Introduction to Systems Biology

Study Notes

Systems biology is a holistic approach to understanding biological systems, recognizing that the whole is greater than the sum of its parts.
It involves understanding the networks that form living organisms, which are integrated at and communicate on multiple scales.
Biological systems consist of many networks, from the genome to molecules and cells, organs, and the individual in their environment.

It requires integration of multiple scientific disciplines, including biology, computer science, engineering, bioinformatics, and physics.
The approach involves investigating the components of cellular networks and their interactions, applying experimental and high-throughput techniques, and integrating computational methods with experimental efforts.

Genomics is the study of the structure and function of genomic sequences and downstream biological products, and their influence on biological behavior.
Genomics uses recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the structure and function of genomes.
NGS is a technology used to determine the sequence of DNA to study genetic variation associated with diseases or other biological phenomena.
The NGS workflow consists of DNA extraction, library preparation, sequencing, and analysis.

DNA extraction: isolating DNA from samples using a DNA isolation kit.
Library preparation: fragmenting genomic DNA and ligating specialized adapters to both ends of the fragment ends.
Sequencing: loading libraries onto the sequencer, where chemically modified nucleotides bind to the DNA template strand through natural complementarity.
Analysis: aligning sequencing reads to a reference genomic sequence with bioinformatics software, identifying similarities and differences between the reference genome and the newly sequenced reads.

It requires a cross-disciplinary environment, where biologists, chemists, computer scientists, engineers, mathematicians, and others come together in teams.
The virtuous cycle of systems biology involves solving challenging biological problems, developing new technologies, and generating new data types that require novel analytical tools.

Integration of complex datasets: systems-level measurements of information flow from all components of the system.
Computational analysis of large data sets to draw insights into the workings of the cell and organism.