In Silico Biology - Volume Pre-press, issue Pre-press
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ISSN 1386-6338 (P)
ISSN 1434-3207 (E)
In Silico Biology is a scientific research journal for the advancement of computational models and simulations applied to complex biological phenomena. We publish peer-reviewed leading-edge biological, biomedical and biotechnological research in which computer-based (i.e.,
) modeling and analysis tools are developed and utilized to predict and elucidate dynamics of biological systems, their design and control, and their evolution. Experimental support may also be provided to support the computational analyses.
In Silico Biology aims to advance the knowledge of the principles of organization of living systems. We strive to provide computational frameworks for understanding how observable biological properties arise from complex systems. In particular, we seek for integrative formalisms to decipher cross-talks underlying systems level properties, ultimate aim of multi-scale models.
Studies published in
In Silico Biology generally use theoretical models and computational analysis to gain quantitative insights into regulatory processes and networks, cell physiology and morphology, tissue dynamics and organ systems. Special areas of interest include signal transduction and information processing, gene expression and gene regulatory networks, metabolism, proliferation, differentiation and morphogenesis, among others, and the use of multi-scale modeling to connect molecular and cellular systems to the level of organisms and populations.
In Silico Biology also publishes foundational research in which novel algorithms are developed to facilitate modeling and simulations. Such research must demonstrate application to a concrete biological problem.
In Silico Biology frequently publishes special issues on seminal topics and trends. Special issues are handled by Special Issue Editors appointed by the Editor-in-Chief. Proposals for special issues should be sent to the Editor-in-Chief.
About In Silico Biology
is a pendant to
(in the living system) and
(in the test tube) biological experiments, and implies the gain of insights by computer-based simulations and model analyses.
In Silico Biology (ISB) was founded in 1998 as a purely online journal. IOS Press became the publisher of the printed journal shortly after. Today, ISB is dedicated exclusively to biological systems modeling and multi-scale simulations and is published solely by IOS Press. The previous online publisher, Bioinformation Systems, maintains a website containing studies published between 1998 and 2010 for archival purposes.
We strongly support open communications and encourage researchers to share results and preliminary data with the community. Therefore, results and preliminary data made public through conference presentations, conference proceeding or posting of unrefereed manuscripts on preprint servers will not prohibit publication in ISB. However, authors are required to modify a preprint to include the journal reference (including DOI), and a link to the published article on the ISB website upon publication.
Abstract: Quantitative modeling is quickly becoming an integral part of biology, due to the ability of mathematical models and computer simulations to generate insights and predict the behavior of living systems. Single-cell models can be incapable or misleading for inferring population dynamics, as they do not consider the interactions between cells via metabolites or physical contact, nor do they consider competition for limited resources such as nutrients or space. Here we examine methods that are commonly used to model and simulate cell populations. First, we cover simple models where analytic solutions are available, and then move on to more complex scenarios…where computational methods are required. Overall, we present a summary of mathematical models used to describe cell population dynamics, which may aid future model development and highlights the importance of population modeling in biology.
Keywords: Mathematical modeling, multiscale simulation algorithms, cell population dynamics, evolution
Abstract: Angiogenesis, a formation of blood vessels from an existing vasculature, plays a key role in tumor growth and its progression into cancer. The lining of blood vessels consists of endothelial cells (ECs) which proliferate and migrate, allowing the capillaries to sprout towards the tumor to deliver the needed oxygen. Various treatments aiming to suppress or even inhibit angiogenesis have been explored. Mesenchymal stem cells (MSCs) have recently been undergoing development in cell-based therapy for cancer due to their ability to migrate towards the capillaries and induce the apoptosis of the ECs, causing capillary degeneration. However, further investigations in this direction…are needed as it is usually difficult to preclinically assess the efficacy of such therapy. We develop a hybrid multiscale model that integrates molecular, cellular, tissue and extracellular components of tumor system to investigate angiogenesis and tumor growth under MSC-mediated therapy. Our simulations produce angiogenesis and vascular tumor growth profiles as observed in the experiments. Furthermore, the simulations show that the effectiveness of MSCs in inducing EC apoptosis is density dependent and its full effect is reached within several days after MSCs application. Quantitative agreements with experimental data indicate the predictive potential of our model for evaluating the efficacy of cell-based therapies targeting angiogenesis.