Nature release recently a series of reviews on systems biology. I have long been hoping to read these papers, however cannot help becoming lazy in leisure senior grades.
Today my eye is caught by the opening line of Collecting and organizing systematic sets of protein data. It states, "The goals of systems biology are orthogonal to large-scale efforts to catalogue genomes, proteomes and interactomes.". I found it a novel expression because I nearly be used to the tone of "omics", and I have a strong feeling that there is always a new idea behind a novel expression. I continue with the paper.
Following the striking opening line comes a sound argument: organism is heterogenous and biological process is dynamic; thus, systems biology require dynamic, spatially resolved data on gene and protein function; This type of data is complex, thus data must be collected with reference to specific, quantitative models.
The authors say practical trade-offs must be considered when selecting what to measure and how frequently to measure it. I wonder whether we can build a model to model the experimental process instead of a preliminary experiment, or at least the experiment model give some insight into the process before the indispensable preliminary experiment.
About the third point data fusion, no single method is sufficient to measure the full diversity of protein signals. On the other hand, even there really exist a general method, how can we believe it gives the right data, given the inaccuracy of biological experiment. Therefore, data fusion also means error detection.
About mass spectrometry, the biggest limitation is not the instrumentation, but rather inadequate software and the need to confirm peptide assignments by hand. Further reading needed to confirm whether it is a rich land.
Computed metrics: In the paper analysis of cellular biology, I made a analog that the change of magnetic field incites electronic field, we biologist have long focus on the absolute level of protein or gene, but the change may make difference, however we have no a method to characterize the change until now. The section express similar idea.
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