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Processes
Special Issues
Next-Generation Methods and Simulation Tools for Systems Biology
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Next-Generation Methods and Simulation Tools for Systems Biology

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Processes and Systems".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 4344

Special Issue Editor

Dr. Akira Funahashi

E-Mail Website
Guest Editor
Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi Kouhoku-ku, Yokohama 223-8522, Japan
Interests: systems biology; quantitative biology; computational biology; mathematical modeling; machine learning; parallel processing

Special Issue Information

Dear Colleagues,

Ever since Isaac Newton compiled the laws of motion, mathematical modeling and model-based simulations have always facilitated our understanding of natural phenomena. This concept has also been applied to biology, creating a field called Systems Biology. Advances in data collection techniques such as next-generation sequencers and high-throughput imaging with microscopy have enabled advanced modeling in biology, i.e., spatial modeling and whole-cell modeling. Currently, new simulation and analysis methods for such models need to be proposed in order to reach deeper insights into natural phenomena. 

This Special Issue focuses on various methods (i.e., large-scale modeling, spatial modeling, image processing, and deep learning) to provide both fundamental and applied analytical methods and simulation tools to extract critical information from large amounts of data in the field of Systems Biology.

Dr. Akira Funahashi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Processes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • ODE model
  • Stochastic model
  • Boolean model
  • Spatial model
  • Numerical calculation
  • Parameter estimation
  • Bifurcation analysis
  • Image processing
  • Machine learning

Published Papers (1 paper)

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Research

10 pages, 3305 KiB  
Article
SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
by Takahiro G. Yamada, Kaito Ii, Matthias König, Martina Feierabend, Andreas Dräger and Akira Funahashi
Processes 2021, 9(10), 1830; https://doi.org/10.3390/pr9101830 - 15 Oct 2021
Viewed by 3672
Abstract
In systems biology, biological phenomena are often modeled by Ordinary Differential Equations (ODEs) and distributed in the de facto standard file format SBML. The primary analyses performed with such models are dynamic simulation, steady-state analysis, and parameter estimation. These methodologies are mathematically formalized, [...] Read more.
In systems biology, biological phenomena are often modeled by Ordinary Differential Equations (ODEs) and distributed in the de facto standard file format SBML. The primary analyses performed with such models are dynamic simulation, steady-state analysis, and parameter estimation. These methodologies are mathematically formalized, and libraries for such analyses have been published. Several tools exist to create, simulate, or visualize models encoded in SBML. However, setting up and establishing analysis environments is a crucial hurdle for non-modelers. Therefore, easy access to perform fundamental analyses of ODE models is a significant challenge. We developed SBMLWebApp, a web-based service to execute SBML-based simulation, steady-state analysis, and parameter estimation directly in the browser without the need for any setup or prior knowledge to address this issue. SBMLWebApp visualizes the result and numerical table of each analysis and provides a download of the results. SBMLWebApp allows users to select and analyze SBML models directly from the BioModels Database. Taken together, SBMLWebApp provides barrier-free access to an SBML analysis environment for simulation, steady-state analysis, and parameter estimation for SBML models. SBMLWebApp is implemented in Java™ based on an Apache Tomcat® web server using COPASI, the Systems Biology Simulation Core Library (SBSCL), and LibSBMLSim as simulation engines. SBMLWebApp is licensed under MIT with source code freely available. At the end of this article, the Data Availability Statement gives the internet links to the two websites to find the source code and run the program online. Full article
(This article belongs to the Special Issue Next-Generation Methods and Simulation Tools for Systems Biology)
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