Biomedical Engineering Reference
In-Depth Information
understanding of how organisms operate at the molecular level, and more
importantly how they fail to operate properly and how that might be fi xed. The
key realization in systems biology is that none of these omics stand alone—it
is not enough to determine “what this gene does” or “what that protein is for.”
All these mechanisms interact within the system that is an organism, and
systems biology attempts to understand that interaction. Modeling the behav-
ior of a living organism at the molecular level is an undertaking of breathtak-
ing complexity made possible only by the advent of inexpensive and powerful
computers. The simultaneous rise of systems biology and the Internet is no
coincidence—the study of interconnectedness demands interconnectedness to
meet the scale of the problem. The scope of systems biology is too great to be
attacked without collaboration between researchers.
The author's company, Insilicos, has been very active in maintenance, inte-
gration, and improvement of various open-source software tools used by the
proteomics research community, most notably the
Trans - Proteomic Pipeline
(TPP), originally developed at the Institute for Systems Biology (ISB), and
LabKey Software's laboratory information management and data analysis
system
LabKey Server
(Insilicos, ISB, and LabKey are all located in Seattle,
WA). This is the keyhole through which the author views the systems biology
world — as a scientifi c software toolmaker, as opposed to a scientifi c research
practitioner.
14.2
TRADITION OF NOT VERY COLLABORATIVE SCIENCE
Since the early days of the Royal Society, science has largely advanced on a
model of serial scientifi c collaboration. New scientifi c papers reference previ-
ously published papers, and the body of knowledge is built block by block. The
intent of peer-reviewed publication is a marketplace of ideas which will result
in the best being advanced and the worst being weeded out. However, the
competitive nature of the scientifi c marketplace sometimes results in less than
full disclosure of the ideas in question. Often the reader of a paper fi nds that
promised data (and now, software) fail to appear or, when they do appear,
their inner workings (raw data, source code) are not made available. A chari-
table view is that these habits of semicooperation are simply a result of the
traditional inconvenience of handling physical media when sharing data and
code. But in disciplines such as systems biology, which have largely arisen in
the Internet age and in which code and data are the fundamental artifacts,
there are new expectations as to what constitutes full disclosure.
14.3 IMPACT OF OPEN - SOURCE SOFTWARE ON TRULY
COLLABORATIVE SCIENCE
The Internet has made collaboration in human endeavors possible in new ways
and at unprecedented scale. The growing body of free and open-source general-
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