Introduction to Bioinformatics - COIN81
COIN 81 Week Ten
Systems Biology and Metabolic Pathways are two relatively newer additions to bioinformatics, and in particular with the advent of higher order modeling, such as CellML and BioCyc, MetaCyc, and e-cell computational modeling.
Systems Biology - is a relatively new biological field of study, focusing on the systematic study of complex interactions in biological systems, using the perspective of integration instead of reduction to study them. Since the year 2000 and onwards, the term is used widely in the biosciences, and in particular bioinformatics.
Metabolic pathways - in metabolism, a pathway is a series of chemical reactions occurring within a cell, where in each pathway, a principal chemical is modified by chemical reactions, driven principally by enzymatic reactions.
KEGG - Kyoto Encyclopedia of Genes and Genomes, is a database of pathways, showing where enzymes act on substrates, and with each other, to complete a complex set of linked chemical reactions.
NCBI - NCBI has a pathways database that mirrors KEGG.
Enzymatic pathways - Enzymatic pathways is a fundamental learning unit. You may have been exposed to this in biochemistry, cell biology, or molecular biology. You will study individual enzymes in BRENDA, an enzyme database.
CellML - CellML is a representational language which uses XML to store mathematical models of cellular processes.
BioCyc - BioCyc is a collection of 371 Pathway/Genome Databases. Each Pathway/Genome Database in the BioCyc collection describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms.
MetaCyc - MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains over 900 pathways from more than 900 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and, secondary metabolism, as well as associated compounds, enzymes, and genes.
e-cell - E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.