Portfolio:Planning for Disruptions in Laboratory Operations - Revision history

Shawndouglas: Shawndouglas moved page LII:Planning for Disruptions in Laboratory Operations to Portfolio:Planning for Disruptions in Laboratory Operations without leaving a redirect: Namespace change

2024-06-21T01:59:06Z

Shawndouglas moved page LII:Planning for Disruptions in Laboratory Operations to Portfolio:Planning for Disruptions in Laboratory Operations without leaving a redirect: Namespace change

← Older revision

Revision as of 18:59, 20 June 2024

Shawndouglas: Tweaks

2024-06-21T01:58:39Z

Tweaks

← Older revision		Revision as of 18:58, 20 June 2024
Line 6:		Line 6:

	'''Publication date''': March 2022		'''Publication date''': March 2022

			NOTE: This was originally published on [https://www.limswiki.org/index.php/LII:Planning_for_Disruptions_in_Laboratory_Operations LIMSwiki.org] and is reproduced here using the same license.


	==Introduction==		==Introduction==
Line 76:		Line 79:
	Despite the advantages of automation in this scenario, just saying “automation can be a solution” doesn’t say much until you consider all of the ramifications of what those words mean, and what it will take to make them a reality. That’s where we’re going with this.		Despite the advantages of automation in this scenario, just saying “automation can be a solution” doesn’t say much until you consider all of the ramifications of what those words mean, and what it will take to make them a reality. That’s where we’re going with this.

	Before we get too deep into this, I'd like to point out that a lot of what we’ll be discussing is based on ''[[~~LII~~:Considerations in the Automation of Laboratory Procedures\|Considerations in the Automation of Laboratory Procedures]]'', published in January 2021. That work notes that in order for someone to pursue the automation of a procedure or method, there are a few requirements to consider<ref name="LiscouskiConsid21">{{cite web \|title=[[LII:Considerations in the Automation of Laboratory Procedures\|Considerations in the Automation of Laboratory Procedures]] \|author=Liscouski, J. \|date=22 January 2021}}</ref>:		Before we get too deep into this, I'd like to point out that a lot of what we’ll be discussing is based on ''[[Portfolio:Considerations in the Automation of Laboratory Procedures\|Considerations in the Automation of Laboratory Procedures]]'', published in January 2021. That work notes that in order for someone to pursue the automation of a procedure or method, there are a few requirements to consider<ref name="LiscouskiConsid21">{{cite web \|title=[[LII:Considerations in the Automation of Laboratory Procedures\|Considerations in the Automation of Laboratory Procedures]] \|author=Liscouski, J. \|date=22 January 2021}}</ref>:

	#The method under consideration must be proven, validated, and stable (i.e., not changing, with no moving targets).		#The method under consideration must be proven, validated, and stable (i.e., not changing, with no moving targets).
Line 82:		Line 85:
	#The automated procedure should be in use over a long enough period of time to justify the work and make the project financially justifiable.		#The automated procedure should be in use over a long enough period of time to justify the work and make the project financially justifiable.

	It's important to note that the concept of "scientific development" ends with the first consideration. In other words, method development, modification, adjustment, and add-ons end once a documented, proven process for accomplishing a lab task is fully developed. The other two considerations involve work post-scientific-development, specifically process engineering, as a sub-heading under the concept of "laboratory systems engineering" (as discussed in ''[[~~LII~~:Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering\|Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering]]''). That's not to say that over time changes won't be needed. There may be improvements required (i.e., "evolutionary operations," as described in ''[[~~LII~~:Directions in Laboratory Systems: One Person's Perspective\|Directions in Laboratory Systems: One Person's Perspective]]''), but at least get the initial system working well before you tweak it.		It's important to note that the concept of "scientific development" ends with the first consideration. In other words, method development, modification, adjustment, and add-ons end once a documented, proven process for accomplishing a lab task is fully developed. The other two considerations involve work post-scientific-development, specifically process engineering, as a sub-heading under the concept of "laboratory systems engineering" (as discussed in ''[[Profile:Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering\|Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering]]''). That's not to say that over time changes won't be needed. There may be improvements required (i.e., "evolutionary operations," as described in ''[[Profile:Directions in Laboratory Systems: One Person's Perspective\|Directions in Laboratory Systems: One Person's Perspective]]''), but at least get the initial system working well before you tweak it.

	That said, let's look at the automation of lab processes from two viewpoints: “fully” automated laboratory processes and manually or partially automated lab processes, as shown in Figure 2.		That said, let's look at the automation of lab processes from two viewpoints: “fully” automated laboratory processes and manually or partially automated lab processes, as shown in Figure 2.
Line 437:		Line 440:

	<!---Place all category tags here-->		<!---Place all category tags here-->
	[[Category~~:LII~~:Guides, white papers, and other publications]]		[[Category:Guides, white papers, and other publications]]

Shawndouglas: 14 revisions imported: Importing my work from LIMSwiki, using the same CC license

2024-06-18T20:27:52Z

14 revisions imported: Importing my work from LIMSwiki, using the same CC license

← Older revision

Revision as of 13:27, 18 June 2024

Shawndouglas: Text replacement - "\[\[Baytek International, Inc.(.*)" to "[[Vendor:Baytek International, Inc.$1"

2024-04-03T19:10:57Z

Text replacement - "\[\[Baytek International, Inc.(.*)" to "[[Vendor:Baytek International, Inc.$1"

← Older revision		Revision as of 12:10, 3 April 2024
Line 170:		Line 170:
	*TSI Incorporated's ''Laboratory Design Handbook''<ref name="TSILab14">{{cite web \|url=http://www.mtpinnacle.com/pdfs/2980330C-LabControlsHandbook.pdf \|format=PDF \|title=Laboratory Design Handbook \|publisher=TSI Incorporated \|date=2014 \|accessdate=17 March 2022}}</ref>		*TSI Incorporated's ''Laboratory Design Handbook''<ref name="TSILab14">{{cite web \|url=http://www.mtpinnacle.com/pdfs/2980330C-LabControlsHandbook.pdf \|format=PDF \|title=Laboratory Design Handbook \|publisher=TSI Incorporated \|date=2014 \|accessdate=17 March 2022}}</ref>

	Another option is to separate functions such as sample preparation, holding, and distribution. [[Baytek International, Inc.\|Baytek International]] markets a product called the TurboTube, which is a distribution system for sample vials primarily used in [[gas chromatography]] (the system isn’t limited to gas chromatography; it’s a matter of vial sizing). The system provides an intelligent routing and holding system, with an option for disposal. If a prepared sample needs multiple tests, the sample can be passed from one system to another, returned to a holding area, and retested if needed.<ref name="BaytekTurboTube">{{cite web \|url=https://www.baytekinternational.com/products/turbotube \|title=TurboTube for Baytek LIMS software \|publisher=Baytek International, Inc \|accessdate=17 March 2022}}</ref> A diagram from a 2009 presentation is shown in Figure 6.		Another option is to separate functions such as sample preparation, holding, and distribution. [[Vendor:Baytek International, Inc.\|Baytek International]] markets a product called the TurboTube, which is a distribution system for sample vials primarily used in [[gas chromatography]] (the system isn’t limited to gas chromatography; it’s a matter of vial sizing). The system provides an intelligent routing and holding system, with an option for disposal. If a prepared sample needs multiple tests, the sample can be passed from one system to another, returned to a holding area, and retested if needed.<ref name="BaytekTurboTube">{{cite web \|url=https://www.baytekinternational.com/products/turbotube \|title=TurboTube for Baytek LIMS software \|publisher=Baytek International, Inc \|accessdate=17 March 2022}}</ref> A diagram from a 2009 presentation is shown in Figure 6.

Shawndouglas: /* Abbreviations, acronyms, and initialisms */ Tweak

2022-03-21T17:58:20Z

Abbreviations, acronyms, and initialisms: Tweak

← Older revision		Revision as of 10:58, 21 March 2022
Line 412:		Line 412:
	'''BHT''': butylated hydroxytoluene (BHT)		'''BHT''': butylated hydroxytoluene (BHT)

	'''CDS''': ~~Chromatography~~ data system		'''CDS''': chromatography data system

	'''ELN''': ~~Electronic~~ laboratory notebook		'''ELN''': electronic laboratory notebook

	'''GLP''': good laboratory practice		'''GLP''': good laboratory practice
Line 420:		Line 420:
	'''GMP''': good manufacturing practice		'''GMP''': good manufacturing practice

	'''IT''': ~~Information~~ technology		'''IT''': information technology

	'''LIMS''': ~~Laboratory~~ information management system		'''LIMS''': laboratory information management system

	'''LSE''': ~~Laboratory~~ systems engineer		'''LSE''': laboratory systems engineer

	'''QC''': quality control		'''QC''': quality control

Shawndouglas: Final edit

2022-03-21T17:35:58Z

Final edit

Show changes

Shawndouglas: Saving and adding more.

2022-03-18T22:46:26Z

Saving and adding more.

@@ Line 63: / Line 63: @@
 {| border="0" cellpadding="5" cellspacing="0" width="700px"
   |-
-   | style="background-color:white; padding-left:10px; padding-right:10px;" |<blockquote>'''Figure 1.''' Basic laboratory workflows. While this leans toward research (both pure and applied to testing), the commercial testing and QC labs can still easily be seen within this framework.</blockquote>
+   | style="background-color:white; padding-left:10px; padding-right:10px;" |<blockquote>'''Figure 1.''' Basic laboratory workflows. While this leans toward research (both pure and applied to testing), the commercial testing and [[quality control]] (QC) labs can still easily be seen within this framework.</blockquote>
   |-
 |}
@@ Line 351: / Line 351: @@
 |}
 Meteorological issues can cause problems with infrastructure. When facilities are planned and built, critical infrastructure controls may be relegated to the basement or lower levels of the facility. Consider moving them above projected high-water levels. Wiring can be protected by conduits, and steps can be taken to mitigate water damage to those wires. Control systems that people interact with may need to be moved so that controlled shutdowns and startups can occur without risk to personnel.
@@ Line 372: / Line 373: @@
 |}
 |}
 ==References==

Shawndouglas: Saving and adding more.

2022-03-18T22:11:32Z

Saving and adding more.

← Older revision		Revision as of 15:11, 18 March 2022
Line 325:		Line 325:
	Flexible work environments and hours may be needed to accommodate individual needs. The recent shift in the economy and loss of access to childcare services, for example, may force people to work off-site to take care of children or other family members. Sudden school closures due to fears or the reality of potential infections (i.e., unplanned events) may require schedule changes. Instead of adding stress to the system, relieve it. A day off is one thing, but shifting work hours and working from home while still achieving goals is another. As this is being written, I’m reminded of one manager who had a unique approach to personnel management: her job, as she saw it, was to give us whatever resources we needed to let us get our work done. In the 1980s this was unusual. If you needed to work from home, take a day off, leave early, borrow equipment, or something else, she trusted you to get your work done, and her employees delivered. The group worked well together and met its goals routinely.		Flexible work environments and hours may be needed to accommodate individual needs. The recent shift in the economy and loss of access to childcare services, for example, may force people to work off-site to take care of children or other family members. Sudden school closures due to fears or the reality of potential infections (i.e., unplanned events) may require schedule changes. Instead of adding stress to the system, relieve it. A day off is one thing, but shifting work hours and working from home while still achieving goals is another. As this is being written, I’m reminded of one manager who had a unique approach to personnel management: her job, as she saw it, was to give us whatever resources we needed to let us get our work done. In the 1980s this was unusual. If you needed to work from home, take a day off, leave early, borrow equipment, or something else, she trusted you to get your work done, and her employees delivered. The group worked well together and met its goals routinely.

			Offices, including lab offices, are going to change. According to Eric Mosley, the CEO and co-founder of Workhuman, a "new normal" for the office can be distilled down to several factors<ref name="MosleyOffices22">{{cite web \|url=https://www.inc.com/eric-mosley/offices-in-2022-heres-what-new-normal-may-look-like.html \|title=Offices in 2022: Here's What the 'New Normal' May Look Like \|author=Mosley, E. \|work=Inc \|date=24 December 2021 \|accessdate=18 March 2022}}</ref>:

			* The advent of the "Great Resignation" will act as a true wake-up call for society.
			* Going forward, work will need to be hybrid, agile, and interdependent.
			* When recruiting and retaining personnel, employers will have to be more inclusive and diverse.
			* Getting women back to the workforce has its own set of challenges.

			The last item is important. Caregiving largely falls on women's shoulders. Some may elect to fill those caregiver roles while also still desiring a career, while others may be in position to forego caregiving or find a way to make work-from-home or hybrid arrangements work. In some cases, there is no other choice but to forgo work. One thing that companies can do to facilitate women getting back to the workplace is to provide on-site child care. There is a cost (which could be shared between the organization and the employee), but if it helps retain valuable people and reduces the stress in their lives, it may be worth it. A lot depends on the nature of the facility. In many cases, on-site care may not work because of exposure to hazardous materials. An alternative would be to contract with a nearby facility that provides the needed services.

			All of this depends on the nature of the lab’s operations (e.g., research, testing, QC, etc.) and the lab's ability to support/tolerate non-traditional working styles. Additionally, considering and planning for the points noted above has more to do with factors beyond the immediate COVID-19 pandemic.

			==External factors disrupting lab operations==
			Numerous issues can affect a lab's ability to function (Figure 9). A lot depends on where you are located geographically. Climate change is a major issue since it affects wide areas and its effect can range from annoying to devastating. Many of the issues in this figure do not warrant comment; you are living through them. The issue is how do we prepare for them in the near future.


			[[File:Fig9 Liscouski PlanDisruptLabOper2022.png\|1000px]]
			{{clear}}
			{\|
			\| style="vertical-align:top;" \|
			{\| border="0" cellpadding="5" cellspacing="0" width="1000px"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;" \|<blockquote>'''Figure 9.''' Mindmap showing potential disruptions to laboratory operations.</blockquote>
			\|-
			\|}
			\|}

			Meteorological issues can cause problems with infrastructure. When facilities are planned and built, critical infrastructure controls may be relegated to the basement or lower levels of the facility. Consider moving them above projected high-water levels. Wiring can be protected by conduits, and steps can be taken to mitigate water damage to those wires. Control systems that people interact with may need to be moved so that controlled shutdowns and startups can occur without risk to personnel.

			If an increase in severe and tornadic storms is anticipated, have plans in place so that non-essential personnel can work from home without risking themselves traveling. Those who are essential may require local housing for the same reason: eliminate travel and have them close to the site. As previously suggested, another option is to run controlled shutdowns where feasible to reduce potential damage.

			Power loss due to storms, earthquakes, floods, and accidents is one of the simpler issues to address. One obvious answer is to add a generator to a facility; however, you have to take into account what happens when power is lost and then restored, and over what period of time. When power is lost, do operations fail safely or dangerously? What type of experiments and procedures are you running, and what are the consequence of losing power for each step of the process? When power is finally restored, does restoring power create an unsafe condition as a result of an unplanned shut down? Will something jam in automated workflow? Keep in mind that components with electronic settings (rather than mechanical) may be reset to the manufacturer's default conditions instead of your normal operating settings. Also consider whether equipment that has to be taken off-line, cleaned, and restarted can be done so safely if power is dropping then quickly restored and lost again before it fails.

			Regarding generators, a couple things must be kept in mind: the quality of the power provided and the delay in providing it. Not all generators provide the clean power needed for modern electronics. Electrical noise can adversely affect computers, instruments, and other electronic equipment.

			One of the characteristics of power loss is the way it is lost. It may be a single sudden event, or it may be lost, come back, and be lost again in cycles until it finally is restored or drops out entirely. In order to keep generators from chaotically starting and stopping for each of the cycles in the latter situation, you may want the generators to wait for a period of time after power is lost before starting up. Note that this may take several minutes. Your equipment needs to be protected during that phase (Figure 10) or it can sustain electrical damage or worse. An uninterruptable power source (UPS), which acts as a temporary power supply, can fill the gap by either being instantly available or quickly available (down to a two-millisecond delay, depending on model). Some can also filter electrical noise from generators and further protect equipment.


			[[File:Fig10 Liscouski PlanDisruptLabOper2022.png\|600px]]
			{{clear}}
			{\|
			\| style="vertical-align:top;" \|
			{\| border="0" cellpadding="5" cellspacing="0" width="600px"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;" \|<blockquote>'''Figure 10.''' Visualization of power supply needs during external power loss.</blockquote>
			\|-
			\|}
			\|}

	==References==		==References==

Shawndouglas: Saving and adding more.

2022-03-18T21:28:00Z

Saving and adding more.

@@ Line 250: / Line 250: @@
 {|
   | style="vertical-align:top;" |
-{| border="0" cellpadding="5" cellspacing="0" width="5000px"
+{| border="0" cellpadding="5" cellspacing="0" width="500px"
   |-
    | style="background-color:white; padding-left:10px; padding-right:10px;" |<blockquote>'''Figure 7.''' The data integrity stack.</blockquote>
@@ Line 286: / Line 286: @@
 As noted earlier, this is analogous to production lines in general. They face the same issues of producing quality products efficiently with minimum waste. People with process engineering backgrounds can be invaluable to making things function. The major difference between a production line making products and laboratory workflows is that those manufactured products can be tested and examined to separate those products that meet desired characteristics from those that don’t. For the most part, the results of laboratory work can’t directly be "tested and examined"; laboratory quality has to be inferred by external factors (e.g., using reference samples, etc.). Re-running a sample and getting the same result can just mean the same error was repeated. (Note, however, that a reference sample is different than running an instrument calibration standard. The latter only evaluates an instrument's detector response, whereas the former is subjected to the entire process.)

Shawndouglas: Saving and adding more.

2022-03-18T20:22:06Z

Saving and adding more.

← Older revision		Revision as of 13:22, 18 March 2022
Line 242:		Line 242:
	\|}		\|}

			===6. Sample processing modes===
			Some of the differences between full and partial automation and the issues around duration don’t fully come to light until we consider operating modes, and later, process control and management. The goal isn’t just to process samples and experiments, it’s to produce high-quality results, which depends on the [[data integrity]] stack (Figure 7). In short, data integrity depends upon system integrity, which in turn is a function of design decisions for automating the process.


			[[File:Fig7 Liscouski PlanDisruptLabOper2022.png\|500px]]
			{{clear}}
			{\|
			\| style="vertical-align:top;" \|
			{\| border="0" cellpadding="5" cellspacing="0" width="5000px"
			\|-
			\| style="background-color:white; padding-left:10px; padding-right:10px;" \|<blockquote>'''Figure 7.''' The data integrity stack.</blockquote>
			\|-
			\|}
			\|}

			What we’ve introduced is two modes of operation: sequential processing of samples (i.e., Method 1) and batch processing of samples (i.e., Method 2; each microplate is a batch). On the surface, the differences between the two are straightforward. In Method 1, samples are prepared and processed by the instrument one at a time. In Method 2, plates are treated as a unit (batch), but the individual sample cells may be processed in different steps: one cell at a time, a row or column at a time, or a plate at a time, depending on the implementation (full or partial automation, manual or equipment-assisted).

			There are two consequences to this. First, in either batch or sequential methods, the more steps that are done manually, the more opportunity there is for error and variability. Manual execution has a higher variability than automated systems, and if you are pipetting material into a 96-well plate, that’s 96 operations instead of one for an automated plate-at-a-time reagent addition. Depending on the type of pipette used, as many as six wells can be accessed at a time. (Note that typical microplates have as few as six wells, or as many as 384 or 1536; higher densities are available in tape-based formats. Microplates with more than 96 wells are normally used in robotic equipment.)

			The second is a matter of when results become available. In Method 1, each result is available as soon as the computer processes the chromatographic output. They can be examined for anomalies and against expected norms (deviations can cause the system to halt) and determine if everything is operating properly, and then continue. This reduces waste of materials, samples, and processing time. Method 2’s batch mode doesn’t give us that luxury; the results for a full plate become available at the same time, and if there are problems, the entire batch may be wasted.

			There are a couple of other issues with batch systems. One is flexibility: what happens when a series of batches are set up, programmed into the system, and a rush sample comes in? Can the system accommodate that? Another issue relates to the minimum number of samples that have to be run to make the system cost effective to operate.

			Finally, sequential systems have their own issues. They are slower processing material, and more expensive to replicate if the sample volume increases significantly due to the cost of the measuring and support equipment.

			===7. Process control and management===
			One characteristic of production lines is that they can run for extended periods of time and provide [[Quality (business)\|quality]] products. The quality of a product can be tested by comparing the item or material produced against its specifications. Size, shape, and composition are just a few characteristics that can be measured against the ideal standard. What if your “products” are measurements, numbers, and descriptors? How do you know if the expected level of quality is there, and what does that really mean? What does that mean for automated laboratory processes?

			What we have to be able to demonstrate is that we have confidence in the results that laboratory procedures yield. Whether it is a research or testing lab, a QC or a contract lab, the bottom line is the same: how do I know that the process as executed is giving me results that I can trust? We can only do that by inference, an inference that is built on a foundation of facts and history:

			* The process is a fully validated implementation of a proven validated method. This is not a good laboratory practice/good manufacturing practice (GLP/GMP) or similar issue, just a matter of proper engineering practices.
			* Those working with the system are fully qualified.
			* We have a history of running reference samples that shows that the procedure's execution is under control.
			* In-process check points provide an early warning if the process is changing in an uncontrolled manner.

			This is another area where the duration of run is a factor. If it is all within a shift, people can periodically check the execution and see if it is working properly, taking corrective action when needed. Longer runs, particularly if unattended for periods of time, would require more robust process control and management.

			Wherever possible, checkpoints should be built into the process. For example, if liquids are being dispensed, are they being used at a rate consistent with the number of samples processed? Too much liquid used could mean a leak, too little could be a plugged dispenser. The nature of the checkpoints will depend on the characteristics of the process. The appearance of a solution can be checked to see if it is the right color, turbidity, clarity, etc. Bubble traps can be used and monitored to make sure air (for example) isn’t being drawn into the system and interfering with flows and measurements.

			Another opportunity can be found with remote access to the process monitors. This can be a database of control measurements, or in the case of instrument systems, logging into the system and looking at the results of completed analysis, including digitized analog data. Some organizations prohibit remote logins to data systems with good reason; if you can get in so can someone else. It should be possible to balance security with access so that you can have confidence that things are working well. If that isn’t possible, then checks will be left to people on-site.

			The extent of having built-in process checks, running reference samples, and implementing statistical process control, etc. should be subjected to a risk-based cost-benefit analysis. The goals are simple: process lab procedures economically and efficiently, manage costs, and develop a system whose results you can have confidence in.

			As noted earlier, this is analogous to production lines in general. They face the same issues of producing quality products efficiently with minimum waste. People with process engineering backgrounds can be invaluable to making things function. The major difference between a production line making products and laboratory workflows is that those manufactured products can be tested and examined to separate those products that meet desired characteristics from those that don’t. For the most part, the results of laboratory work can’t directly be "tested and examined"; laboratory quality has to be inferred by external factors (e.g., using reference samples, etc.). Re-running a sample and getting the same result can just mean the same error was repeated. (Note, however, that a reference sample is different than running an instrument calibration standard. The latter only evaluates an instrument's detector response, whereas the former is subjected to the entire process.)