scholarly journals Systems interface biology

2006 ◽  
Vol 3 (10) ◽  
pp. 603-616 ◽  
Author(s):  
Francis J Doyle ◽  
Jörg Stelling
Keyword(s):  
Systems Biology ◽  
Systems Engineering ◽  
Biological Networks ◽  
Biological Systems ◽  
Mutual Benefit ◽  
Systems Approaches ◽  
The Rich ◽  
Complex Biological Networks

The field of systems biology has attracted the attention of biologists, engineers, mathematicians, physicists, chemists and others in an endeavour to create systems-level understanding of complex biological networks. In particular, systems engineering methods are finding unique opportunities in characterizing the rich behaviour exhibited by biological systems. In the same manner, these new classes of biological problems are motivating novel developments in theoretical systems approaches. Hence, the interface between systems and biology is of mutual benefit to both disciplines.

scholarly journals Biocharts: a visual formalism for complex biological systems

2009 ◽  
Vol 7 (48) ◽  
pp. 1015-1024 ◽  
Author(s):  
Hillel Kugler ◽  
Antti Larjo ◽  
David Harel
Keyword(s):  
Systems Engineering ◽  
Biological Networks ◽  
Biological Systems ◽  
Computational Modelling ◽  
Bacterial Chemotaxis ◽  
Visual Language ◽  
Modelling Effort ◽  
High Level ◽  
Natural Way ◽  
Modelling Approach

We address one of the central issues in devising languages, methods and tools for the modelling and analysis of complex biological systems, that of linking high-level (e.g. intercellular) information with lower-level (e.g. intracellular) information. Adequate ways of dealing with this issue are crucial for understanding biological networks and pathways, which typically contain huge amounts of data that continue to grow as our knowledge and understanding of a system increases. Trying to comprehend such data using the standard methods currently in use is often virtually impossible. We propose a two-tier compound visual language, which we call Biocharts , that is geared towards building fully executable models of biological systems. One of the main goals of our approach is to enable biologists to actively participate in the computational modelling effort, in a natural way. The high-level part of our language is a version of statecharts, which have been shown to be extremely successful in software and systems engineering. The statecharts can be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the pathways and networks. We illustrate the language and our general modelling approach using the well-studied process of bacterial chemotaxis.

scholarly journals Closing the gap between formats for storing layout information in systems biology

2019 ◽  
Vol 21 (4) ◽  
pp. 1249-1260 ◽  
Author(s):  
David Hoksza ◽  
Piotr Gawron ◽  
Marek Ostaszewski ◽  
Jan Hasenauer ◽  
Reinhard Schneider
Keyword(s):  
Systems Biology ◽  
Biological Networks ◽  
Software Tools ◽  
Molecular Network ◽  
Large Networks ◽  
Software Libraries ◽  
Closing The Gap ◽  
Rest Api ◽  
High Level ◽  
Complex Biological Networks

Abstract The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.

Target controllability with minimal mediators in complex biological networks

Genomics ◽  
2020 ◽  
Vol 112 (6) ◽  
pp. 4938-4944 ◽  
Author(s):  
Ali Ebrahimi ◽  
Abbas Nowzari-Dalini ◽  
Mahdi Jalili ◽  
Ali Masoudi-Nejad
Keyword(s):  
Biological Networks ◽  
Complex Biological Networks

Social networks to biological networks: systems biology of Mycobacterium tuberculosis

2013 ◽  
Vol 9 (7) ◽  
pp. 1584 ◽  
Author(s):  
Rohit Vashisht ◽  
Anshu Bhardwaj ◽  
OSDD Consortium ◽  
Samir K. Brahmachari
Keyword(s):  
Social Networks ◽  
Mycobacterium Tuberculosis ◽  
Systems Biology ◽  
Biological Networks

Modern Technologies and Approaches for Decoding Non-Coding Rna-Mediated Biological Networks in Systems Biology and Their Applications

2016 ◽  
pp. 106-132
Author(s):  
Devyani Samantarrai ◽  
Mousumi Sahu ◽  
Garima Singh ◽  
Jyoti Roy ◽  
Chandra Bhushan ◽  
...  
Keyword(s):  
Systems Biology ◽  
Biological Networks ◽  
Non Coding Rna ◽  
Modern Technologies

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 A Spiral Curriculum Approach To The Implementation Of Instrumentation In Biological Systems Engineering

2020 ◽  
Author(s):  
Kumar Mallikarjunan ◽  
Anand Lakshmikanth ◽  
John Cundiff ◽  
Andrew Fulton
Keyword(s):  
Systems Engineering ◽  
Biological Systems ◽  
Spiral Curriculum
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