Improving DNA Manufacturing Through Standardization

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This manuscript was submitted for presentation at IWBDA 2013. It was not accepted. The reviews we received are copied below. The manuscript will eventually be revised and published elsewhere.

----------------------- REVIEW 1 ---------------------
 PAPER: 11
 TITLE: Improving DNA Manufacturing Through Standardization
 AUTHORS: Gregory T. Purdy, Christopher Overend, David Ball, Mandy L. Wilson, Jaime A. Camelio, Kimberly P. Ellis and Jean Peccoud
OVERALL EVALUATION: 1 (weak accept)
 REVIEWER'S CONFIDENCE: 3 (medium)
----------- REVIEW -----------
 Process standards fashions come and go, but behind them is common sense. If the field of DNA
 nanotechnology is to reach maturity, technicians and not PhDs will do the work in
 the lab, and they may benefit from order (Fig. 1) as opposed to "creative chaos".
 Therefore this abstract promises a useful oral presentation.
There is a confusing contradiction in Section 2. Under "shine" we have that worker
 ownership of their station is encouraged. On the other hand, "no individual 'owns'
 a station".
Figure 2 is illegible and therefore useless. Please do not have a slide like this figure.
Minor: "praxes" is not a word in English. Perhaps write "practices".
----------------------- REVIEW 2 ---------------------
 PAPER: 11
 TITLE: Improving DNA Manufacturing Through Standardization
 AUTHORS: Gregory T. Purdy, Christopher Overend, David Ball, Mandy L. Wilson, Jaime A. Camelio, Kimberly P. Ellis and Jean Peccoud
OVERALL EVALUATION: 3 (strong accept)
 REVIEWER'S CONFIDENCE: 4 (high)
----------- REVIEW -----------
 5S and process mapping are well-accepted methods in industrial engineering, and used to streamline and standardize complex processes.  The authors present their experiences with applying 5S and process mapping methods from industrial engineering to a research-based synthetic biology laboratory.  The authors give convincing evidence that laboratory processes are well-suited and apt to benefit from the application of these methods.
The abstract is well written, providing adequate background on the 5S and process mapping methods from industrial engineering.  The application of these methods to research-based synthetic biology laboratory practices are clearly illustrated in Figure 1 and 2.  Figure 2 in particular provides nice insight into the actual complexity of a "simple" procedure like Sanger sequencing, and well motivates the importance of this work.
This work resonates with the problems faced by any quantitative biological laboratory, and the authors do great job bridging the communication gap between industrial engineering and laboratory procedure.  I recommend this paper for a strong accept as an oral presentation.
----------------------- REVIEW 3 ---------------------
 PAPER: 11
 TITLE: Improving DNA Manufacturing Through Standardization
 AUTHORS: Gregory T. Purdy, Christopher Overend, David Ball, Mandy L. Wilson, Jaime A. Camelio, Kimberly P. Ellis and Jean Peccoud
OVERALL EVALUATION: -1 (weak reject)
 REVIEWER'S CONFIDENCE: 5 (expert)
----------- REVIEW -----------
 The author's present the tenets of lean as applied to gene synthesis. It is not clear if they are advocating that a research lab follow this principle or this is appropriate for mass production in industry.
How does automation fit into the picture?
Most labs have standard protocols that are followed to more or less of a degree, however they do not specify the exact location of the pipette box. Would a left-handed user be required to use the same setup?
There is no data presented showing that this approach works well or not for biological research in general or even gene synthesis in particular.
The paper is well written but is prescriptive rather than providing any evidence-based result.
For example, Lean has many limitations. The elimination of 'waste' also may eliminate flexibility and real options that have value when the outcome is less predictable.
Figure 2 is unreadable.
----------------------- REVIEW 4 ---------------------
 PAPER: 11
 TITLE: Improving DNA Manufacturing Through Standardization
 AUTHORS: Gregory T. Purdy, Christopher Overend, David Ball, Mandy L. Wilson, Jaime A. Camelio, Kimberly P. Ellis and Jean Peccoud
OVERALL EVALUATION: 1 (weak accept)
 REVIEWER'S CONFIDENCE: 3 (medium)
----------- REVIEW -----------
 This paper proposes a combination of gene synthesis and industrial engineering approaches to streamline DNA fabrication. The approach relies on the 5S methodology to reduce resource wastage, and the introduction of process standardization and process mapping tools.
The 5S methodology seem reasonable though somewhat generic: sort, straighten, shine, standardize and sustain, could be interpreted in many different ways. This paper shows how these concepts can be applied to a molecular biology laboratory. The online resources indicate that this has been given careful thought, and the ideas would be beneficial for a laboratory that does not have an existing standardised setup in place. The proposals seem reasonable, though it's not clear whether there are better alternatives out there. The process mapping proposal also seems to be a good way of formalising the steps of a protocol. Both the 5S and process mapping concepts could be interesting discussion topics for IWBDA. The issue with standards is that they need to be agreed upon and adopted by a majority of practitioners, and the decision of which standards to adopt can be quite subjective. I would have liked the paper to mention the existence of alternative standards, and some justificati!
 on of why the proposed standards should be adopted over these alternatives. My impression though is that there just aren't that many alternatives out there, so this seems like a good starting point.
Note that the resolution of Figure 2 should be increased, so that it is legible when zoomed in.

Description

 

By framing gene synthesis as a manufacturing problem, it is possible to utilize common Industrial Engineering (IE) principles that have been applied to numerous macroscale systems in the burgeoning realm of DNA fabrication. These techniques have been successfully employed in an academic research laboratory and include: the implementation of the 5S methodology to reduce wasted resources; the introduction of process standardization and awareness, both at the system and discrete process level; and the use of process mapping tools to encourage best practices. The direct results of this collaboration between IE and gene synthesis are the continual improvement of processes in the academic research labs. The long-term impact is a scalable approach, both in design and organization, of gene synthesis enterprises for academic and large-scale industrial biotechnology laboratories.

This work is supported by NSF Award 1241328

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