Foundations of Systems Biology

Foundations of Systems Biology

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Today, as hundreds of genomes have been sequenced and thousands of proteins and more than ten thousand metabolites have been identi?ed, navigating safely through this wealth of information without getting completely lost has become crucial for research in, and teaching of, molecular biology. Consequently, a considerable number of tools have been developed and put on the market in the last two decades that describe the multitude of potential/putative interactions between genes, proteins, metabolites, and other biologically relevant compounds in terms of metabolic, genetic, signaling, and other networks, their aim being to support all sorts of explorations through bio-data bases currently called Systems Biology. As a result, navigating safely through this wealth of information-processing tools has become equally crucial for successful work in molecular biology. To help perform such navigation tasks successfully, this book starts by providing an extremely useful overview of existing tools for ?nding (or designing) and inv- tigating metabolic, genetic, signaling, and other network databases, addressing also user-relevant practical questions like a€c Is the database viewable through a web browser? a€c Is there a licensing fee? a€c What is the data type (metabolic, gene regulatory, signaling, etc. )? a€c Is the database developed/maintained by a curator or a computer? a€c Is there any software for editing pathways? a€c Is it possible to simulate the pathway? It then goes on to introduce a speci?c such tool, that is, the fabulous a€œCell - lustrator 3. 0a€ tool developed by the authors.This program creates the GIFs and SVGs of the pathways according to the data created by curators called a€œPathway Authoritiesa€. ... Cytoscape is a software tool designed to visualize the molecular interactions as a network diagram (http:// ... of California San Diego as well as some other institutions such as the Pasteur Institute, MSKCC, Agilent, and UCSF as an open source project.

Title:Foundations of Systems Biology
Author:Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
Publisher:Springer Science & Business Media - 2009-04-21


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