaboration. We create a publicly available end-to-end continuum- and line imaging pipeline for MeerKAT and other…
DL_MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation.…
This work presents a guide for the use of some of the functions of the R package "multiColl" for the detection of near multicollinearity. The main contribution, in comparison to other existing packages in R or other econometric software, is…
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including…
\pkg{multiplex} is a computer program that provides algebraic tools for the analysis of multiple network structures within the \proglang{R} environment. Apart from the possibility to create and manipulate multivariate data representing…
Motivated by modeling and analysis of mass-spectrometry data, a semi- and nonparametric model is proposed that consists of a linear parametric component for individual location and scale and a nonparametric regression function for the…
Technology aided platforms provide reliable tools in almost every field these days. These tools being supported by computational power are significant for applications that need sensitive and precise data analysis. One such important…