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Revision as of 20:19, 25 October 2012
Data Sheet
In many fields of engineering, such as electrical engineering, data sheets are a mechanism to document part data such that the behavior of a part is captured and can be shared with other groups. Ideally, the information on these sheets should be robust enough to allow any group to use the part in a different context effectively, given the information captured on these data sheets.
Canton et al. 2008 Arkin 2008
Several groups have started developing the ideas that should be on such a data sheet for DNA parts. Canton et. al included information such as performance, reliability and compatibility. Arkin suggested that general device data, cell-cell communication measurements, DNA-binding protein domain measurements and therapeutic measurements could be documented and shared as well. A sharing standard is sought, but there is still no standard mechanism for sharing part information amongst synthetic biologists.
Our approach to sharing characterization data through a data sheet is to break information into four major sections: General Datasheet Information, Growth/Measurement Conditions, Part Information and Data Analysis.
General Datasheet Information: Here a brief abstract of the findings of the characterization, author, and date information are included in addition to other relevant comments and conclusions. Also included here would be links or references to related parts and datasheets.
Growth/Measurement Conditions: In this section, all experimental growth conditions and measurement settings are documented. The experimental conditions include controls used and is similar to an abbreviated methods section in a journal article. This includes who built the parts and what assembly method/protocol are used. It also includes when during the process things are tested and how. Some popular measurement techniques are based on fluorescence of a molecular fluorophore such as microscopy, flow data, or plate reading. Other measurements such as gel imaging and DNA sequencing are taken and these measurements are listed here.
Part Information: Here we include all part and device information. If the device consists of multiple parts, all parts are listed and if parts have special features, these are also be defined. Additionally, the assembly method and any scars created by the assembly and the vector backbone are defined in this section. This section has enough information to trace back to a full sequence while including abstract functions of these sequences.
Data Analysis: This section includes a variety of analyses based on the data collected. All analysis in this section derive from the experimental settings described in the Growth/Measurement Conditions section. Depending upon the device, the appropriate analyses might differ, but we start a basic set of analyses such as gel images, sequencing data and flow cytometry bar graphs or curves. For more complicated circuits such as signaling circuits, other analyses might be more appropriate to define its function.
Currently our datasheet are intended only for human consumption, but we are working on developing them to be consumable by a computer program
[1] B. Canton et al. “Refinement and standardization...” Nature Biotech 26(7). 2008.
[2] A. Arkin "Setting the standard in synthetic biology" Nature Biotech 26(7). 2008.
