In a breakthrough effort for computational biology, the world’s first complete computer model of an organism has been completed, Stanford researchers reported…A team led by Markus Covert, assistant professor of bioengineering, used data from more than 900 scientific papers to account for every molecular interaction that takes place in the life cycle of Mycoplasma genitalium, the world’s smallest free-living bacterium.
By encompassing the entirety of an organism in silico, the paper fulfills a longstanding goal for the field. Not only does the model allow researchers to address questions that aren’t practical to examine otherwise, it represents a stepping-stone toward the use of computer-aided design in bioengineering and medicine.
“This achievement demonstrates a transforming approach to answering questions about fundamental biological processes,” said James M. Anderson…”Comprehensive computer models of entire cells have the potential to advance our understanding of cellular function and, ultimately, to inform new approaches for the diagnosis and treatment of disease…”
Biology over the past two decades has been marked by the rise of high-throughput studies producing enormous troves of cellular information. A lack of experimental data is no longer the primary limiting factor for researchers. Instead, it’s how to make sense of what they already know.
Most biological experiments, however, still take a reductionist approach to this vast array of data: knocking out a single gene and seeing what happens…
This situation has resulted in a yawning gap between information and understanding that can only be addressed by “bringing all of that data into one place and seeing how it fits together,” according to Stanford bioengineering graduate student and co-first author Jayodita Sanghvi.
Integrative computational models clarify data sets whose sheer size would otherwise place them outside human ken.
“You don’t really understand how something works until you can reproduce it yourself,” Sanghvi said…
Computational analysis leading to computer simulations as thorough and complete as climate projections, stress testing in engineering design, pre-production cost analysis in consumer goods – or more so – is methodology that’s been waiting in the wings for biology, bio-engineering.
This is a process that not only can bring greater understanding to biology; but, rational design.