12 papers · ranked by Valyu relevance
Daniel Castaño-Díez
A technical description of the Dynamo software package for subtomogram averaging is provided. Details are given on advanced MATLAB libraries, parallelization strategies, the use of GPUs and accessibility though the Amazon cloud computing services.
Yuliya V Karpievitch, Jonas S Almeida
Background Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed…
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…
Jason S. Sherfey, Austin E. Soplata, Salva Ardid, Erik A. Roberts + 3 more
'David A. Stanley' 'Benjamin R. Pittman-Polletta' 'Nancy J. Kopell'] DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or…
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…
Ruijie Ren, Xiang-e Sun, Lin Hu
Currently, using MATLAB Web App Server to deploy MATLAB Web applications for hosting and sharing interactive Web applications involves the following problems: slow loading of applications, incompatibility with some browser versions, and various shortcomings of deployment tools, such as poor scalability and difficulty…
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…
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…
Matthew J. Wade, Jordan Oakley, Sophie Harbisher, Nicholas G. Parker + 2 more
'Jan Dolfing' 'Jérémie Bourdon'] Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates…
Matthew B. Biggs, Jason A. Papin, Michael Hensel
Multiscale modeling is used to represent biological systems with increasing frequency and success. Multiscale models are often hybrids of different modeling frameworks and programming languages. We present the MATLAB-NetLogo extension (MatNet) as a novel tool for multiscale modeling. We demonstrate the utility of the…
Chen Zhao, Aleksander S. Popel
Title: Summary The ability to measure and analyze the complex dynamic multi-marker features of macrophages is critical for the understanding of their diverse phenotypes and functions in health and disease. To that end, we have recently developed a multi-pathway computational model that for the first time enables a…