24 papers · ranked by Valyu relevance
Lukyanenko, R., Pastor, O. + 2 more
Background: All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support researchers and scientists in conducting their work, conceptual…
John W. Sheppard
This book is focused on the broad issues surrounding "realizing complex integrated systems." What do we mean by this? It might be helpful to break down our title, one word at a time. To do this, we start at the end. What is a "system"? We start this introductory chapter by addressing that question. We pose a number of…
Johannes Reich
A system model is developed where the criterion to partition the world into a system and a rest is based on the functional relation between its states. This approach implies that the gestalt of systems becomes very dynamic. Especially interactions between systems may create temporary super systems "on the fly". The…
Felix Tretter, Henriette Löffler-Stastka
Clinical fields of the “sciences of the mind” (psychotherapy, psychiatry, etc.) lack integrative conceptual frameworks that have explanatory power. Mainly descriptive-classificatory taxonomies like DSM dominate the field. New taxonomies such as Research Domain Criteria (RDoC) aim to collect scientific knowledge…
Vladimir A. Likić, Malcolm J. McConville, Trevor Lithgow, Antony Bacic
Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i) mathematical and computational modeling; (ii) the application of traditional engineering practices in the analysis of biochemical systems; and in the past decade increasingly (iii)…
Andrew C Ahn, Muneesh Tewari, Chi-Sang Poon, Russell S Phillips
In the first of a two part series, Ahn and colleagues discuss the reductionist approach pervading medicine and explain how a systems approach (as advocated by systems biology) may complement reductionism.
David Blockley, Gordon Stirrat, Kirsty Alexander, Sabrina Phillips
Background A recent UK Government draft Heath White Paper follows the NHS England long term plan when it states that NHS England requires “a new framework that builds on changes already being made as well as building in the flexibility to support the system to tackle challenges of the future”. At present the structure…
Richard Berlin, Russell Gruen, James Best
This paper presents a brief history of Systems Theory, progresses to Systems Biology, and its relation to the more traditional investigative method of reductionism. The emergence of Systems Medicine represents the application of Systems Biology to disease and clinical issues. The challenges faced by this transition…
Lindsay M Edwards, Ines Thiele
Systems biology is defined in this review as ‘an iterative process of computational model building and experimental model revision with the aim of understanding or simulating complex biological systems’. We propose that, in practice, systems biology rests on three pillars: computation, the omics disciplines and…
Joseph Sifakis
A key idea is to compensate the lack of human intervention by adaptive control. This is instrumental for system resilience: it allows both coping with uncertainty and managing mixed criticality services. Our proposal for knowledge-based design seeks a compromise: preserving rigorousness despite the fact that essential…
Tihana Galinac Grbac
This is part I of the follow-up lecture notes of the lectures given by the authors at the Three "CO" (Composability, Comprehensibility, Correctness) Winter School held in Koˇsice, Slovakia, in January 2018, and Summer School held in Budapest, Hungary, in June 2019. In this part we explain the role of functional…
Jan-Hendrik S. Hofmeyr
As shown by Hofmeyr, the processes in the living cell can be divided into three classes of efficient causes that produce each other, so making the cell closed to efficient causation, the hallmark of an organism. They are the enzyme catalysts of covalent metabolic chemistry, the intracellular milieu that drives the…
Lei Xie, Eli J. Draizen, Philip E. Bourne
Systems pharmacology aims to holistically understand genetic, molecular, cellular, organismal, and environmental mechanisms of drug actions through developing mechanistic or predictive models. Data-driven modeling plays a central role in systems pharmacology, and has already enabled biologists to generate novel…
Craig E Kuziemsky, Mustafa Ozkaynak, Kim M Unertl, Saira Haque
Health system pursuits, such as collaborative care delivery, public health and wellness, and patient-centered care, extend beyond individual factors, including technologies, users, policies, or contexts. While taking stock of individual system components in biomedical informatics (BMI) research is necessary and…
Andres M. Bran, Peter F. Stadler, Juergen Jost, Guillermo Restrepo
The periodic system emerges by intertwining order and similarity relationships among chemical elements, which in turn arise from known substances at a given time that constitute the chemical space. Although the system has been adjusted to accommodate new elements, the connection with the chemical space has been largely…
Amro M. Farid
Systems-of-Systems Authors: ['Amro M. Farid'] Our modern life has grown to depend on many and nearly ubiquitous large complex engineering systems. Many disciplines now seemingly ask the same question: "In the face of assumed disruption, to what degree will these systems continue to perform and when will they be able to…
Authors not listed
Diversity and properties of ring systems contained in small molecules are of high interest for applications such as drug discovery or material sciences. In the present work we extract, analyse and classify ring systems found in small molecule compounds of open access databases such as PubChem, ChEMBL, DrugCentral…
Eric Smith, Harrison B. Smith, Jakob Lykke Andersen
We consider problems in the functional analysis and evolution of combinatorial chemical reaction networks as rule-based, or three-level systems. The first level consists of rules, realized here as graph-grammar representations of reaction mechanisms. The second level consists of stoichiometric networks of molecules and…
Jordan C Rozum, Réka Albert
We present a technique applicable in any dynamical framework to identify control-robust subsets of an interacting system. These robust subsystems, which we call stable modules, are characterized by constraints on the variables that make up the subsystem. They are robust in the sense that if the defining constraints are…
Authors not listed
Despite the promise of self-driving laboratories to accelerate discovery, their widespread implementation is hindered by prohibitive cost and technical complexity. We introduce BrickSDLab, a fully functional self-driving lab platform built entirely from LEGO® components, designed to bridge this accessibility gap.…
Authors not listed
Embedding mechanophores into polymer matrices to activate mechanochemical reactions has been extensively employed to realize diverse functional applications. Spiropyran (SP) is a widely used mechanophore that undergoes force-induced isomerization into its activated merocyanine (MC) form, accompanied by a color change.…
Oleksii Zozulia, Kriebisch Kriebisch, Brigitte Kriebisch, Héctor Soria Carrera + 3 more
Lipids can spontaneously assemble into vesicle-forming membranes. Such vesicles serve as compartments for even the simplest living systems. Vesicles have been extensively studied for constructing synthetic cells or as models for protocells—the cells hypothesized to have existed before life. These compartments exist…
Authors not listed
Self-organizing tissues, such as organoids, offer transformative potential beyond healthcare by enabling the sustainable production of advanced materials. Resource scarcity and global warming drive the need for innovative fabrication solutions. This prospective review explores developmental biology as a manufacturing…
Juan G. Diaz Ochoa
Explanations based on low level interacting elements are valuable and powerful since they contribute to identify the key mechanisms of biological functions. However, many dynamic systems based on low level interacting elements with unambiguous, finite and complete information of initial states generate future states…