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Systems and Synthetic Biology

, Volume 7, Issue 4, pp 221–227 | Cite as

An attempt to construct a (general) mathematical framework to model biological “context-dependence”

  • Anirban Banerji
Research Article

Abstract

Context-dependent nature of biological phenomena is well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various (particular) facets of biological context-dependence, a formal and general mathematical construct to model the wide spectrum of context-dependence, eludes the students of biology. Such an objective model, from both ‘bottom-up’ as well as ‘top-down’ perspective, is proposed here to serve as the template to describe the various kinds of context-dependence that we encounter in different branches of biology. Interactions between biological contexts was found to be transitive but non-commutative. It is found that a hierarchical nature of dependence among the biological contexts models the emergent biological properties efficiently. Reasons for these findings are provided in a general model to describe biological reality. Scheme to algorithmically implement the hierarchic structure of organization of biological contexts was proposed with a construct named ‘Context tree’. A ‘Context tree’ based analysis of context interactions among biophysical factors influencing protein structure was performed.

Keywords

Biological contexts Mathematical model Hierarchical organization Emergence Thread-mesh model Context tree Protein structure Structural dependencies 

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Bioinformatics CentreUniversity of PunePuneIndia

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