22 papers · ranked by Valyu relevance
Matthew J. K. Vince, Kristin A. Hughes, Anastasiya Buzuk, Deborah L. Perlstein + 2 more
Machine learning (ML) is rapidly gaining traction in many areas of experimental molecular science for elucidating relationships and patterns in large or complex data sets. Historically, ML was largely the preserve of those with specialized training in fields such as statistics or cheminformatics. Increasingly, however…
Theodore J. Perkins
The Matlab programming language is widely used for both teaching and research in engineering, computer science, and mathematics. Despite its many strengths, it has never been a dominant language in computational genomics or bioinformatics more generally. Here, we introduce COGEM, a long-term project to develop…
James J Cai, David K Smith, Xuhua Xia, Kwok-yung Yuen
Background MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and…
Samuel Okyere, Joseph Ackora-Prah, Ebenezer Bonyah, Samuel Akwasi Adarkwa
'Samuel Akwasi Adarkwa'] Background: This paper presents a newly developed Matlab code for the numerical simulation of compartmental/deterministic models. It addresses modeling and simulation issues concerning compartmental models. The code is easy to understand and edit for the simulation of compartmental models. An…
Alberto Gómez
This paper presents a Matlab toolbox to perform basic image processing and visualization tasks, particularly designed for medical image processing. The functionalities available are similar to basic functions found in other non-Matlab widely used libraries such as the Insight Toolkit (ITK). The toolbox is entirely…
Harold F. Gómez, Michael Hucka, Sarah M. Keating, German Nudelman + 2 more
'Dagmar Iber' 'Stuart C. Sealfon'] Summary: MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can…
Ayesha Gauhar, Adnan Rashid, Osman Hasan, João Bispo + 2 more
MATLAB is a software based analysis environment that supports a high-level programing language and is widely used to model and analyze systems in various domains of engineering and sciences. Traditionally, the analysis of MATLAB models is done using simulation and debugging/testing frameworks. These methods provide…
Bernard C. Wang, Anthony M. Norcia, Blair Kaneshiro
MatClassRSA is a Matlab toolbox that performs M/EEG classification and produces various visualizations of the resulting confusion matrices. This toolbox is aimed toward cognitive neuroscience researchers who wish to apply classification-style analyses to repeated trials of data. The functionalities of the toolbox fall…
Zaid Abdi Alkareem Alyasseri
— Matlab is one of the most widely used mathematical computing environments in technical computing. It has an interactive environment which provides high performance computing (HPC) procedures and easy to use. Parallel computing with Matlab has been an interested area for scientists of parallel computing researches for…
Stewart Heitmann, Matthew Aburn, Michael Breakspear
The Brain Dynamics Toolbox provides a graphical tool for simulating user-defined dynamical systems in matlab. It supports three classes of differential equations commonly used in computational neuroscience: Ordinary Differential Equations, Delay Differential Equations and Stochastic Differential Equations. The design…
Vardan Andriasyan, Yauhen Yakimovich, Artur Yakimovich
Scientific legacy code in MATLAB/Octave not compatible with modernization of research workflows is vastly abundant throughout academic community. Performance of non-vectorized code written in MATLAB/Octave represents a major burden. A new programming language for technical computing Julia, promises to address these…
Ilija Dukovski, Djordje Bajić, Jeremy M. Chacón, Michael Quintin + 9 more
'Jean C. C. Vila' 'Snorre Sulheim' 'Alan R. Pacheco' 'David B. Bernstein' 'William J Rieh' 'Kirill S. Korolev' 'Álvaro Sánchez' 'William R. Harcombe' 'Daniel Segrè'] - 2 Biological Design Center, Boston University, Boston, MA, USA - 3 Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA - 4…
Tomasz Markiewicz
Background The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks…
Mohammad Mahdi Moayeri, Mohammad Hemami, Jamal Amani Rad, Kourosh Parand
The study of synchronous or asynchronous in (stochastic) neuronal populations is an important concept both in theory and in practice in neuroscience. The NPDS toolbox provides an interactive simulation platform for exploring such processes in Matlab looking through the lens of nonlinear dynamical systems. NPDS includes…
Bruno Iannazzo, Mehdi Najafi Kalyani, Federico Poloni
We introduce the mmatrix toolbox, a Matlab software package for componentwise accurate computations with M-matrices described through left or right triplet representations. The core of the toolbox is a Fortran implementation, in the Lapack style, of the unblocked, recursive, and blocked versions of the GTH algorithm…
Authors not listed
This paper presents the Multi Cell-line Kinetic Model (MCKM), a novel generalised kinetic mechanistic model specifically tailored for Ambr15™ fed-batch cultivations of multiple Chinese Hamster Ovary (CHO) cell lines producing different recombinant monoclonal antibodies (mAbs). Unlike traditional models that requires…
Alan Veliz-Cuba, Stephen Randal Voss, David Murrugarra
A primary challenge in building predictive models from temporal data is selecting the appropriate network and the regulatory functions that describe the data. Software packages are available for equation learning of continuous models, but not for discrete models. In this paper we introduce a method for building model…
Bryan Wong, Cameron Chevalier
We present an open-source software package, HADOKEN (High-level Algorithms to Design, Optimize, and Keep Electrons in Nanowires), for predicting electron confinement/localization effects in nanowires with various geometries, arbitrary number of concentric shell layers, doping densities, and external boundary…
MARCO TODISCO
Determining the distribution of multiple chemical species at equilibrium for a given system is a common problem that must be routinely addressed by scholars. While simple systems consisting of a few species and reactions can be solved manually, most of these problems require the definition and solution of higher-order…
harry gray
The matrix exponential method as implemented in MATLAB is demonstrated as a facile tool for solving the time-dependent concentrations of an arbitrary chemically reactive network modelled as a coupled linear system of first-order differential equations. The method is used to verify a 10 species network incorporating…
Anzhi Zhang, Massimiliano Fasi
TypedMatrices.jl is a Julia package to organize test matrices. By default, the package comes with a number of built-in matrices and interfaces to help users select test cases based on their properties. The package is designed to be extensible, allowing users to define their own matrix types. We discuss the design and…
Authors not listed
As a prove of concept for experimental geochemistry, an advanced 3D numerical framework, here and after called Digital Twin (DT), of a diffusion experiment conducted at a synchrotron beamline, has been implemented using in-situ measurements data, physics-based modelling, a machine learning (ML) model, and parameter…