Portfolio:Directions in Laboratory Systems: One Person's Perspective - Revision history

Shawndouglas: Note

2024-06-21T00:07:01Z

Note

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	'''Publication date''': November 2021		'''Publication date''': November 2021

			NOTE: This was originally published on [https://www.limswiki.org/index.php/LII:Directions_in_Laboratory_Systems:_One_Person%27s_Perspective LIMSwiki.org] and is reproduced here using the same license.


	==Introduction==		==Introduction==

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Shawndouglas: /* About the content */

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About the content

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	This material follows in the footsteps of more than 15 years of writing and presentation on the topic. That writing and presentation—[[Book:LIMSjournal - Laboratory Technology Special Edition\|compiled here]]—includes:		This material follows in the footsteps of more than 15 years of writing and presentation on the topic. That writing and presentation—[[Book:LIMSjournal - Laboratory Technology Special Edition\|compiled here]]—includes:

	*[[~~LII~~:Are You a Laboratory Automation Engineer?\|''Are You a Laboratory Automation Engineer?'' (2006)]]		*[[Portfolio:Are You a Laboratory Automation Engineer?\|''Are You a Laboratory Automation Engineer?'' (2006)]]
	*[[~~LII~~:Elements of Laboratory Technology Management\|''Elements of Laboratory Technology Management'' (2014)]]		*[[Portfolio:Elements of Laboratory Technology Management\|''Elements of Laboratory Technology Management'' (2014)]]
	*[[LII:~~A Guide for Management~~: ~~Successfully Applying Laboratory Systems to Your Organization's Work\|~~''A Guide for Management: Successfully Applying Laboratory Systems to Your Organization's Work'' (2018)]]		*[https://www.limswiki.org/index.php/LII:A_Guide_for_Management:_Successfully_Applying_Laboratory_Systems_to_Your_Organization%27s_Work ''A Guide for Management: Successfully Applying Laboratory Systems to Your Organization's Work'' (2018)]
	*[[LII:~~Laboratory Technology Management & Planning\|~~''Laboratory Technology Management & Planning'' (2019)]]		*[https://www.limswiki.org/index.php/LII:Laboratory_Technology_Management_%26_Planning ''Laboratory Technology Management & Planning'' (2019)]
	*[[~~LII~~:Notes on Instrument Data Systems\|''Notes on Instrument Data Systems'' (2020)]]		*[[Portfolio:Notes on Instrument Data Systems\|''Notes on Instrument Data Systems'' (2020)]]
	*[[~~LII~~:Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering\|''Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering'' (2020)]]		*[[Portfolio:Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering\|''Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering'' (2020)]]
	*[[~~LII~~:Considerations in the Automation of Laboratory Procedures\|''Considerations in the Automation of Laboratory Procedures'' (2021)]]		*[[Portfolio:Considerations in the Automation of Laboratory Procedures\|''Considerations in the Automation of Laboratory Procedures'' (2021)]]
	*[[~~LII~~:The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies\|''The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies'' (2021)]]		*[[Portfolio:The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies\|''The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies'' (2021)]]


	While that material covers some of the “where do we go from here” discussions, I want to bring a lot of it together in one spot so that we can see what the entire picture looks like, while still leaving some of the details to the titles above. Admittedly, there have been some changes in thinking over time from what was presented in those pieces. For example, the concept of "laboratory automation engineering" has morphed into "laboratory systems engineering," given that in the past 15 years the scope of laboratory automation and computing has broadened significantly. Additionally, references to "scientific manufacturing" are now replaced with "scientific production," since laboratories tend to produce ideas, knowledge, results, information, and data, not tangible widgets. And as the state of laboratories continues to dynamically evolve, there will likely come more changes.		While that material covers some of the “where do we go from here” discussions, I want to bring a lot of it together in one spot so that we can see what the entire picture looks like, while still leaving some of the details to the titles above. Admittedly, there have been some changes in thinking over time from what was presented in those pieces. For example, the concept of "laboratory automation engineering" has morphed into "laboratory systems engineering," given that in the past 15 years the scope of laboratory automation and computing has broadened significantly. Additionally, references to "scientific manufacturing" are now replaced with "scientific production," since laboratories tend to produce ideas, knowledge, results, information, and data, not tangible widgets. And as the state of laboratories continues to dynamically evolve, there will likely come more changes.

Shawndouglas: Shawndouglas moved page LII:Directions in Laboratory Systems: One Person's Perspective to Portfolio:Directions in Laboratory Systems: One Person's Perspective without leaving a redirect: Namespace change

2024-06-20T23:54:15Z

Shawndouglas moved page LII:Directions in Laboratory Systems: One Person's Perspective to Portfolio:Directions in Laboratory Systems: One Person's Perspective without leaving a redirect: Namespace change

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Revision as of 16:54, 20 June 2024

Shawndouglas: 21 revisions imported: Importing my work from LIMSwiki, using the same CC license

2024-06-18T15:44:05Z

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

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Revision as of 08:44, 18 June 2024

test>Shawndouglas: Text replacement - "\[\[PerkinElmer Inc.(.*)" to "[[Vendor:PerkinElmer Inc.$1"

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

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	===1.2 The beginning of laboratory informatics systems===		===1.2 The beginning of laboratory informatics systems===
	In the early 1970s, [[PerkinElmer Inc.\|PerkinElmer]] described its instrument supporting computers as “data stations.” Then they announced the “laboratory information management system” or "LIMS," and the next level of informatics hit the lab market. However, “laboratory information management system” was a problematic name for a product that did sample and test tracking. The customers thought it would take into account all of a lab's information, including personnel records, scheduling, budgets, documents, anything that “information” could be attached to, ultimately promising more than it could deliver. It took some time, but eventually something like that happened. From a marketing standpoint, it got people’s attention.		In the early 1970s, [[Vendor:PerkinElmer Inc.\|PerkinElmer]] described its instrument supporting computers as “data stations.” Then they announced the “laboratory information management system” or "LIMS," and the next level of informatics hit the lab market. However, “laboratory information management system” was a problematic name for a product that did sample and test tracking. The customers thought it would take into account all of a lab's information, including personnel records, scheduling, budgets, documents, anything that “information” could be attached to, ultimately promising more than it could deliver. It took some time, but eventually something like that happened. From a marketing standpoint, it got people’s attention.

	Several other vendors, consulting companies, startups, and computer vendors began LIMS development projects (computer vendors felt that database systems were their turf). This was viewed as a strategic offering: the testing lab's operations would revolve around the LIMS, and that gave the LIMS vendor whose product was chosen a strong marketing position in that company.		Several other vendors, consulting companies, startups, and computer vendors began LIMS development projects (computer vendors felt that database systems were their turf). This was viewed as a strategic offering: the testing lab's operations would revolve around the LIMS, and that gave the LIMS vendor whose product was chosen a strong marketing position in that company.

test>Shawndouglas: Cats

2022-02-09T19:44:35Z

Cats

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	==References==		==References==
	{{Reflist\|colwidth=30em}}		{{Reflist\|colwidth=30em}}

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

test>Shawndouglas: /* It can make routine work easier and more productive, reducing costs and improving ROI */ Table 2 fix

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It can make routine work easier and more productive, reducing costs and improving ROI: Table 2 fix

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	{\| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="100%"		{\| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="100%"
	\|-		\|-
	\| colspan="4" style="background-color:white; padding-left:10px; padding-right:10px;" \|'''Table 2.''' Productivity of labor-processing area<br /> <br />FTE = Full-time equivalent; TLA = Total laboratory		\| colspan="4" style="background-color:white; padding-left:10px; padding-right:10px;" \|'''Table 2.''' Productivity of labor-processing area<br /> <br />FTE = Full-time equivalent; TLA = Total laboratory automation
	\|-		\|-
	! style="padding-left:10px; padding-right:10px;" \|Ratio		! style="padding-left:10px; padding-right:10px;" \|Ratio

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	The combination of robotics and microplates also worked well in biotechnology because of the prevalence of liquid samples; this point can not be stressed enough. We are good at working with fluids, including measuring amounts, transferring them, dispensing them, and so on. Solids can be a problem because of cross-contamination if equipment isn’t cleaned, if the solid is tacky, if the particle size isn’t right for the equipment, if it has a tendency to roll, and so on. Solids also have the potential for problems with homogeneity. (You can get layering in liquids, but that can be solved in “two shakes.”)		The combination of robotics and microplates also worked well in biotechnology because of the prevalence of liquid samples; this point can not be stressed enough. We are good at working with fluids, including measuring amounts, transferring them, dispensing them, and so on. Solids can be a problem because of cross-contamination if equipment isn’t cleaned, if the solid is tacky, if the particle size isn’t right for the equipment, if it has a tendency to roll, and so on. Solids also have the potential for problems with homogeneity. (You can get layering in liquids, but that can be solved in “two shakes.”)

	====Two approaches to sample processing with robotics====		====1.3.1 Two approaches to sample processing with robotics====
	Broadly speaking, there are two approaches to sample processing with robotics: batching and sample-at-a-time runs. The microplate is an example of batch processing. Each tray is handled (dilution, sealing, reading, etc.) at a station, and you don’t have an opportunity to evaluate the results until the analysis for a tray is completed and reported. Other methods such as ICP, mass spectrometry, chromatography, etc. that use auto-injectors can behave in a similar fashion, or be evaluated on a sample-at-a-time basis. It depends on how the process is planned and implemented, and at what stage the results are evaluated.		Broadly speaking, there are two approaches to sample processing with robotics: batching and sample-at-a-time runs. The microplate is an example of batch processing. Each tray is handled (dilution, sealing, reading, etc.) at a station, and you don’t have an opportunity to evaluate the results until the analysis for a tray is completed and reported. Other methods such as ICP, mass spectrometry, chromatography, etc. that use auto-injectors can behave in a similar fashion, or be evaluated on a sample-at-a-time basis. It depends on how the process is planned and implemented, and at what stage the results are evaluated.

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	In short, you have to have control of your samples and be able to ensure their integrity.		In short, you have to have control of your samples and be able to ensure their integrity.

	====The nature of incoming samples====		====1.4.1 The nature of incoming samples====
	Considerations about the nature of incoming samples don’t get as much press as they deserve. For example, if you are in quality control, the nature of your incoming samples is going to be consistent and determined by the production process. In fact, sample preparation is likely to be integrated with the test procedure’s automation. If the samples are fluids, the impact on an automation process may be small compared to working with solids. One complicating factor with fluids is the need to remove extraneous material so that downstream problems aren’t created. That removal may be accomplished by filtering, settling, centrifugal separation, batch centrifugation, or other means depending on the amount of material and its composition.		Considerations about the nature of incoming samples don’t get as much press as they deserve. For example, if you are in quality control, the nature of your incoming samples is going to be consistent and determined by the production process. In fact, sample preparation is likely to be integrated with the test procedure’s automation. If the samples are fluids, the impact on an automation process may be small compared to working with solids. One complicating factor with fluids is the need to remove extraneous material so that downstream problems aren’t created. That removal may be accomplished by filtering, settling, centrifugal separation, batch centrifugation, or other means depending on the amount of material and its composition.

test>Shawndouglas: Finished adding rest of content.

2021-11-17T23:39:17Z

Finished adding rest of content.

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	This material follows in the footsteps of more than 15 years of writing and presentation on the topic. That writing and presentation—[[Book:LIMSjournal - Laboratory Technology Special Edition\|compiled here]]—includes:		This material follows in the footsteps of more than 15 years of writing and presentation on the topic. That writing and presentation—[[Book:LIMSjournal - Laboratory Technology Special Edition\|compiled here]]—includes:

	*[[~~LII~~:Are You a Laboratory Automation Engineer?\|''Are You a Laboratory Automation Engineer?'' (2006)]]		*[[Portfolio:Are You a Laboratory Automation Engineer?\|''Are You a Laboratory Automation Engineer?'' (2006)]]
	*[[~~LII~~:Elements of Laboratory Technology Management\|''Elements of Laboratory Technology Management'' (2014)]]		*[[Portfolio:Elements of Laboratory Technology Management\|''Elements of Laboratory Technology Management'' (2014)]]
	*[[LII:~~A Guide for Management~~: ~~Successfully Applying Laboratory Systems to Your Organization's Work\|~~''A Guide for Management: Successfully Applying Laboratory Systems to Your Organization's Work'' (2018)]]		*[https://www.limswiki.org/index.php/LII:A_Guide_for_Management:_Successfully_Applying_Laboratory_Systems_to_Your_Organization%27s_Work ''A Guide for Management: Successfully Applying Laboratory Systems to Your Organization's Work'' (2018)]
	*[[LII:~~Laboratory Technology Management & Planning\|~~''Laboratory Technology Management & Planning'' (2019)]]		*[https://www.limswiki.org/index.php/LII:Laboratory_Technology_Management_%26_Planning ''Laboratory Technology Management & Planning'' (2019)]
	*[[~~LII~~:Notes on Instrument Data Systems\|''Notes on Instrument Data Systems'' (2020)]]		*[[Portfolio:Notes on Instrument Data Systems\|''Notes on Instrument Data Systems'' (2020)]]
	*[[~~LII~~:Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering\|''Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering'' (2020)]]		*[[Portfolio:Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering\|''Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering'' (2020)]]
	*[[~~LII~~:Considerations in the Automation of Laboratory Procedures\|''Considerations in the Automation of Laboratory Procedures'' (2021)]]		*[[Portfolio:Considerations in the Automation of Laboratory Procedures\|''Considerations in the Automation of Laboratory Procedures'' (2021)]]
	*[[~~LII~~:The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies\|''The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies'' (2021)]]		*[[Portfolio:The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies\|''The Application of Informatics to Scientific Work: Laboratory Informatics for Newbies'' (2021)]]


	While that material covers some of the “where do we go from here” discussions, I want to bring a lot of it together in one spot so that we can see what the entire picture looks like, while still leaving some of the details to the titles above. Admittedly, there have been some changes in thinking over time from what was presented in those pieces. For example, the concept of "laboratory automation engineering" has morphed into "laboratory systems engineering," given that in the past 15 years the scope of laboratory automation and computing has broadened significantly. Additionally, references to "scientific manufacturing" are now replaced with "scientific production," since laboratories tend to produce ideas, knowledge, results, information, and data, not tangible widgets. And as the state of laboratories continues to dynamically evolve, there will likely come more changes.		While that material covers some of the “where do we go from here” discussions, I want to bring a lot of it together in one spot so that we can see what the entire picture looks like, while still leaving some of the details to the titles above. Admittedly, there have been some changes in thinking over time from what was presented in those pieces. For example, the concept of "laboratory automation engineering" has morphed into "laboratory systems engineering," given that in the past 15 years the scope of laboratory automation and computing has broadened significantly. Additionally, references to "scientific manufacturing" are now replaced with "scientific production," since laboratories tend to produce ideas, knowledge, results, information, and data, not tangible widgets. And as the state of laboratories continues to dynamically evolve, there will likely come more changes.

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	:''C.'' Issues that need concerted attention:		:''C.'' Issues that need concerted attention:
	::1. Education for lab management and lab personnel		::1. Education for lab management and lab personnel
	::2. The conversion of manual methods to semi- or full-automated methods (see [[~~LII~~:Considerations in the Automation of Laboratory Procedures\|''Considerations in the Automation of Laboratory Procedures'']] for more)		::2. The conversion of manual methods to semi- or full-automated methods (see [[Portfolio:Considerations in the Automation of Laboratory Procedures\|''Considerations in the Automation of Laboratory Procedures'']] for more)
	::3. Long-term usable access to lab information in databases without vendor controls (i.e., the impact of [[software as a service]] and other software subscription models)		::3. Long-term usable access to lab information in databases without vendor controls (i.e., the impact of [[software as a service]] and other software subscription models)
	::4. Archived instrument data in standardized formats and standardized vendor software (requires tamper-proof formats)		::4. Archived instrument data in standardized formats and standardized vendor software (requires tamper-proof formats)
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	Laboratory work has become a merger of two disciplines: science and information technology (including robotics). Without the first, nothing happens; without the second, work will proceed but at a slower more costly pace. There are different levels of education requirements. For those working at the lab bench, not only do they need to understand the science, but also how the instrumentation and supporting computers systems (if any, including those embedded in the instrument) make and transform measurements into results. “The computer did it” is not a satisfactory answer to “how did you get that result,” nor is “magic," or maintaining willful ignorance of exactly how the instrument measurements are taken. Laboratorians are responsible and accountable for the results, and they should be able to explain the process of how they were derived, including how settings on the instrument and computer software affect that work. Lab managers should understand the technologies at the functional level and how the systems interact with each other. They are accountable for the overall integrity of the systems and the data and information they contain. IT personnel should understand how lab systems differ from office applications and why business-as-usual for managing office applications doesn’t work in the lab environment. The computer systems are there to support the instruments, and any changes that may affect that relationship should be initiated with care; the instrument vendor’s support for computer systems upgrades is essential.		Laboratory work has become a merger of two disciplines: science and information technology (including robotics). Without the first, nothing happens; without the second, work will proceed but at a slower more costly pace. There are different levels of education requirements. For those working at the lab bench, not only do they need to understand the science, but also how the instrumentation and supporting computers systems (if any, including those embedded in the instrument) make and transform measurements into results. “The computer did it” is not a satisfactory answer to “how did you get that result,” nor is “magic," or maintaining willful ignorance of exactly how the instrument measurements are taken. Laboratorians are responsible and accountable for the results, and they should be able to explain the process of how they were derived, including how settings on the instrument and computer software affect that work. Lab managers should understand the technologies at the functional level and how the systems interact with each other. They are accountable for the overall integrity of the systems and the data and information they contain. IT personnel should understand how lab systems differ from office applications and why business-as-usual for managing office applications doesn’t work in the lab environment. The computer systems are there to support the instruments, and any changes that may affect that relationship should be initiated with care; the instrument vendor’s support for computer systems upgrades is essential.

	As such, we need a new personnel position, that of the laboratory systems engineer or LSE, to provide support for the informatics architecture. This isn’t simply an IT person; it should be someone who is fluent in both the science and the information technology applied to lab work. (See [[~~LII~~:Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering\|''Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering'']] for more on this topic.)		As such, we need a new personnel position, that of the laboratory systems engineer or LSE, to provide support for the informatics architecture. This isn’t simply an IT person; it should be someone who is fluent in both the science and the information technology applied to lab work. (See [[Portfolio:Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering\|''Laboratory Technology Planning and Management: The Practice of Laboratory Systems Engineering'']] for more on this topic.)

	===C-3. Long-term usable access to lab information in databases without vendor controls===		===C-3. Long-term usable access to lab information in databases without vendor controls===
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	'''Key point''': ''Today, people’s attitudes about work have changed, and with it the world has changed; the [[COVID-19]] [[pandemic]] has forced us to re-evaluate models of work. If nothing else, even though we’re talking about science, the use of technology to conduct scientific work is going to take on a new importance. This won’t be solved one lab at a time, but on an industry-by-industry basis. We need to think about key concepts and their implementation as a community if truly effective solutions are to be found and put into practice.''		'''Key point''': ''Today, people’s attitudes about work have changed, and with it the world has changed; the [[COVID-19]] [[pandemic]] has forced us to re-evaluate models of work. If nothing else, even though we’re talking about science, the use of technology to conduct scientific work is going to take on a new importance. This won’t be solved one lab at a time, but on an industry-by-industry basis. We need to think about key concepts and their implementation as a community if truly effective solutions are to be found and put into practice.''

	In [[~~LII~~:Considerations in the Automation of Laboratory Procedures\|''Considerations in the Automation of Laboratory Procedures'']], the criteria for "automation readiness" were described. Two significant points were that a laboratory procedure must both be stable and have a duration of use sufficiently long enough to justify the cost of automation. Beyond that, additional concerns such as safety may come into play, but those two points were the most critical. From those points we can roughly derive the automation needs of research, testing, quality control, and contract laboratories.		In [[Portfolio:Considerations in the Automation of Laboratory Procedures\|''Considerations in the Automation of Laboratory Procedures'']], the criteria for "automation readiness" were described. Two significant points were that a laboratory procedure must both be stable and have a duration of use sufficiently long enough to justify the cost of automation. Beyond that, additional concerns such as safety may come into play, but those two points were the most critical. From those points we can roughly derive the automation needs of research, testing, quality control, and contract laboratories.

	'''Research laboratory''': Automation in research is going to be predominately at the task level, i.e., portions of a process being done by automated instruments and devices rather than end-to-end automation. This is due to the two key points noted above: research labs often change procedures, with some being very short-lived, and the cost of full-automation (including validation) may not be worth it unless the equipment is designed to be modular, interconnected, and easily programmed. One exception can be seen with Bayer.<ref name="CNNMicro15">{{cite web \|url=https://www.youtube.com/watch?v=_PuTKH7143c \|title=Micro robots drive Bayer's high-tech vision \|author=CNN Business \|work=YouTube \|date=17 April 2015 \|accessdate=17 November 2021}}</ref> They are using robotics and microplate technology to automate a high-throughput screen system that couldn’t—in their words—be done practically by people; it's too slow and too expensive. Could something like this become more commonplace?		'''Research laboratory''': Automation in research is going to be predominately at the task level, i.e., portions of a process being done by automated instruments and devices rather than end-to-end automation. This is due to the two key points noted above: research labs often change procedures, with some being very short-lived, and the cost of full-automation (including validation) may not be worth it unless the equipment is designed to be modular, interconnected, and easily programmed. One exception can be seen with Bayer.<ref name="CNNMicro15">{{cite web \|url=https://www.youtube.com/watch?v=_PuTKH7143c \|title=Micro robots drive Bayer's high-tech vision \|author=CNN Business \|work=YouTube \|date=17 April 2015 \|accessdate=17 November 2021}}</ref> They are using robotics and microplate technology to automate a high-throughput screen system that couldn’t—in their words—be done practically by people; it's too slow and too expensive. Could something like this become more commonplace?
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	<!---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]]