Portfolio:A Science Student's Guide to Laboratory Informatics - Revision history

Shawndouglas: Added summary.

2024-06-21T02:10:24Z

Added summary.

Shawndouglas: Shawndouglas moved page LII:A Science Student's Guide to Laboratory Informatics to Portfolio:A Science Student's Guide to Laboratory Informatics without leaving a redirect: Namespace change

2024-06-21T02:06:02Z

Shawndouglas moved page LII:A Science Student's Guide to Laboratory Informatics to Portfolio:A Science Student's Guide to Laboratory Informatics without leaving a redirect: Namespace change

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Revision as of 19:06, 20 June 2024

Shawndouglas: 16 revisions imported: Importing my work from LIMSwiki, using the same CC license

2024-06-18T20:28:00Z

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

← Older revision

Revision as of 13:28, 18 June 2024

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

2024-03-29T16:17:35Z

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

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	That same facility is available through an IDS, but only for the devices that the IDS is connected to, e.g., chromatographs, spectrometers, etc. In addition to that function, IDSs support instrumental data collection, analysis, and reporting. They can also be linked to LIMS and ELNs by electronically receiving worklists and then electronically sending the results back, thus avoiding the need for entering the data manually.		That same facility is available through an IDS, but only for the devices that the IDS is connected to, e.g., chromatographs, spectrometers, etc. In addition to that function, IDSs support instrumental data collection, analysis, and reporting. They can also be linked to LIMS and ELNs by electronically receiving worklists and then electronically sending the results back, thus avoiding the need for entering the data manually.

	The LES is also an aid to the laboratory, ensuring that laboratory methods and procedures are carried out correctly, with documented support for each step in the method. They can be seen as a quasi-automation system, except instead of automation hardware doing the work, the laboratorian is doing it, guided step-by-step by strict adherence to the method as embedded in software. The problem that this type of system, originally styled as an “electronic laboratory notebook” by Velquest Inc. (later purchased by [[Accelrys, Inc.\|Accelrys]]) was to ensure that there was documented evidence that every step in a lab procedure was properly carried out by qualified personnel, using calibrated/maintained instruments, current reagents, with all data electronically captured with potential links to LIMS or other systems. That system would provide bullet-proof support for data and information generated by procedures in regulated environments. That in turn means that the data/information produced is reliable and can stand up to challenges.		The LES is also an aid to the laboratory, ensuring that laboratory methods and procedures are carried out correctly, with documented support for each step in the method. They can be seen as a quasi-automation system, except instead of automation hardware doing the work, the laboratorian is doing it, guided step-by-step by strict adherence to the method as embedded in software. The problem that this type of system, originally styled as an “electronic laboratory notebook” by Velquest Inc. (later purchased by [[Vendor:Accelrys, Inc.\|Accelrys]]) was to ensure that there was documented evidence that every step in a lab procedure was properly carried out by qualified personnel, using calibrated/maintained instruments, current reagents, with all data electronically captured with potential links to LIMS or other systems. That system would provide bullet-proof support for data and information generated by procedures in regulated environments. That in turn means that the data/information produced is reliable and can stand up to challenges.

	Implementations of LES have ranged from stand-alone applications that linked to LIMS, ELNs, and SDMS, to programmable components of LIMS and ELNs. Instead of having a stand-alone framework to implement an LES, as with Velquest's product, embedded systems provide a scripting (i.e., programming by the user) facility within a LIMS that has access to the entire LIMS database, avoiding the need to interface two products. That embedded facility put a lot of pressure on the programmer to properly design, test, and validate each procedure in an isolated structure, separate from the active LIMS so that programming errors didn’t compromise the integrity of the database. Note: procedure execution in stand-alone systems requires validation as well.		Implementations of LES have ranged from stand-alone applications that linked to LIMS, ELNs, and SDMS, to programmable components of LIMS and ELNs. Instead of having a stand-alone framework to implement an LES, as with Velquest's product, embedded systems provide a scripting (i.e., programming by the user) facility within a LIMS that has access to the entire LIMS database, avoiding the need to interface two products. That embedded facility put a lot of pressure on the programmer to properly design, test, and validate each procedure in an isolated structure, separate from the active LIMS so that programming errors didn’t compromise the integrity of the database. Note: procedure execution in stand-alone systems requires validation as well.

Shawndouglas: LIMS FAQ to Q&A

2024-02-23T22:57:22Z

LIMS FAQ to Q&A

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	*'''American Association for Laboratory Accreditation (A2LA)''': This includes guidelines and accreditation requirements that labs must adhere to as part of accrediting to a particular standard. This includes standards like the [[ISO 9000]] family of standards and [[ISO/IEC 17025]]. The ISO 9000 family is a set of five QMS standards that help organizations ensure that they meet customer and other stakeholder needs within statutory and regulatory requirements related to a product or service. ISO/IEC 17025 ''General requirements for the competence of testing and calibration laboratories'' is the primary standard used by testing and calibration laboratories, and there are special technology considerations to be made when complying. (See ''[[LII:LIMS Selection Guide for ISO/IEC 17025 Laboratories\|LIMS Selection Guide for ISO/IEC 17025 Laboratories]]'' for more on this topic.) In most countries, ISO/IEC 17025 is the standard for which most labs must hold accreditation to be deemed technically competent.		*'''American Association for Laboratory Accreditation (A2LA)''': This includes guidelines and accreditation requirements that labs must adhere to as part of accrediting to a particular standard. This includes standards like the [[ISO 9000]] family of standards and [[ISO/IEC 17025]]. The ISO 9000 family is a set of five QMS standards that help organizations ensure that they meet customer and other stakeholder needs within statutory and regulatory requirements related to a product or service. ISO/IEC 17025 ''General requirements for the competence of testing and calibration laboratories'' is the primary standard used by testing and calibration laboratories, and there are special technology considerations to be made when complying. (See ''[[LII:LIMS Selection Guide for ISO/IEC 17025 Laboratories\|LIMS Selection Guide for ISO/IEC 17025 Laboratories]]'' for more on this topic.) In most countries, ISO/IEC 17025 is the standard for which most labs must hold accreditation to be deemed technically competent.

	A comment should be made about the interplay of regulations, standards, and guidelines. The difference between regulations and standards is that regulations have the law to support their enforcement.<ref name="PankoninReg21">{{cite web \|url=https://www.aem.org/news/regulations-vs-standards-clearing-up-the-confusion \|title=Regulations vs. Standards: Clearing up the Confusion \|author=Pankonin, M. \|publisher=Association of Equipment Manufacturers \|date=27 May 2021 \|accessdate=17 November 2023}}</ref> Standards are consensus agreements that companies, industries, and associations use to define “best practices.” Guidelines are proposed standards of organizational behavior that may or may not eventually become regulations. The FDA regulations for example, began as guidelines, underwent discussion and modification, and eventually became regulations under 21 CFR Part 11. For a more nuanced discussion in one particular lab-related area, materials science, see ''[[LIMS ~~FAQ~~:What standards and regulations affect a materials testing laboratory?\|What standards and regulations affect a materials testing laboratory?]]''.		A comment should be made about the interplay of regulations, standards, and guidelines. The difference between regulations and standards is that regulations have the law to support their enforcement.<ref name="PankoninReg21">{{cite web \|url=https://www.aem.org/news/regulations-vs-standards-clearing-up-the-confusion \|title=Regulations vs. Standards: Clearing up the Confusion \|author=Pankonin, M. \|publisher=Association of Equipment Manufacturers \|date=27 May 2021 \|accessdate=17 November 2023}}</ref> Standards are consensus agreements that companies, industries, and associations use to define “best practices.” Guidelines are proposed standards of organizational behavior that may or may not eventually become regulations. The FDA regulations for example, began as guidelines, underwent discussion and modification, and eventually became regulations under 21 CFR Part 11. For a more nuanced discussion in one particular lab-related area, materials science, see ''[[LIMS Q&A:What standards and regulations affect a materials testing laboratory?\|What standards and regulations affect a materials testing laboratory?]]''.

	===Meeting the needs of data governance, data integrity, and regulatory compliance===		===Meeting the needs of data governance, data integrity, and regulatory compliance===

Shawndouglas: Cat

2024-01-04T15:45:37Z

Cat

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	<!---Place all category tags here-->		<!---Place all category tags here-->
	[[Category:LII:Guides, white papers, and other publications\|A Science Student's Guide to Laboratory Informatics]]		[[Category:LII:Guides, white papers, and other publications\|Science Student's Guide to Laboratory Informatics]]

Shawndouglas: About the author

2023-11-18T14:34:32Z

About the author

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	==In closing...==		==In closing...==
	The purpose of this document is to give the student a high-level overview of the purpose and use of the major informatics systems that are commonly used in industrial research and service laboratories. This is an active area of development, with new products and platforms being released annually, usually around major conferences. The links included are starting points to increasing the depth of the material.		The purpose of this document is to give the student a high-level overview of the purpose and use of the major informatics systems that are commonly used in industrial research and service laboratories. This is an active area of development, with new products and platforms being released annually, usually around major conferences. The links included are starting points to increasing the depth of the material.

			==About the author==
			Initially educated as a chemist, author Joe Liscouski (joe dot liscouski at gmail dot com) is an experienced laboratory automation/computing professional with over forty years of experience in the field, including the design and development of automation systems (both custom and commercial systems), LIMS, robotics and data interchange standards. He also consults on the use of computing in laboratory work. He has held symposia on validation and presented technical material and short courses on laboratory automation and computing in the U.S., Europe, and Japan. He has worked/consulted in pharmaceutical, biotech, polymer, medical, and government laboratories. His current work centers on working with companies to establish planning programs for lab systems, developing effective support groups, and helping people with the application of automation and information technologies in research and quality control environments.

	==References==		==References==

Shawndouglas: /* Systems development: tinkering vs. engineering */

2023-11-18T01:30:48Z

Systems development: tinkering vs. engineering

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	AI offers a great deal of potential benefits to laboratory work, something marketers are going to exploit to attract more customers. Product offerings need to be viewed skeptically as supposed benefits may be less than promised, or not as fully tested as needed. Unlike dealing with spelling checkers that consistently make improper word substitutions, AI-generated errors in data analysis are dangerous because they may go undetected.		AI offers a great deal of potential benefits to laboratory work, something marketers are going to exploit to attract more customers. Product offerings need to be viewed skeptically as supposed benefits may be less than promised, or not as fully tested as needed. Unlike dealing with spelling checkers that consistently make improper word substitutions, AI-generated errors in data analysis are dangerous because they may go undetected.

	==Systems development: ~~tinkering~~ vs. engineering==		==Systems development: Tinkering vs. engineering==
	One common practice in laboratory work, particularly in research, is modifying equipment or creating new configurations of equipment and instruments to get work done. That same thought pattern often extends to software development; components such as spreadsheets, compilers, database systems, and so on are common parts of laboratory computer systems. Many people include programming as part of their list of skills. That can lead to the development of special purpose software to solve issues in data handling and analysis.		One common practice in laboratory work, particularly in research, is modifying equipment or creating new configurations of equipment and instruments to get work done. That same thought pattern often extends to software development; components such as spreadsheets, compilers, database systems, and so on are common parts of laboratory computer systems. Many people include programming as part of their list of skills. That can lead to the development of special purpose software to solve issues in data handling and analysis.

Shawndouglas: Finished updates.

2023-11-18T01:25:48Z

Finished updates.

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	'''Publication date''': November 2023		'''Publication date''': November 2023

	~~{{ombox~~
	~~\| type = notice~~
	~~\| image = [[Image:Emblem-important-yellow.svg\|40px]]~~
	~~\| style = width: 500px;~~
	~~\| text = This article should be considered a work in progress and incomplete. Consider this article incomplete until this notice is removed.~~
	}}

	==Introduction==		==Introduction==
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	The LES is also an aid to the laboratory, ensuring that laboratory methods and procedures are carried out correctly, with documented support for each step in the method. They can be seen as a quasi-automation system, except instead of automation hardware doing the work, the laboratorian is doing it, guided step-by-step by strict adherence to the method as embedded in software. The problem that this type of system, originally styled as an “electronic laboratory notebook” by Velquest Inc. (later purchased by [[Accelrys, Inc.\|Accelrys]]) was to ensure that there was documented evidence that every step in a lab procedure was properly carried out by qualified personnel, using calibrated/maintained instruments, current reagents, with all data electronically captured with potential links to LIMS or other systems. That system would provide bullet-proof support for data and information generated by procedures in regulated environments. That in turn means that the data/information produced is reliable and can stand up to challenges.		The LES is also an aid to the laboratory, ensuring that laboratory methods and procedures are carried out correctly, with documented support for each step in the method. They can be seen as a quasi-automation system, except instead of automation hardware doing the work, the laboratorian is doing it, guided step-by-step by strict adherence to the method as embedded in software. The problem that this type of system, originally styled as an “electronic laboratory notebook” by Velquest Inc. (later purchased by [[Accelrys, Inc.\|Accelrys]]) was to ensure that there was documented evidence that every step in a lab procedure was properly carried out by qualified personnel, using calibrated/maintained instruments, current reagents, with all data electronically captured with potential links to LIMS or other systems. That system would provide bullet-proof support for data and information generated by procedures in regulated environments. That in turn means that the data/information produced is reliable and can stand up to challenges.

	Implementations of LES have ranged from stand-alone applications that linked to LIMS, ELNs, and SDMS, to programmable components of LIMS and ELNs. Instead of having a stand-alone framework to implement an LES as with Velquest's product, embedded systems provide a scripting (i.e., programming by the user) facility within a LIMS that has access to the entire LIMS database, avoiding the need to interface two products. That embedded facility put a lot of pressure on the programmer to properly design, test, and validate each procedure in an isolated structure, separate from the active LIMS so that programming errors didn’t compromise the integrity of the database. Note: procedure execution in stand-alone systems requires validation as well.		Implementations of LES have ranged from stand-alone applications that linked to LIMS, ELNs, and SDMS, to programmable components of LIMS and ELNs. Instead of having a stand-alone framework to implement an LES, as with Velquest's product, embedded systems provide a scripting (i.e., programming by the user) facility within a LIMS that has access to the entire LIMS database, avoiding the need to interface two products. That embedded facility put a lot of pressure on the programmer to properly design, test, and validate each procedure in an isolated structure, separate from the active LIMS so that programming errors didn’t compromise the integrity of the database. Note: procedure execution in stand-alone systems requires validation as well.

	As for the IDS, instrument vendors of the late 1960s explored the benefits of connecting laboratory instruments to computer systems to see what could be gained from that combination. One problem they wanted to address was the handling of the large volumes of data that instruments produced. At that time, analog instrument output was often recorded on chart paper, and a single sample through a chromatograph might be recorded on a chart that was one or more feet long. A day’s work generated a lot of paper that had to be evaluated manually, which proved time-consuming and labor-intensive. Vendors have since successfully developed computer-instrument combinations that automatically transform the instrument's analog output to a digital format, and then store and process that data to produce useful information (results), eliminating the manual effort and making labs more cost-effective in the process. This was the first step in instrument automation; the user was still required to introduce the sample into the device. The second step solved that problem in many instances through the creation of automatic samplers that moved the samples into position for analysis. This includes auto-injectors, flow-through cells, and other autosamplers, depending on the analytical technique.		As for the IDS, instrument vendors of the late 1960s explored the benefits of connecting laboratory instruments to computer systems to see what could be gained from that combination. One problem they wanted to address was the handling of the large volumes of data that instruments produced. At that time, analog instrument output was often recorded on chart paper, and a single sample through a chromatograph might be recorded on a chart that was one or more feet long. A day’s work generated a lot of paper that had to be evaluated manually, which proved time-consuming and labor-intensive. Vendors have since successfully developed computer-instrument combinations that automatically transform the instrument's analog output to a digital format, and then store and process that data to produce useful information (results), eliminating the manual effort and making labs more cost-effective in the process. This was the first step in instrument automation; the user was still required to introduce the sample into the device. The second step solved that problem in many instances through the creation of automatic samplers that moved the samples into position for analysis. This includes auto-injectors, flow-through cells, and other autosamplers, depending on the analytical technique.
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	==Systems development: tinkering vs. engineering==		==Systems development: tinkering vs. engineering==
			One common practice in laboratory work, particularly in research, is modifying equipment or creating new configurations of equipment and instruments to get work done. That same thought pattern often extends to software development; components such as spreadsheets, compilers, database systems, and so on are common parts of laboratory computer systems. Many people include programming as part of their list of skills. That can lead to the development of special purpose software to solve issues in data handling and analysis.

			That activity in an industrial lab is potentially problematic. Organizations have controls over what software development is permitted so that organizational security isn’t compromised and that the development activities do not create problems with organizational or regulatory requirements and guidelines.

			If a need for software develops, there are recognized processes for defining, implementing, and validating those projects. One of the best-known in laboratory science comes from ISPE's GAMP guidelines.<ref name="ISPEWhatIsGAMP" /> There is also a discussion of the methodology in ''[[LII:Considerations in the Automation of Laboratory Procedures\|Considerations in the Automation of Laboratory Procedures]]''.

			The development process begins with a “needs analysis” that describes why the project is being undertaken and what it is supposed to accomplish, along with the benefits of doing it. That is followed by a user-requirements document that has to be agreed upon before the project begins. Once that is done, a prototype system(s) can be developed that will give you a chance to explore different options for development, project requirements, etc., that will form the basis of a design specification for the development of the actual project (whereupon the prototype is scrapped). At this point, the rest of the GAMP process is followed through the completion of the project. The end result is a proven, working, documented system that can be relied upon (based on evidence) to work and be supported. If changes are needed, the backup documentation is there to support that work.

			This is an engineering approach to systems development. Those systems may result in software, a sample preparation process, or the implementation of an automated test method. It is needed to ensure that things work, and if the developer is no longer available, the project can still be used, supported, modified, etc., as needed. The organizations investment is protected, the data and information produced can be supported and treated as reliable, and all guidelines and regulations are being met.

			==In closing...==
			The purpose of this document is to give the student a high-level overview of the purpose and use of the major informatics systems that are commonly used in industrial research and service laboratories. This is an active area of development, with new products and platforms being released annually, usually around major conferences. The links included are starting points to increasing the depth of the material.

	==References==		==References==

Shawndouglas: Saving and adding more.

2023-11-18T01:14:59Z

Saving and adding more.

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