Process Algebra Models in Biology

2011 ◽  
pp. 197-219
Author(s):  
Ozan Kahramanogullari
Keyword(s):  
Stochastic Process ◽  
Systems Biology ◽  
Programming Languages ◽  
Biological Systems ◽  
Point Of View ◽  
Process Algebras ◽  
Modeling And Analysis ◽  
Simulation Tools ◽  
Biological Phenomena ◽  
Evolutionarily Conserved

Process algebras are formal languages, which were originally designed to study the properties of complex reactive computer systems. Due to highly parallelized interactions and stochasticity inherit in biological systems, programming languages that implement stochastic extensions of processes algebras are gaining increasing attention as modeling and simulation tools in systems biology. The author discusses stochastic process algebras from the point of view of their broader potential as unifying instruments in systems biology. They argue that process algebras can help to complement conventional more established approaches to systems biology with new insights that emerge from computer science and software engineering. Along these lines, the author illustrates on examples their capability of addressing a spectrum of otherwise challenging biological phenomena, and their capacity to provide novel techniques and tools for modeling and analysis of biological systems. For the example models, they resort to phagocytosis, an evolutionarily conserved process by which cells engulf larger particles.

scholarly journals On Strengthening the Interest of Architecture Students in Bio-informed Solutions: A Systematic Approach for Learning from Nature

2021 ◽  
Vol 13 (4) ◽  
pp. 2138
Author(s):  
Semra Arslan Selçuk ◽  
Güneş Mutlu Avinç
Keyword(s):  
Design Education ◽  
Architectural Design ◽  
Systematic Approach ◽  
Point Of View ◽  
System Thinking ◽  
Sustainable Solutions ◽  
Research Areas ◽  
Biological Phenomena ◽  
Architectural Structures ◽  
Interdisciplinary Relationships

The bio-informed concept, which means “designing by learning from nature’s best ideas” as an approach, method, tool, discipline or strategy, is one of the most important research areas of today. It does not only shape designs, but also is based on collaborative/interactive/creative methods in education and can be integrated with contemporary educational approaches. This paper questions how to translate the bio-knowledge, which can be an effective and useful method for developing designers’ skills such as system-thinking, innovative thinking and problem-based learning, to design education in an easy and understandable way. In this context, the method of determining and applying biological phenomena/systems into architectural design process through the “natural language approach” is investigated. With this research, it is aimed to open the way to reach more innovative and sustainable solutions by establishing a bridge between architectural and biological terminology while creating architectural structures. It has been shown how to increase the biodiversity utilized for bio-informed solutions in the architectural field by proposing a systematic approach to search for biological systems. From this point of view, this study emphasizes the importance of promoting the bio-informed design approach, increasing interdisciplinary relationships and orienting individuals to nature for creativity and sustainability.

scholarly journals Implementation of BIM Modelling and Simulation Tools in Reducing Annual Energy Consumption of Multifamily Dwellings

2020 ◽  
Vol 170 ◽  
pp. 01002
Author(s):  
Subbarao Yarramsetty ◽  
MVN Siva Kumar ◽  
P Anand Raj
Keyword(s):  
Energy Efficient ◽  
Energy Use ◽  
Construction Materials ◽  
Residential Building ◽  
Energy Simulation ◽  
Point Of View ◽  
Rotational Angle ◽  
Existing Building ◽  
Simulation Tools ◽  
Efficient Option

In current research, building modelling and energy simulation tools were used to analyse and estimate the energy use of dwellings in order to reduce the annual energy use in multifamily dwellings. A three-story residential building located in Kabul city was modelled in Revit and all required parameters for running energy simulation were set. A Total of 126 experiments were conducted to estimate annual energy loads of the building. Different combinations from various components such as walls, roofs, floors, doors, and windows were created and simulated. Ultimately, the most energy efficient option in the context of Afghan dwellings was figured out. The building components consist of different locally available construction materials currently used in buildings in Afghanistan. Furthermore, the best energy efficient option was simulated by varying, building orientation in 15-degree increments and glazing area from 10% to 60% to find the most energy efficient combination. It was found that combination No. 48 was best option from energy conservation point of view and 120-degree rotational angle from north to east, of the existing building was the most energy-efficient option. Also, it was observed that 60% glazing area model consumed 24549 kWh more electricity compared to the one with 10% glazing area.

scholarly journals A standard-enabled workflow for synthetic biology

2017 ◽  
Vol 45 (3) ◽  
pp. 793-803 ◽  
Author(s):  
Chris J. Myers ◽  
Jacob Beal ◽  
Thomas E. Gorochowski ◽  
Hiroyuki Kuwahara ◽  
Curtis Madsen ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Markup Language ◽  
Design Tools ◽  
Data Standards ◽  
Data Repositories ◽  
Simulation Tools ◽  
Systems Biology Markup Language ◽  
Visualization Tools ◽  
Synthetic Biology Open Language

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

scholarly journals A virtual model of a vascularized bone matrix for biofabrication

2019 ◽  
Author(s):  
Maria Bolina Kersanach ◽  
Jorge Vicente Lopes da Silva ◽  
Janaina de Andrea Dernowsek
Keyword(s):  
Programming Languages ◽  
Bone Matrix ◽  
Good Alternative ◽  
Basic Unit ◽  
Cellular Interactions ◽  
Daily Lives ◽  
Biological Phenomena ◽  
Highly Correlated ◽  
Vascularized Bone

Increasingly, biofabrication is seen as a promising strategy in the tissue engineering and regenerative medicine fields. It proves to be a good alternative for drug and cosmetics testing and even for transplantation tissues and organs in humans. However, long before we dream with this science impacting our daily lives, we need to know it more on a smaller scale - the cellular interactions involved, the biomolecules, the transcription factors, the differentiation phases - it is all highly correlated, sensitive and complex. With the aim of reducing the investments of large sums of money and time with in vitro experiments, this work proposes the creation of a predictive model to the biological structures that will be biofabricated. From the use of mathematical and computational methods, simulations of biological phenomena are made through the translation of the biological processes described in the literature into logical processes written in programming languages. These in silico strategies make possible to iteratively refine physical and biochemical parameters before the in vitro stage. To exemplify this approach, an osteogenesis and angiogenesis implementation is shown in a virtual tissue spheroid (the bioprinting basic unit) - from mesenchymal and endothelial cells to a vascularized bone matrix.

scholarly journals Modeling Biological Systems Using Crowdsourcing

2018 ◽  
Vol 43 (3) ◽  
pp. 219-243 ◽  
Author(s):  
Szymon Wasik
Keyword(s):  
Systems Biology ◽  
Serious Games ◽  
Domain Knowledge ◽  
Biological Systems ◽  
Effective Technique ◽  
Design Models ◽  
Modeling Systems ◽  
Vast Network

Abstract Crowdsourcing is a very effective technique for outsourcing work to a vast network usually comprising anonymous people. In this study, we review the application of crowdsourcing to modeling systems originating from systems biology. We consider a variety of verified approaches, including well-known projects such as EyeWire, FoldIt, and DREAM Challenges, as well as novel projects conducted at the European Center for Bioinformatics and Genomics. The latter projects utilized crowdsourced serious games to design models of dynamic biological systems, and it was demonstrated that these models could be used successfully to involve players without domain knowledge. We conclude the review of these systems by providing 10 guidelines to facilitate the efficient use of crowdsourcing.

scholarly journals Markov Stochastic Processes in Biology and Mathematics -- the Same, and yet Different

2018 ◽  
Vol 14 (1) ◽  
pp. 7540-7559
Author(s):  
MI lOS lAWA SOKO
Keyword(s):  
Stochastic Process ◽  
Stochastic Processes ◽  
Discrete Time ◽  
Stochastic Matrix ◽  
Random Number Generator ◽  
Point Of View ◽  
State Transitions ◽  
Similar Principle ◽  
Probabilistic Space ◽  
And Mathematics

Virtually every biological model utilising a random number generator is a Markov stochastic process. Numerical simulations of such processes are performed using stochastic or intensity matrices or kernels. Biologists, however, define stochastic processes in a slightly different way to how mathematicians typically do. A discrete-time discrete-value stochastic process may be defined by a function p : X0 × X → {f : Î¥ → [0, 1]}, where X is a set of states, X0 is a bounded subset of X, Î¥ is a subset of integers (here associated with discrete time), where the function p satisfies 0 < p(x, y)(t) < 1 and  EY p(x, y)(t) = 1. This definition generalizes a stochastic matrix. Although X0 is bounded, X may include every possible state and is often infinite. By interrupting the process whenever the state transitions into the X −X0 set, Markov stochastic processes defined this way may have non-quadratic stochastic matrices. Similar principle applies to intensity matrices, stochastic and intensity kernels resulting from considering many biological models as Markov stochastic processes. Class of such processes has important properties when considered from a point of view of theoretical mathematics. In particular, every process from this class may be simulated (hence they all exist in a physical sense) and has a well-defined probabilistic space associated with it.

scholarly journals Stochastic Process Algebras: From Individuals to Populations

2011 ◽  
Vol 55 (7) ◽  
pp. 866-881 ◽  
Author(s):  
J. Hillston ◽  
M. Tribastone ◽  
S. Gilmore
Keyword(s):  
Stochastic Process ◽  
Process Algebras ◽  
Stochastic Process Algebras
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