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| text      = This is sublevel2 of my sandbox, where I play with features and test MediaWiki code. If you wish to leave a comment for me, please see [[User_talk:Shawndouglas|my discussion page]] instead.<p></p>
| text      = This is sublevel9 of my sandbox, where I play with features and test MediaWiki code. If you wish to leave a comment for me, please see [[User_talk:Shawndouglas|my discussion page]] instead.<p></p>
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==Sandbox begins below==
==Sandbox begins below==
{{Infobox journal article
|name        =
|image        =
|alt          = <!-- Alternative text for images -->
|caption      =
|title_full  = The development and application of bioinformatics core competencies to improve bioinformatics training and education
|journal      = ''PLOS Computational Biology''
|authors      = Mulder, Nicola; Schwartz, Russell; Brazas, Michelle, D.; Brooksbank, Carth; Gaeta, Bruno; Morgan, Sarah L.;<br />Pauley, Mark A.; Rosenwald, Anne; Rustici, Gabriella; Sierk, Michael; Warnow, Tandy; Welch, Lonnie
|affiliations = University of Cape Town, Carnegie Mellon University, Ontario Institute for Cancer Research, Wellcome Genome Campus, University of New South Wales, University<br />of Nebraska at Omaha, Georgetown University, University of Cambridge, Saint Vincent College, University of Illinois at Urbana-Champaign, Ohio University
|contact      = Email: nicola dot mulder at uct dot ac dot za
|editors      = Troyanskaya, Olga G.
|pub_year    = 2018
|vol_iss      = '''14'''(2)
|pages        = e1005772
|doi          = [http://10.1371/journal.pcbi.1005772 10.1371/journal.pcbi.1005772]
|issn        = 1553-7358
|license      = [http://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International]
|website      = [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005772 http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005772]
|download    = [http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005772&type=printable http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005772&type=printable] (PDF)
}}
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| text      = This article should not be considered complete until this message box has been removed. This is a work in progress.
}}
==Abstract==
[[Bioinformatics]] is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.


==Introduction==
==1. Introduction to manufacturing laboratories==
The need for bioinformatics education and training is immense, but it is also diverse. There is a wide range of audiences who are potential recipients of training, each of which has different needs in terms of what skills or knowledge they require and at what depth. For example, someone training to be a bioinformatics engineer (which we define as someone who will actively be involved in the development and application of bioinformatics algorithms) requires in-depth knowledge of existing algorithms, how they work, how to critically evaluate them, and how to interpret the results. By contrast, a bioinformatics user (which we define as someone making use of bioinformatics resources in an applied context, such as in medical practice) would need a basic level of understanding of the methods and a stronger focus on the interpretation of the outputs. In a recent publication<ref name="WelchApplying16">{{cite journal |title=Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee) |journal=PLOS Computational Biology |author=Welch, L.; Brooksban, C.; Schwartz, R. et al. |volume=12 |issue=5 |page=e1004943 |year=2016 |doi=10.1371/journal.pcbi.1004943 |pmid=27175996 |pmc=PMC4866758}}</ref>, the ISCB Education Committee’s Curriculum Task Force described the potential for refinement and application of bioinformatics core competencies for different user groups. Here, we describe the further refinement of these competencies and provide a series of use cases illustrating their applications to different bioinformatics education and training programs globally.
According to McKinsey & Company, the U.S. manufacturing industry represents only 11 percent of U.S. gross domestic product (GDP) and eight percent of direct employment, yet it "makes a disproportionate economic contribution, including 20 percent of the nation’s capital investment, 35 percent of productivity growth, 60 percent of exports, and 70 percent of business R&D spending."<ref name="CarrDeliver22">{{cite web |url=https://www.mckinsey.com/capabilities/operations/our-insights/delivering-the-us-manufacturing-renaissance |title=Delivering the US manufacturing renaissance |author=Carr, T.; Chewning, E.; Doheny, M. et al. |work=McKinsey & Company |date=29 August 2022 |accessdate=24 March 2023}}</ref> These categories of economic contribution are important as many of them indirectly point to how the work of [[Laboratory|laboratories]] is interwoven within the manufacturing industry. As we'll discuss later in this chapter, manufacturing-based laboratories primarily serve three roles: research and development (R&D), pre-manufacturing and manufacturing, and post-production regulation and security (e.g., through exports and trade). We can be sure that if U.S. manufacturers' efforts represent huge chunks of total business R&D spending, trade, and capital expenditure (capex), a non-trivial amount of laboratory effort is associated with that spending. Why? Because R&D, trade, and manufacturing [[quality control]] (QC) activities rarely can occur without laboratories backing up their work.<ref>{{Cite journal |last=Ischi |first=H. P. |last2=Radvila |first2=P. R. |date=1997-01-17 |title=Accreditation and quality assurance in Swiss chemical laboratories |url=http://link.springer.com/10.1007/s007690050092 |journal=Accreditation and Quality Assurance |volume=2 |issue=1 |pages=36–39 |doi=10.1007/s007690050092 |issn=0949-1775}}</ref><ref>{{Cite book |last=Crow |first=Michael M. |last2=Bozeman |first2=Barry |date=1998 |title=Limited by design: R&D laboratories in the U.S. national innovation system |url=https://books.google.com/books?hl=en&lr=&id=OVPZvqz2e6UC |chapter=Chapter 1: The Sixteen Thousand: Policy Analysis, R&D Laboratories, and the National Innovation System |publisher=Columbia University Press |place=New York |pages=1–40 |isbn=978-0-585-04137-7}}</ref><ref>{{Cite journal |last=Grochau |first=Inês Hexsel |last2=ten Caten |first2=Carla Schwengber |date=2012-10 |title=A process approach to ISO/IEC 17025 in the implementation of a quality management system in testing laboratories |url=http://link.springer.com/10.1007/s00769-012-0905-3 |journal=Accreditation and Quality Assurance |language=en |volume=17 |issue=5 |pages=519–527 |doi=10.1007/s00769-012-0905-3 |issn=0949-1775}}</ref><ref>{{Cite journal |last=Ribeiro, À.S.; Gust, J.; Vilhena, A. et al. |year=2019 |title=The role of laboratories in the international development of accreditation |url=https://www.imeko.info/index.php/proceedings/7687-the-role-of-laboratories-in-the-international-development-of-accreditation |journal=Proceedings of the 16th IMEKO TC10 Conference "Testing, Diagnostics & Inspection as a comprehensive value chain for Quality & Safety" |pages=56–9}}</ref>
 
Labs in the manufacturing sector provide vital services, including but not limited to [[quality assurance]] (QA), QC, production control, regulatory trade control (e.g., authenticity and adulteration), safety management, label claim testing, and packaging analysis. These activities occur in a wide array of manufacturing industries. Looking to the North American Industry Classification System (NAICS), employed by the U.S. Bureau of Labor Statistics (BLS), manufacturing industries and sub-industries include<ref name="BLSManufact23">{{cite web |url=https://www.bls.gov/iag/tgs/iag31-33.htm |title=Manufacturing: NAICS 31-33 |work=Industries at a Glance |publisher=U.S. Bureau of Labor Statistics |date=24 March 2023 |accessdate=24 March 2023}}</ref>:
 
*apparel (e.g., knitted goods, cut-and-sew clothing, buttons and clasps)
*chemical (e.g., pesticides, fertilizers, paints, cleaning products, adhesives, electroplating solutions)
*electric power (e.g., light bulbs, household appliances, energy storage cells, transformers)
*electronics (e.g., sensors, semiconductors, electrodes, mobile phones, computers)
*food and beverage (e.g., baked goods, probiotics, preservatives, wine)
*furniture (e.g., mattresses, sofas, window blinds, light fixtures)
*leather (e.g., purses, saddles, footwear, bookbinding hides)
*machinery (e.g., mining augers, air conditioning units, turbines, lathes)
*materials (e.g., ceramics, cements, glass, nanomaterials)
*medical equipment and supplies (e.g., ventilators, implants, lab equipment, prosthetics, surgical equipment)
*metal forming and casting (e.g., steel beams, aluminum ingots, shipping containers, hand tools, wire)
*paper and printing (e.g., cardboard, sanitary items, stationery, books, bookbinding papers)
*petrochemical (e.g., solvents, fuel additives, biofuels, lubricants)
*pharmaceutical and medicine (e.g., antivenom, vaccines, lab-on-a-chip diagnostic tests, cannabis products, nutraceuticals)
*plastics and rubbers (e.g., dinnerware, tires, storage and shelving, outdoor furniture)
*textiles (e.g., carpeting, upholstery, bulk fabric, yarn)
*vehicular and aerospace (e.g., electric vehicles, reusable rocketry, railroad rolling stock, OEM auto parts)
*wood (e.g., plywood, flooring, lumber, handrails)
 
If you've ever used a sophisticated two-part epoxy adhesive to repair a pipe crack, used an indoor sun lamp, gotten a lot of mileage out of a pair of leather gloves, received a medical implant, taken a medication, eaten a Twinkie, or ridden on Amtrak, one or more laboratories were involved somewhere in the manufacturing process before using that item. From endless research and testing of prototypes to various phases of quality and safety testing, laboratory science was involved. The importance of the laboratory in manufacturing processes can't be understated.
 
But what of the history of the manufacturing-focused lab? What of the roles played and testing conducted in them? What do they owe to safety and quality? This chapter more closely examines these questions and more.
 
 
===1.1 Manufacturing labs, then and now===
In 1852, the ''Putnam's Home Cyclopedia: Hand-Book of the Useful Arts'' was published as a dictionary-like source of scientific terms. Its definition of a laboratory at that time in U.S. history is revealing (for more on the equipment typically described with a laboratory of that time period, see the full definition)<ref name="AntisellPutnamArts52">{{cite book |url=https://books.google.com/books?id=vsI0AAAAMAAJ&pg=PA284 |title=Putnam's Home Cyclopedia: Hand-Book of the Useful Arts |author=Antisell, T. |publisher=George P. Putnam |volume=3 |pages=284-5 |year=1852 |accessdate=31 March 2023}}</ref>:
 
<blockquote>'''Laboratory'''. The workshop of a chemist. Some laboratories are intended for private research, and some for the manufacture of chemicals on the large scale. Hence it is almost impossible to give a description of the apparatus and disposition of a laboratory which would be generally true of all. A manufacturing laboratory necessarily occupies a large space, while that of the scientific man is necessarily limited to a peculiar line of research. Those who study in organic chemistry have different arrangements than that of the mineral analyst.</blockquote>
 
This definition highlights the state of laboratories at the time: typically you either had a small private laboratory for experiments in the name of research and development (R&D) and producing prototype solutions, or you had a slightly larger "manufacturing laboratory" that was responsible for the creation of chemicals, reagents, or other substances for a wider customer base.<ref name="AntisellPutnamArts52" /><ref name="PorterTheChem30">{{cite book |url=https://books.google.com/books?id=zy8aAAAAYAAJ&pg=PA17&dq=manufacturing+laboratory |title=The Chemistry of the Arts; being a Practical Display of the Arts and Manufactures which Depend on Chemical Principles |chapter=Chemistry Applied to the Arts |author=Porter, A.L. |publisher=Carey & Lea |year=1830 |pages=17–18 |accessdate=06 April 2023 |quote=The larger laboratories, or workshops, which are used only in particular branches of business, and the necessary apparatus attached to them, will be considered under the several substances which are prepared in them. Besides the workshop, every operative chemist ought to devote some part of his premises as a small general elaboratory, fitted up with some furnaces and other apparatus as may enable him to make any experiment seemingly applicable to the improvement of his manufacturing process without loss of time, and immediately upon its inception.}}</ref><ref name="MarshSpeech46">{{cite book |url=https://books.google.com/books?id=ptg-AAAAYAAJ&pg=PA11&dq=manufacturing+laboratory |title=Speech of Mr. Marsh, of Vermont, on the Hill for Establishing the Smithsonian Institution, Delivered in The House of Representatives of the U. States, April 22, 1846 |author=Marsh, G. P. |publisher=J. & G.S. Gideon |year=1846 |page=11 |accessdate=06 April 2023 |quote=How are new substances formed, or the stock of a given substance increased, by the chemistry of nature or of art? By new combinations or decompositions of known and pre-existing elements. The products of the experimental or manufacturing laboratory are no new creations; but their elements are first extracted by the decomposition of old components, and then recombined in new forms.}}</ref> These laboratory types date back further than the mid-1800s, to be sure, though they also saw great change leading up to and after this time period. This is best characterized by the transition from the humble apothecary lab to the small-scale manufacturing laboratory before the mid-1800s, to the full-scale pharmaceutical manufacturing lab and facility well beyond the mid-1800s.
 
====1.1.1 From apothecary to small-scale manufacturing laboratory====
A critical area to examine in relation to the evolution of manufacturing laboratories involves pharmaceuticals and the apothecary, which is steeped in the tradition of making pharmaceutical preparations, as well as prescribing and dispensing them to customers. The idea of an individual who attempted to make medical treatments dates back to at least to 2000 BC, from which Sumerian documents reveal compounding formulas for various medicinal dosage types.<ref name="AllenAHist11">{{cite journal |url=https://www.perrigo.com/business/pdfs/Sec%20Artem%2011.3.pdf |archiveurl=https://web.archive.org/web/20130128014521/https://www.perrigo.com/business/pdfs/Sec%20Artem%2011.3.pdf |format=PDF |title=A History of Pharmaceutical Compounding |journal=Secundum Artem |author=Allen Jr., L.V. |volume=11 |issue=3 |year=2011 |archivedate=28 January 2013 |accessdate=06 April 2023}}</ref> By 1540, Swiss physician and chemist Paracelsus made a significant contribution to the early apothecary, influencing "the transformation of pharmacy from a profession based primarily on botanic science to one based on chemical science."<ref name="AllenAHist11" /> Thanks to Paracelsus and other sixteenth century practitioners, the concept of the apothecary became more formalized and chemistry-based in the early seventeenth century. With this formalization came the need for the regulation of apothecaries to better ensure the integrity of the profession. For example, the Master, Wardens and Society of the Art and Mystery of Pharmacopolites of the City of London was founded in 1617 through the Royal Charter of James the First, requiring an aspiring apothecary to conduct an apprenticeship or pay a fee, followed by taking an examination proving the individual's knowledge, skill, and science in the art.<ref name="AllenAHist11" /><ref name="Plough97">{{cite journal |url=https://www.google.com/books/edition/Pharmaceutical_Journal/ScDyXwC8McwC?hl=en&gbpv=1&dq=manufacturing+laboratory&pg=PA164&printsec=frontcover |title=The Plough Court Pharmacy |journal=The Pharmaceutical Journal |publisher=Pharmaceutical Society of Great Britain |volume=LVIII |pages=164–7, 247–51 |date=January to June 1897 |accessdate=06 April 2023}}</ref>
 
However, despite this sort of early regulation, medical practitioners took exception to apothecaries encroaching upon the medical practitioners' own services, and apothecaries took exception to the untrained and uncertified druggists who were still performing the work of pharmacists. (As it turns out, these sorts of recriminations would continue on in some form or another into the beginning of the twenty-first century, discussed later.) But as an 1897 article from ''The Pharmaceutical Journal'' portrayed, the apothecaries likely wanted to have their cake and eat it too. "[W]hile the apothecaries urged, in the interest of the public, the desirability of a guarantee for the the competences of every person authorised to practise pharmacy," the journal noted, "they also sought, in their own interest, to extend the scope of their medical practice."<ref name="Plough97" /> This led to further debate and changes over time, including British Parliament declaring medicinal preparations as "very proper objects for taxation" in 1783, while at the same time requiring non-apprenticed apothecaries to apply annually for a license. By this time, most apprenticed apothecaries ceased being perceived as mere pharmacists and more as medical practitioners, though the Society's power of conferring medical qualifications, given to them in 1617, were by this point largely lost.<ref name="Plough97" />
 
By the end of the eighteenth century, apothecaries and druggists were setting up their own manufacturing laboratories to make chemical and pharmaceutical products. However, these labs were likely still limited in scope. In 1897, ''The Pharmaceutical Journal'' portrayed manufacturing labs as such, in the scope of the growing Plough Court Pharmacy run by William Allen and Luke Howard<ref name="Plough97" />:
 
<blockquote>It is, however, difficult to at the present time to realise what must have been the position of a manufacturing chemist in 1797, or to comprehend, without some reflection, how limited was the range of his operations and how much his work was beset with difficulties which are now scarecely conceivable. At that time chemical industry was confined to the production of soap, the mineral acids, and some saline compounds then used in medicine. Among the latter, mercurial preperations held an important place, and some of these appear to have first received attention by the firm of Allen and Howard. The early laboratory account books of the firm mention ammoniacals, caustic potash, borax, argentic nitrate, and cream of tartar, as well as ether, benzoic acid, and refine camphor, which were then articles of the materia medics, citric, tartatic and oxalic acids, etc.</blockquote>
 
To be sure, other types of manufacturing were occurring during the rise and dominance of the apothecary, not just pharmaceutical manufacture. But, retrospectively, the pharmaceutical manufacturing lab in general was likely not in the best of shape as the nineteenth century approached. With several changes in Europe and United States in the early 1800s, the apothecary's manufacturing lab arguably saw more formalized and regulated activity, through various releases of pharmacopoeias<ref name="AllenAHist11" /><ref name="AndersonPharm13">{{cite web |url=http://www.histpharm.org/ISHPWG%20UK.pdf |format=PDF |title=Pharmacopoeias of Great Britain |work=A History of the Pharmacopoeias of the World |author=Anderson, S.C. |publisher=International Society for the History of Pharmacy |pages=1–8 |year=2013 |accessdate=06 April 2023}}</ref>, openings of new pharmacy schools (though still limited in scope)<ref name="DCTheEarly18">{{cite journal |url=https://books.google.com/books?id=P3kgAQAAMAAJ&pg=RA2-PA243-IA1&dq=manufacturing+laboratory |title=The Early Days of Pharmaceutical |journal=The Druggists Circular |volume=LXII |issue=6 |pages=244–5 |date=June 1918 |accessdate=06 April 2023}}</ref>, publishing of books<ref name="DCTheEarly18" />, and additional formalization of regulating legislation (such as Britain's Apothecaries Act of 1815).<ref name="Plough97" /> By the time the ''United States Pharmacopeia'' came upon the scene in 1820, the apothecary was viewed as "competent at collecting and identifying botanic drugs and preparing from them the mixtures and preparations required by the physician."<ref name="AllenAHist11" /> Pharmaceutical historian Loyd Allen, Jr. refers to this time period as "a time that would never be seen again," a sort of Golden Age of the apothecary, given the increasingly rapid rate that scientific and technological discoveries were being made soon after, particularly in synthetic organic chemistry.<ref name="AllenAHist11" />
 
Of course, the manufacturing lab—pharmaceutical and otherwise—had other issues as well. For example, just because a small-scale experimental R&D process yielded a positive result didn't mean that process was scalable to large-scale manufacturing. "Frequently, things work well on a small scale, and failure results when mass action comes into effect," noted Armour Fertilizer Company's president Charles McDowell in April 1917, while discussing American research methods.<ref name="McDowellAmerican17">{{cite journal |url=https://books.google.com/books?id=8pMPAQAAIAAJ&pg=PA546&dq=manufacturing+laboratory |title=American Research Methods |journal=Journal of the Western Society of Engineers |author=McDowell, C.A. |volume=XXII |issue=8 |year=1917 |pages=546–65 |accessdate=06 April 2023}}</ref> Sometimes a process was sufficiently simple that switching to more robust and appropriate apparatuses was all that was needed to scale up from experiment to full production.<ref name="RobertsonDesulph43">{{cite journal |url=https://books.google.com/books?id=3u01AQAAMAAJ&pg=RA1-PA444&dq=manufacturing+laboratory |title=Desulphuration of Metals |journal=Mechanics' Magazine, Museum, Register, Journal, and Gazette |editor=Robertson, J.C. |volume=38 |date=01 July 1843 |page=444 |accessdate=06 April 2023}}</ref> In other cases, a full-scale manufacturing laboratory process had yet to be developed, let alone the experiments conducted to develop a proof-of-concept solution in the experimental lab.<ref name="JacksonChemical43">{{cite journal |url=https://books.google.com/books?id=hrYxAQAAMAAJ&pg=PA379&dq=manufacturing+laboratory |title=Chemical Salts as Fertilizers |journal=New England Farmer, and Horticultural Register |author=Jackson, C.T. |publisher=Joseph Breck & Co |volume=XXL |issue=48 |page=379 |date=31 May 1843 |accessdate=06 April 2023}}</ref>
 
Another challenge the manufacturing lab had was in ensuring the stability of any laboratory manufactured solution. Discussing the British Pharmacopoeia-introduced substance of sulphurous acid for afflictions of the throat, Fellow of the Chemical Society Charles Umney noted the stability considerations of the substance when made in the manufacturing laboratory<ref name="UmneySulphurous69">{{cite journal |url=https://books.google.com/books?id=POkKAAAAYAAJ&pg=PA516&dq=manufacturing+laboratory |title=Sulphurous Acid |journal=Pharmaceutical Journal and Transactions |author=Umney, C. |publisher=John Churchill and Sons |volume=X |issue=IX |pages=516–20 |year=1869 |accessdate=06 April 2023}}</ref>:
 
<blockquote>Now the Pharmacopoeia solution (which is about 37 volumes) was designedly made nearly one of saturation at the average summer temperature of this country, and, if one may be excused for making a guess, we described from calculations made from the above data of Bunsen's, and not practically worked out to see whether such a solution could be ordinarily obtained in the manufacturing laboratory without chance of failure, and, when made, be kept without great alteration in the various stages it would have to pass through, even if only from the manufacturer to the wholesale druggist, then to the pharmacists, in whose store it might retain for a year or more, being perhaps placed in a temperature many degrees above the point at which it was saturated, thereby causing expansion, liberation of gas, and inconvenience.</blockquote>
 
Difficulties aside, as the 1800s progressed, the resources of a collaboratory manufacturing laboratory were often greater than those of the individual private laboratory, with enterprising businesses increasingly turning to larger labs for greater and more high-quality quantities of materials. For example, in a letter from the Royal Institution of Great Britain, editor William Crookes discussed the discovery of thallium, noting that the manufacturing lab of noted manufacturing chemists Hopkin and Williams were able to prepare chloride of thallium for him from two hundredweight (cwt) in less time than it took Crookes to make 10 pounds of sulfur in his private laboratory.<ref name="CrookesOnThe63">{{cite journal |url=https://books.google.com/books?id=0JHOIc5pHYwC&pg=PA172&dq=manufacturing+laboratory |title=On the Discovery of the Metal Thallium |journal=The Chemical News and Journal of Physical Chemistry |author=Crookes, W. |volume=VII |issue=175 |pages=172–6 |date=April 1863 |accessdate=06 April 2023}}</ref> This trend would continue into the late 1800s, for pharmaceutical and other manufactured goods.
 
====1.1.2 From small-scale private manufacturing lab to larger-scale industrial manufacturing lab====
By the 1860s, numerous changes to the paradigm of the manufacturing lab were beginning to take shape, with noticeable momentum away from the small-scale private manufacturing labs to those larger in scope and output, putting competitive pressures on the smaller manufacturing labs.<ref name="PearsonThePrep11">{{cite journal |url=https://books.google.com/books?id=GyFFAQAAMAAJ&pg=PA415&dq=manufacturing+laboratory |title=The Preparation and Testing of Drugs |journal=The Journal of the Franklin Institute of the State of Pennsylvania |author=Pearson, W.A. |volume=CLXXI |issue=4 |pages=415–21 |date=April 1911 |accessdate=12 April 2023 |quote=All the large drug laboratories have been developed since 1860 ... The increase in number of manufacturing laboratories and the consequent increase in competition exerted an influence on the wholesale druggist.}}</ref> Take, for example, one of the largest U.S.-based enameled brick factories for its time, in 1896, which "[i]n addition to their manufacturing laboratory for slips, enamels and glazes, they maintain an analytical chemical laboratory, and have two chemists in their employ."<ref name="LockingtonEnamled96">{{cite journal |url=https://books.google.com/books?id=lj9PAQAAIAAJ&pg=RA1-PA350&dq=manufacturing+laboratory |title=Enamled Brick at Oaks, PA |journal=The Clay-Worker |author=Lockington, W.P. |volume=XXV |issue=4 |pages=350–51 |date=April 1896 |accessdate=07 April 2023}}</ref> Ten years prior, a report on the visit to the experimental and manufacturing laboratories of Louis Pasteur highlights the need for a more sizeable facility for meeting demand for the anthrax vaccine<ref name="RobertsonReport86">{{cite journal |url=https://books.google.com/books?id=a-AfAQAAIAAJ&pg=PA223&dq=manufacturing+laboratory |title=Report of Visit to the Laboratories of M. Pasteur at Paris |journal=The Veterinary Journal and Annals of Comparative Pathology |author=Robertson, W. |volume=XXIII |pages=223–7 |year=1886 |accessdate=07 April 2023}}</ref>:
 
<blockquote>To meet the demands upon the laboratory work for the supply of anthrax vaccine, the preparation of this is now carried out in an establishment apart from the experimental laboratory in connection with the Ecole Normale, where it was originally started. In the Rue Vaquelin, under the charge of educated assistants, M. Chamberland carries out the preparation on a large scale—the necessity for this being apparent when regard is had to the statement of the quantity demanded for France and other countries.</blockquote>
 
The author, William Robertson, then goes into greater detail of the many rooms and floors of the building housing the manufacturing laboratory and its apparatuses, highlighting the grandness of the lab's efforts.
 
The change from small-scale private to larger-scale industrial manufacturing labs—in turn seemingly being supplanted by analytical laboratories<ref name="TWDDrugClerks02">{{cite journal |url=https://books.google.com/books?id=qG8gAQAAMAAJ&pg=PA405&dq=manufacturing+laboratory |title=Drug Clerks and Labor Unions |journal=The Western Druggist |author=The Western Druggist |volume=XXIV |issue=7 |page=405 |date=July 1902 |accessdate=12 April 2023}}</ref>—is arguably best seen in the transition from the apothecary and pharmacist to the large-scale pharmaceutical manufacturer. During this time of change in the late 1800s, laws dictating higher manufacturing quality, educational requirements, and restrictions on who can sell medicines were derided, debated, or cheered, depending on who was involved.<ref name="LillyTheRel83">{{cite journal |url=https://books.google.com/books?id=VlyFy6zJQpUC&pg=RA2-PA258&dq=manufacturing+laboratory |title=The Relation of Manufacturing Pharmacists to Pharmacy Laws |journal=The Pharmacist and Chemist |author=Lilly, J.K. |volume=XVI |issue=1 |pages=258–9 |date=January 1883 |accessdate=06 April 2023}}</ref><ref name="ParkerSomeAsp96">{{cite journal |url=https://books.google.com/books?id=bSnnAAAAMAAJ&pg=PA183&dq=manufacturing+laboratory |title=Some Aspects of Technical Pharmacy |journal=American Druggist and Pharmaceutical Record |author=Parker, C.E. |volume=XXVIII |issue=6 |pages=183–4 |date=25 March 1896 |accessdate=12 April 2023}}</ref>
 
Reading for a meeting at the Kings County Pharmaceutical Society of Ohio, Charles E. Parker had the following to say about the state of the apothecary-turned-pharmacist in 1896, which fully highlights the transition from small-scale private to larger-scale industrial manufacturing of pharmaceuticals<ref name="ParkerSomeAsp96" />:
 
<blockquote>The modern pharmacist succeeds to all the responsibilities and obligations of the ancient apothecary without opposition, but his utmost efforts have not preserved to him his inheritance of former privileges and emoluments ... Technical skill is of no use to the professional side of pharmacy unless it is used, and used for the public welfare as well as that of its possessor. The dispenser is the ''typical'' pharmacist. But where in former years his sphere included many activities and much manipulative expertness in the preparation of drugs, and even the production of many of them, the midern tendancy is for him to become a mere compounder and dispenser. Of course he is expected to know how, but actually is seldom required to perform the operations once a matter of constant routine. Step by step the productive processes of his little laboratory have been transferred to the works of large manufacturers. Year by year the pharmaceutical improvements and useful inventions which would once have conferred reputation and profit upon the dispensing pharmacies where they originated, have found a better market through these same manufacturers ... In addition, it is to be considered that some of the requisites of modern pharmacy are of a nature involving the use of expensive machinery and large plant, which places their production quite beyond the reach of the pharmacy.</blockquote>
 
Writing for the ''Pharmaceutical Review'' in 1897, editor Dr. Edward Kremers penned an editorial on the role of the manufacturing laboratory in the growing pharmaceutical industry, noting that "[d]uring the past hundred years a most remarkable industrial revolution has taken place," and that pharmacy was also victim to that, lamenting that the apothecaries of the beginning of the century—along with the druggists of 1897—had largely become "relics of the past."<ref name="KremersTheManu97">{{cite journal |url=https://books.google.com/books?id=4BU4AQAAMAAJ&pg=PA61&dq=manufacturing+laboratory |title=The Manufacturing Laboratory in the Household of Pharmacy |journal=Pharmaceutical Review |author=Kremers, E. |volume=15 |issue=4 |pages=61–7 |date=April 1897 |accessdate=12 April 2023}}</ref> Kremers also touched upon another complaint popular at the time: that of pharmacy as a money-making venture.<ref name="TWDDrugClerks02" /><ref name="KremersTheManu97" /> In his editorial, Kremers says:
 
<blockquote>It is a hope cherished by some that higher education will revolutionize pharmacy of today and lift her out of her present unenviable situation. The manufacturing industries, however, have revolutionized pharmacy of fifty years ago and are to no small extent coresponsible for the present state of affairs. The pharmaceutical profession as a whole is justified in asking what a particular branch is doing for the general good. Is the pharmaceutical manufacturer in the erection of his buildings, in the equipment of his laboratories and in the selection of his working force simply bent upon making so many thousands of dollars a paying investment, viewed from a merely commercial standpoint, or are his doings influenced to some extent to at least by higher than purely necessary motives.</blockquote>
 
By the early years of 1900, recognition of the sea-level change to the apothecary, pharmacist, and manufacturing laboratory had arguably gained traction, and by 1920 it was largely accepted<ref name="BealAward19">{{cite journal |url=https://books.google.com/books?id=GQlOAAAAMAAJ&pg=PA475&dq=manufacturing+laboratory |title=Award of the Joseph B. Remington Honor Medal |journal=The Midland Druggist and Pharmaceutical Review |author=Diner, J.; Beal, J.H. |volume=LIII |issue=12 |pages=475–9 |date=December 1919 |accessdate=12 April 2023}}</ref>. Writing for ''The Rocky Mountain Druggist'' in 1908, pharmaceutical doctor Geo H. Meeker laid it out in no uncertain terms:
 
<blockquote>Large manufacturing establishments can, for the most part, furnish the druggist at lower prices, with better authentic goods than he himself could produce, assay and guarantee. The inevitable result is that the druggist of today purchases finished products rather than raw materials as did the apothecary of yesterday. It is obvious that a large manufacturing establishment, conducted on ethical lines, employing a complete corps of specialists, buying raw materials to the best advantage and by assay only, making preparations on a large and intelligent technical scale and testing and assying the finished products, does a work that is too immense in its scope for the individual apothecary ... Our present remnant of the drug store laboratory is, as in the past, essentially a manufacturing laboratory. It is of limited and rapidly vanishing scope because the small local laboratory man cannot successfully compete with his rivals, the great and highly-organized factories.</blockquote>
 
Similar comments were being made by Pearson in 1911<ref name="PearsonThePrep11" />, Thiesing in 1915<ref name="Thiesing15">{{cite journal |url=https://books.google.com/books?id=b_5EAQAAMAAJ&pg=PA1203&dq=manufacturing+laboratory |title=Proceedings of the Joint Session of the Commercial Section and Section on Education and Legislation - Chairman Thiesing's Address |journal=The Journal of the Americam Pharmaceutical Association |author=Thiesing, E.H. |volume=IV |issue=10 |pages= |date=October 1915 |accessdate=12 April 2023}}</ref>, and Beal in 1919.<ref name="BealAward19" /> Beal in particular spoke solemnly of the transition, largely complete by the time of his acceptance of the Joseph P. Remington Honor Medal in 1919. Speaking of Remington and his experiences in pharmacy, until his death in 1918, Beal said<ref name="BealAward19" />:
 
<blockquote>Professor Remington's professional experience bridged the space between two distinct periods of pharmaceutical development. When he began his apprenticeship the apothecary, as he was then commonly called, was the principal manufacturer as well as the purveyor of medical supplies ... He lived to see the period when the apothecary ceased to be the principal producer of medicinal compounds and became mainly the purveyor of preparations manufactured by others, and when the medicinal agents in most common use assumed a character that required for the successful production the resources of establishments maintained by large aggregations of capital and employing large numbers of specially trained workers.
 
To those who knew him intimately it was evident that although Professor Remington did not welcome the passing of the manufacturing functions of the apothecary to the large laboratory, he at length came to realize that such a change was inevitable, that it was but a natural step in the process of social evolution, and that the logical action of the apothecary was not to resist that which he could neither prevent nor change, but to readjust himself to the new conditions.</blockquote>


==Development of core competencies for bioinformatics==
Of course, by then, the rise of the industrial research lab within large-scale manufacturing enterprises was in full swing.
The ISCB Curriculum Task Force undertook the task of identifying some of the breadth of needs for bioinformatics education, as described in a series of reports from the task force. This effort arose first from a series of surveys of current training practice and desired training needs<ref name="WelchAReport12">{{cite journal |title=A report of the Curriculum Task Force of the ISCB Education Committee |journal=PLOS Computational Biology |author=Welch, L.R.; Schwartz, R.; Lewitter, F. |volume=8 |issue=6 |page=e1002570 |year=2012 |doi=10.1371/journal.pcbi.1002570 |pmid=22761560 |pmc=PMC3386154}}</ref>, which identified a set of broad categories of training needs but also widespread disparities across programs in what was taught, how, and for what intended target audiences. An outcome of these surveys was the need for identifying a set of core competencies as broad categories of skills and training that cross different programs and training needs and that can provide a basis for discussing similarities and differences between programs and desired outcomes. This led to a further effort to define a set of initial core competencies<ref name="WelchBioinformatics14">{{cite journal |title=Bioinformatics curriculum guidelines: toward a definition of core competencies |journal=PLOS Computational Biology |author=Welch, L.; Lewitter, F; Schwartz, R. et al. |volume=10 |issue=3 |page=e1003496 |year=2014 |doi=10.1371/journal.pcbi.1003496 |pmid=24603430 |pmc=PMC3945096}}</ref> that in turn led to an intensive program of community engagement to refine these competencies to better serve the breadth of needs of the bioinformatics training community.


There were three major steps in the development of the core competencies: (1) defining the competencies needed for using bioinformatics, (2) defining a variety of user profiles describing distinct subgroups in need of training, and (3) defining how the competencies will apply to each user profile (scoring). The core competency framework was developed through an iterative process with input from multiple parties from diverse backgrounds with a connection to bioinformatics. In order to gain a broader appreciation of which competencies the bioinformatics community considers relevant for different bioinformatics user profiles, the ISCB Curriculum Task Force has run several competency workshops (discussion sessions for defining the competencies and their applications) both at ISCB conferences and at other bioinformatics education venues such as the GOBLET (Global Organisation for Bioinformatics Learning, Education and Training) Annual General Meeting. Each iteration of a competency workshop has greatly enhanced not only the competencies themselves but also the definitions of the user profiles<ref name="WelchApplying16" /> and the competency-use case scoring mechanism.
====1.1.3 The rise of the industrial research lab within large-scale manufacturing, and today's manufacturing landscape====
Like the small, privately owned manufacturing labs evolving to large-scale company-run manufacturing labs, so did the research processes of prior days. The individual tinkering with research in their private laboratory and making small batches of product gave way to a collective of individuals with more specialized talents cooperatively working in a large industrial manufacturing center towards a common, often complex research goal, i.e., within the industrial research laboratory.<ref name="MeesTheOrg20">{{cite book |url=https://books.google.com/books?id=rDIuAAAAYAAJ&printsec=frontcover&dq=industrial+research+laboratories |title=The Organization of Industrial Scientific Research |chapter=Chapter 1: Introduction |author=Mees, C.E.K. |publisher=McGraw-Hill Book Company, Inc |pages=4–10 |year=1920 |accessdate=12 April 2023}}</ref><ref name="BoydPutting24">{{cite journal |url=https://books.google.com/books?id=lYkiAQAAMAAJ&pg=RA23-PA22&dq=industrial+research+laboratories |title=Putting Research to Work |journal=A.E.C. Bulletin - Invention and The Engineer's Relation to It |author=Boyd, T.A. |publisher=American Engineering Council |pages=22–9 |date=May 1938 |accessdate=12 April 2023}}</ref> Those larger manufacturing entities that didn't have an industrial research lab were beginning to assess the value of adding one, while smaller enterprises that didn't have the resources to support an extensive collection of manufacturing and research labs were increasingly joining forces "to maintain laboratories doing work for the whole industry."<ref name="MeesTheOrg20" />  


Initially, the mapping of bioinformatics competencies to audiences considered three major user profiles: (1) the bioinformatics user; (2) the bioinformatics scientist; and (3) the bioinformatics engineer. Early competency workshops quickly surmised that these user profiles were too narrow and did not adequately capture the breadth of roles requiring bioinformatics competency and curriculum. Participants spent much of the workshop time defining a bioinformatics user or distinguishing a bioinformatics scientist from a bioinformatics engineer. The use case roles were subsequently expanded to better embody the breadth of bioinformatics users, including physicians, lab technicians, ethicists and biocurators, scientists (which include the discovery biologist, academic bioinformatics researcher, and core facility scientist), and engineers (which may be a bioinformatician in academia, bioinformatician in research institute, or software engineer). This change allowed for subsequent workshop participants to self-select according to the category of user with which they most identified.
But what drove the advance of the industrial research lab? As the National Research Council pointed out in 1940, "individuals working independently could not, for very long, provide the technical and scientific knowledge essential to a rapidly developing industrial nation."<ref name="NRCRsearch40">{{cite book |url=https://nap.nationalacademies.org/read/20233/chapter/4#34 |title=Research—A National Resource, II—Industrial Research |author=National Research Council |publisher=United States Government Printing Office |date=December 1940 |accessdate=13 April 2023}}</ref> Newly emerging industries had a need for new knowledge to feed their growth, and they proved to be the early adopters of establishing separate research departments or divisions in their businesses, unlike businesses in long-established industries. The First World War was also responsible for driving organized research efforts in various industries to solve not only wartime problems but also plant the seed of development in peacetime industries. By 1920, two-thirds of all research workers surveyed by the National Research Council were employed in the emerging electrical, chemical, and rubber industries, though the overall adoption of industrial research approaches was still limited across all companies.<ref name="NRCRsearch40" />


With user profiles better defined, competency workshops then struggled with the competencies themselves and their definitions. Several early competency definitions appeared to overlap. For example, “Apply knowledge of computing appropriate to the discipline (e.g., effectively utilize bioinformatics tools)” closely resembled “Analyze a problem and identify and define the computing requirements appropriate to its solution (e.g., define algorithmic time and space complexities and hardware resources required to solve a problem).” Workshop participants helped to reduce the redundancy in our initial set of bioinformatics competencies from 20 competencies to a refined set of 16 competencies.
In 1917, the previously mentioned Charles McDowell presented his view of American research and manufacturing methods of his time, referring to research as "diligent inquiry."<ref name="McDowellAmerican17" /> In his work, McDowell stated three types of research that leads up to the manufacturing process: pure scientific inquiry, industrial research, and factory research. He noted that of pure scientific inquiry, little thought is typically given to whether the research—often conducted by university professors—will have any real commercial value, though such value is able to emerge from this fundamental research. As for factory research, McDowell characterized it as full-scale factory-level operations that range from haphazard approaches to well-calculated contingency planning, all of which could make or break the manufacturing business.


Competency workshops have additionally helped to revise the scoring of competencies for each user profile. Early workshops scored the applicability of a bioinformatics competency to a particular profile with a simple yes/no response, which did not allow for an appreciation of the depth of the competency necessary for a given profile. Such a scoring approach, while better than no score, would not be helpful when developing a curriculum for a specific user profile. Subsequent workshops used a graded scoring approach, with grades ranging from 1 (no competency required) to 4 (specialist knowledge required). This, too, proved too ambiguous to allow for meaningful discussion and classification. The scoring approach was thus revised again to the current model, which uses the Bloom’s Revised Taxonomy<ref name="AndersonATax01">{{cite book |title=A Taxonomy for Learning, Teaching, and Assessing: A Revision of Bloom's Taxonomy of Educational Objectives |editor=Anderson, L.W.; Krathwohl, D.R. |publisher=Pearson |pages=336 |year=2001 |isbn=9780801319037}}</ref> terms: knowledge, comprehension, application, analysis, synthesis, and evaluation. While the use of Bloom’s Taxonomy has been useful in mapping competency levels to each of the user profiles, this change required refinement of the competency list as several of the earlier competencies incorporated Bloom’s Taxonomy terms.
In regards to the middle category of industrial research, McDowell made several observations that aptly described the state of manufacturing research in the early 1900s. He noted that unlike pure scientific inquiry, industrial research had commercial practicality as a goal, often beginning with small-scale experiments while later seeking how to reproduce those theoretical results into large-scale manufacturing. He also reiterated his point about needing to "have good backing" financially. "The larger manufacturer maintains his own staff and equipment to carry out investigations along any line that may seem desirable," he said, "but the smaller industries are not able to support an establishment and must rely on either consulting engineers or turn their problems over to some equipped public or private laboratory to solve."<ref name="McDowellAmerican17" />  


Overall, competency workshops have been invaluable to the enhancement and refinement of the bioinformatics competencies. Through these workshops, the ISCB Curriculum Task Force has been able to construct a useful set of bioinformatics competencies that curriculum developers can use to develop, compare, and assess impactful bioinformatics training programs for a wide range of audiences and ultimately help establish bioinformatics skills in such audiences.<ref name="WelchBioinformatics14" />
In his 1920 book ''The Organization of Industrial Scientific Research'', Mees presented these three types of research somewhat similarly, though in the context of the industrial laboratory and its operations. Mees argued that industrial laboratories could be classified into three divisions<ref name="MeesTheOrg20" />:


Table 1 reports the current state of the competencies developed and refined through this community engagement process. Tables 2–4 map these refined competencies to a broader set of personas, suggested over the course of the Task Force’s community engagement efforts, via Bloom’s Taxonomy terms. For reference, Table 5 provides examples and definitions of the Bloom's Revised Taxonomy terms. In the next section, we provide some examples of how the competencies have been applied in a variety of training contexts.
*Laboratories "working on pure theory and the fundamental sciences associated with the industry," aligning in part with McDowell's "pure scientific inquiry";
*Work laboratories "exerting analytical control over materials, processes and product," aligning slightly with McDowell's "factory research" but more akin to the modern quality control lab; and
*Industrial laboratories "working on improvements in product and in processes," aligning with McDowell's "industrial research."


Mees argued in particular that those industrial research laboratories that simply improve products and processes were not doing enough; they should, necessarily, also direct some of their goals towards more fully understanding the fundamental and underlying theory of the topic of research.<ref name="MeesTheOrg20" /> In other words, Mees suggested that those labs simply working on theoretical and fundamental science research, as well as those labs conducting industrial research to improve products and processes, shouldn't necessarily function in separate vacuums. "Research work of this fundamental kind involves a laboratory very different from the usual works laboratory and also investigators of a different type from those employed in a purely industrial laboratory," he noted. Of course, this hybrid approach to fundamental and industrial research was largely reserved for the largest of manufacturers, and solutions were needed for smaller manufacturing endeavors. Here, like McDowell in 1917, Mees argued for smaller businesses with limited resources adopting both cooperative laboratory (those businesses that pool resources together for a fully supported research laboratory) and consulting laboratory (a third-party lab with the resources to fully study a problem, undertake investigations, model a manufacturing process, and implement that process into its client's factory, all for a fee) approaches.<ref name="MeesTheOrg20" /> With such solutions, the industrial research laboratory continued to take on a new level of complexity to address emerging industry needs, far from the humble origins of an early nineteenth-century manufacturing laboratory.


[[File:Tab1 Mulder PLOSCompBio2018 14-2.png|800px]]
This growth or industrial research would continue onward from the twentieth century into the twenty-first century. In 1921, some 15 companies maintained research groups of more than 50 people; by 1938, there were 120 such businesses.<ref name="NRCRsearch40" /> By the 1990s, "the share of funding for basic research provided by industry actually grew from 10 percent to 25 percent of the national total, even though basic research accounted for just 5-7 percent of total R&D expenditures by industry."<ref name="UsselmanResearch13">{{cite web |url=https://economics.yale.edu/sites/default/files/usselman_paper.pdf |title=Research and Development in the United States since 1900: An Interpretive History |author=Usselman, S.W. |publisher=Yale University |date=11 November 2013 |accessdate=13 April 2023}}</ref> This trend of large research groups continues today, though with the recognition that smaller teams may still have advantages. In a 2019 article in the ''Harvard Business Review'', Wang and Evans recognize "large teams as optimal engines for tomorrow’s largest advances," while smaller research teams are better poised to ask disruptive questions and make innovative discoveries.<ref name="WangResearch19">{{cite web |url=https://hbr.org/2019/02/research-when-small-teams-are-better-than-big-ones |title=Research: When Small Teams Are Better Than Big Ones |work=Harvard Business Review |authors=Wang, D.; Evans, J.A. |date=21 February 2019 |accessdate=13 April 2023}}</ref>
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{|
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{| border="0" cellpadding="5" cellspacing="0" width="800px"
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  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Table 1.''' Bioinformatics core competencies. This table provides the current competency list following a process of community engagement. It specifically reflects a significant refinement of the competencies designed to accommodate scoring in terms of Bloom’s Taxonomy.</blockquote>
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[[File:Tab2 Mulder PLOSCompBio2018 14-2.png|900px]]
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{| border="0" cellpadding="5" cellspacing="0" width="900px"
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  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Table 2.''' Mapping of competencies to bioinformatics user personas via Bloom’s Taxonomy</blockquote>
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[[File:Tab3 Mulder PLOSCompBio2018 14-2.png|900px]]
===1.2 Laboratory roles and activities in the industry===
{{clear}}
Today, the "manufacturing laboratory" is a complex entity that goes beyond the general idea of a lab making or researching things. Many of the historical aspects discussed prior still hold today, but other aspects have changed. As indicated in the introduction, the world of manufacturing encompasses a wide swath of industries and sub-industries, each with their own nuances. Given the nuances of pharmaceutical manufacturing, food and beverage development, petrochemical extraction and use, and other industries, it's difficult to make broad statements about manufacturing laboratories in general. However, the rest of this guide will attempt to do just that, while at times pointing out a few of those nuances found in specific industries.
{|
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{| border="0" cellpadding="5" cellspacing="0" width="900px"
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  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Table 3.''' Mapping of competencies to bioinformatics scientist personas via Bloom’s Taxonomy</blockquote>
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[[File:Tab4 Mulder PLOSCompBio2018 14-2.png|900px]]
The biggest area of commonality is found, unsurprisingly, in the roles manufacturing-based labs play today, as well as the types of lab activities they're conducting within those roles. These roles prove to be important in the greater scheme of industry activities, in turn providing a number of benefits to society. As gleaned from prior discussion, as well as other sources, these laboratory roles can be broadly broken into three categories: research and development (R&D), pre-manufacturing and manufacturing, and post-production regulation and security. Additionally, each of these categories has its own types of laboratory activities.
{{clear}}
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{| border="0" cellpadding="5" cellspacing="0" width="900px"
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  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Table 4.''' Mapping of competencies to bioinformatics engineer personas via Bloom’s Taxonomy</blockquote>
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[[File:Tab5 Mulder PLOSCompBio2018 14-2.png|900px]]
The scientific disciplines that go into these laboratory roles and activities is as diverse as the manufacturing industries and sub-industries that make up the manufacturing world. For example, the
{{clear}}
food and beverage laboratory taps into disciplines such as [[biochemistry]], [[biotechnology]], [[chemical engineering]], [[chemistry]], fermentation science, materials science, [[microbiology]], molecular gastronomy, and nutrition.<ref name="NolletHand15">{{cite book |url=https://books.google.com/books?id=KtAdCgAAQBAJ&printsec=frontcover |title=Handbook of Food Analysis (Two Volume Set) |editor=Nollet, L.M.L.; Toldrá, F. |publisher=CRC Press |edition=3rd |pages=1568 |year=2015 |isbn=9781482297843}}</ref><ref name="NielsenFood15">{{cite book |url=https://books.google.com/books?id=i5TdyXBiwRsC&printsec=frontcover |title=Food Analysis Laboratory Manual |author=Nielsen, S. |publisher=Springer |pages=177 |edition=2nd |year=2015 |isbn=9781441914620}}</ref><ref name="DouglasTheLabs22">{{cite book |url=https://www.limswiki.org/index.php/LII:The_Laboratories_of_Our_Lives:_Labs,_Labs_Everywhere!/Labs_by_industry:_Part_2 |chapter=Labs by industry: Part 2 |title=The Laboratories of Our Lives: Labs, Labs Everywhere! |author=Douglas, S.E. |publisher=LIMSwiki |edition=2nd |date=July 2022 |accessdate=13 April 2023}}</ref><ref>{{Cite book |last=Bhandari, B.; Roos, Y.H. |date=2012 |editor-last=Bhandari |editor-first=Bhesh |editor2-last=Roos |editor2-first=Yrjö H. |title=Food Materials Science and Engineering |chapter=Chapter 1: Food Materials Science and Engineering: An Overview |publisher=Wiley-Blackwell |place=Chichester, West Sussex, UK ; Ames, Iowa |pages=1–25 |isbn=978-1-4051-9922-3}}</ref> However, the paper and printing industry taps into disciplines such as biochemistry, [[biology]], chemistry, environmental science, engineering, forestry, and physics.<ref name="BajpaiEnviro10">{{cite book |url=https://books.google.com/books?id=zjEeUpwepFMC&printsec=frontcover |title=Environmentally Friendly Production of Pulp and Paper |chapter=Chapter 2: Overview of Pulp and Papermaking Processes |author=Bajpai, P. |publisher=John Wiley & Sons |pages=8–45 |year=2010 |isbn=9780470528105 |accessdate=13 April 2023}}</ref><ref>{{Citation |last=Nykänen |first=Panu |date=2018 |editor-last=Särkkä |editor-first=Timo |editor2-last=Gutiérrez-Poch |editor2-first=Miquel |editor3-last=Kuhlberg |editor3-first=Mark |title=Research and Development in the Finnish Wood Processing and Paper Industry, c. 1850–1990 |url=http://link.springer.com/10.1007/978-3-319-94962-8_3 |work=Technological Transformation in the Global Pulp and Paper Industry 1800–2018 |publisher=Springer International Publishing |place=Cham |volume=23 |pages=35–64 |doi=10.1007/978-3-319-94962-8_3 |isbn=978-3-319-94961-1 |accessdate=2023-04-13}}</ref> By extension, the reader can imagine that these and other industries also have a wide variety of laboratory techniques associated with their R&D, manufacturing, and post-production activities.
{|  
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{| border="0" cellpadding="5" cellspacing="0" width="900px"
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  | style="background-color:white; padding-left:10px; padding-right:10px;"| <blockquote>'''Table 5.''' Bloom’s revised Taxonomy. The table provides, for each term, illustrative examples of skills demonstrating the given level of competency and a general definition.</blockquote>
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==Use cases==
The following subsections more closely examine the three roles manufacturing-based labs can play, as well as a few examples of lab-related activities found within those roles.
To better illustrate the use of the competencies, we present here a series of brief use cases—scenarios in which the competencies have proven valuable already in defining, refining, or assessing a bioinformatics training mechanism. These use cases were selected to highlight a diverse set of training needs, user personas, types of training programs, and educational settings. In this spirit, we present examples grouped into three categories: (1) complete degree programs for which the competencies have proven valuable to overall curriculum design or refinement; (2) supplements to existing degree programs (i.e., specializations, tracks, certificates); and (3) training resources outside the context of specific degree programs.


===Degree programs===
====1.2.1 R&D roles and activities====
====Introductory and masters bioinformatics training in Africa: H3ABioNet====
The National Institute of Standards and Technology (NIST) and its Technology Partnerships Office offer a detailed definition of manufacturing-related R&D as an activity "aimed at increasing the competitive capability of manufacturing concerns," and that "encompasses improvements in existing methods or processes, or wholly new processes, machines or system."<ref name="NISTDefin19">{{cite web |url=https://www.nist.gov/tpo/definition-manufacturing-related-rd |title=Definition of Manufacturing-related R&D |author=Technology Partnerships Office |publisher=National Institute of Standards and Technology |date=31 July 2019 |accessdate=14 April 2023}}</ref> They break this down into four different technology levels<ref name="NISTDefin19" />:
H3ABioNet (www.h3abionet.org), a Pan African bioinformatics network for H3Africa<ref name="MulderH3ABioNet16">{{cite journal |title=H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa |journal=Genome Research |author=Mulder, N.J.; Adebiyi, E.; Alami, R. et al. |volume=26 |issue=2 |pages=271-7 |year=2016 |doi=10.1101/gr.196295.115 |pmid=26627985 |pmc=PMC4728379}}</ref>, has developed a bioinformatics training program for African scientists from the Human Heredity and Health in Africa (www.h3africa.org) consortium. This involves bioinformatics training for a broad range of audiences, primarily in [[genomics]] [[data analysis]], and the development of new bioinformatics degrees to train bioinformatics scientists. Though there are some institutions in Africa offering bioinformatics postgraduate degrees, this was limited to a handful of countries, and many additional institutions expressed a desire to develop and offer such degrees in order to build the next generation of bioinformatics academics. An African Bioinformatics Education Committee was established along with a Curriculum Task Force, which set about designing a bioinformatics master’s program. Topic areas were selected from existing master’s courses and those proposed by Welch ''et al.''.<ref name="WelchBioinformatics14" /> From these, core modules were defined and augmented with additional elective modules relevant to specific institutions, based on their research priorities. The Curriculum Task Force then fleshed out the detailed content of each module and started mapping these to core competencies required of a bioinformatics specialist. Though the focus of some master’s programs may vary from the more biological to a stronger emphasis on software engineering, there were common competencies with which all bioinformatics master’s graduates should be equipped. While some African institutions have specific research focus areas, the feeling was that all students training to be bioinformaticians should be exposed to a set of core subjects, which are in line with the ISCB’s recommendations, and the elective subjects then tend to be dependent on the research focus. The proposed curriculum has been put into practice, with at least two universities in Africa starting their first master’s programs in the last two years.


For bioinformatics users, H3ABioNet has successfully run several specialist short courses to train researchers on next generation sequence analysis, metagenomics, genome-wide association studies, and other topics. However, through interactions with users, there emerged a need for more basic “introduction to bioinformatics” training. In response, H3ABioNet developed an Introduction to Bioinformatics course delivered remotely to classrooms across multiple countries. The curriculum was derived primarily from topics used for the master’s courses, but this time mapping it to competencies for bioinformatics users and removing topics with a modelling or programming focus. The competencies for this audience are thus more focused on a basic understanding of the topic, example algorithms, and how the tools can be applied to answer biological questions. The practicals are also designed to enable users to navigate their way through the tools and learn to interpret the outputs. This course was run successfully for the first time in 2016 and was assessed to determine whether the required core competencies were acquired.
*Unit process-level technologies that create or improve manufacturing processes,
*Machine-level technologies that create or improve manufacturing equipment,
*Systems-level technologies for innovation in the manufacturing enterprise, and
*Environment- or societal-level technologies that improve workforce abilities and manufacturing competitiveness.


Using core competencies for both cases described above enabled course organizers to better define the detailed content, contact hours, and focus for each module, based on the intended audience. We could also use the competencies to define learning outcomes and refine module assessments.
Obviously, this definition applies to actual development of and innovation towards methods of improving and streamlining manufacturing processes. However, this same concept can, in part, can be applied to the actual products made in a manufacturing plant. Not only does product-based R&D focus on improving "existing methods and processes," but it also focuses on "manufacturing competitiveness" by developing new and innovating existing products that meet end users' needs. Laboratories play an manufacturing-based R&D laboratories play an important role in this regard.


====Undergraduate and graduate degree programs in a U.S. research university: Computational biology education at Carnegie Mellon====
The laboratory participating in this role is performing one or more tasks that relate to the development or improvement of a manufactured good. This often leads to a commercial formulation, process, or promising insight into a product. The R&D lab may appear outside the manufacturing facility proper, but not necessarily always. Some manufacturing companies may have an entire research complex dedicated to creating and improving some aspect of their products.<ref name="MonBreak16">{{cite web |url=https://ir.mondelezinternational.com/news-releases/news-release-details/mondelez-international-breaks-ground-new-research-development |title=Mondelez International Breaks Ground for New Research & Development Center in Poland |publisher=Mondelez International |date=08 June 2016 |accessdate=13 April 2023}}</ref> Other companies may take their R&D to a third-party consulting lab dedicated to conducting development and formulation activities for manufacturers.<ref name="BSCommForm">{{cite web |url=https://www.bevsource.com/news/why-you-need-commercial-formula |title=Why You Need A Commercial Formula |publisher=BevSource |date=13 August 2022}}</ref><ref name="GudeSol19">{{cite book |chapter=Solutions Commonly Applied in Industry and Outsourced to Expert Laboratories |title=Food Contact Materials Analysis: Mass Spectrometry Techniques |author=Gude, T. |editor=Suman, M. |publisher=Royal Society of Chemistry |doi=10.1039/9781788012973-00245 |isbn=9781788017190 |year=2019}}</ref> Industrial research activities aren't confined to manufacturers, however. Some higher education institutions provide laboratory-based research and development opportunities to students engaging in work-study programs, often in partnership with some other commercial enterprise.<ref name="HartFoodBev">{{cite web |url=https://www.hartwick.edu/about-us/center-for-craft-food-and-beverage/ |title=Hartwick College Center for Craft Food & Beverage |publisher=Hartwick College |accessdate=13 April 2023}}</ref>
Carnegie Mellon University has long been active in education in computational biology and bioinformatics, providing several opportunities for considering how a general set of competencies can apply to diverse populations. These experiences include degree programs in computational biology at several levels, including a bachelor's of science (BS) in computational biology (since 1989), a masters of science (MS) in computational biology (since 1999), a doctorate (PhD) in computational biology (offered jointly with the University of Pittsburgh since 2005), and required training in computational biology as part of the core of the BS in biological sciences, the university's general undergraduate biology major. While all of these programs predate the ISCB competencies, the competencies provide a basis for considering how well these programs prepare students for work involving computational biology to differing degrees. Two of these programs—the BS in biological sciences and the PhD in computational biology—are discussed as examples of programs with very different student populations and training needs that can be evaluated in light of the competencies.


Carnegie Mellon's BS in biological sciences illustrates one kind of bioinformatics training: for students primarily training for work in experimental biology. Carnegie Mellon took the still unusual step in 2013 of making Introduction to Computational Biology (ICB) a core requirement of every undergraduate biological sciences major, providing an opportunity to explore how one would design a class to be accessible but rigorous and useful to a population of general biology students. Applying these competencies, then, requires working in the context of students who are typically taking a single class on computational biology but within a full undergraduate biology curriculum. Some competencies, primarily those focused on technical aspects of computational biology, can be covered reasonably well at the level needed by an experimental biologist within a single computational biology class (C,D,F,I,J; see Table 1). Other important areas, such as more conventional biological knowledge, are covered thoroughly in other areas of an undergraduate biological sciences curriculum, e.g., in more traditional core classes such as genetics, biochemistry, or cell biology (A,B). Still others, such as the topics that fall broadly under communications and professional development, are covered elsewhere in the curriculum by a variety of mechanisms inside and outside the classroom (M,N,O,P). Still other areas go beyond what can fit in one introductory class but are also not covered elsewhere. Some of these (G,H,K) are competencies that may not be needed by this population but can be flagged for consideration in revisions of ICB. The most interesting topics are those that are crucial for experimental biologists, cannot be covered sufficiently in ICB, and are not covered elsewhere (E, i.e., biostatistics). ICB gives this latter area enough coverage to convey the key ideas needed for bioinformatics work, but the competencies flag it as an area in need of further development in the curriculum as a whole.
The following types of lab-related activities may be associated with the R&D role:


The Carnegie Mellon/University of Pittsburgh joint PhD in computational biology offers an example at another extreme of the spectrum: a full multi-year training program for students expected to become experts in computational biology, who are expected to graduate competent to lead independent research programs in the area, teach computational biology, run bioinformatics core facilities, or pursue similarly demanding jobs. Computational biology programs face a special challenge compared with more traditional degree programs, in that the lack of clear standards for training at the undergraduate level means that there is little one can assume or enforce about background knowledge of incoming students beyond basic competencies in biology, computing, and mathematics. Furthermore, since a PhD program is research-focused and under pressure to limit time to degree, formal training can occupy only a finite amount of a student's time, equivalent to roughly a year of full-time coursework. To a limited degree, the program can rely on admissions standards, remediation, and self-teaching to assume some basics of all students (A,F,I,J). Some competencies can be handled by flexible menu-based requirements to meet a competency in ways appropriate to each student’s individual needs and background (B). In others, every student needs a high level of competency, and this must be met with specialized core classes designed for this population (C,D,E,G,H). Others must be met within the curriculum through specialized professional development mechanisms as well as one-on-one mentorship by the thesis advisor (K,L,M,N,O,P). Nonetheless, some competencies, especially those that depend on the mentorship of the research advisor, may be acquired much more effectively by some students than others. The competencies again suggest that these topics should be flagged for consideration for more formal training in the future. Furthermore, the challenges faced by this program with respect to knowledge of incoming students make clear the value that accepted standards for competencies at the undergraduate level could have in making most effective use of time in graduate school for specialists in the field.
'''Overall product development and innovation''': Jain ''et al.'' noted in their book on managing R&D activities that in 2010, 60 percent of U.S. R&D was focused on product development, while 22 percent focused on applied research and 18 percent on basic research. However, they also argue that any R&D lab worth its weight should have a mix of these activities, while also including customer participation in the needs assessment and innovation activities that take place in product development and other research activities. Jain ''et al.'' define a manufacturer's innovation activities as "combining understanding and invention in the form of socially useful and affordable products and processes."<ref>{{Cite book |url=https://books.google.com/books?id=nSgebaFKwvMC&pg=PA8 |last=Jain |first=Ravi |last2=Triandis |first2=Harry Charalambos |last3=Weick |first3=Cynthia Wagner |date=2010 |title=Managing research, development and innovation: Managing the unmanageable |chapter=Chapter 1: R&D Organizations and Research Categories |edition=3rd |publisher=Wiley |place=Hoboken, N.J |pages=8 |isbn=978-0-470-40412-6}}</ref> As the definition denotes, newly developed products ("offerings") and processes (usually which improve some level of efficiency and effectiveness) come out of innovation activities. Additionally, platforms that turn existing components or building blocks into a new derivative offering (e.g., a new model or "generation" of product), as well as "solutions that solve end-to-end customer problems," can be derived from innovation. Those activities can focus on more risky radical innovation to a new product or take a more cautious incremental approach to improvements on existing products.<ref>{{Cite book |url=https://books.google.com/books?id=nSgebaFKwvMC&pg=PA240 |last=Jain |first=Ravi |last2=Triandis |first2=Harry Charalambos |last3=Weick |first3=Cynthia Wagner |date=2010 |title=Managing research, development and innovation: Managing the unmanageable |chapter=Chapter 12: Models for Implementing Incremental and Radical Innovation |edition=3rd |publisher=Wiley |place=Hoboken, N.J |pages=240–241 |isbn=978-0-470-40412-6}}</ref>


====Undergraduate training in an Australian university: Bioinformatics engineering education at the University of New South Wales (UNSW)====
'''Reformulation''': Reformulation involves the material substitution of one or more raw materials used in the production of a product to accomplish some stated goal. That goal may be anything from reducing the toxicity or volume of wastes generated<ref name=":0">{{Cite book |last=Dupont |first=R. Ryan |last2=Ganesan |first2=Kumar |last3=Theodore |first3=Louis |date=2017 |title=Pollution prevention: sustainability, industrial ecology, and green engineering |url=https://books.google.com/books?id=3m4NDgAAQBAJ&pg=PA382 |edition=Second edition |publisher=CRC Press, Taylor & Francis Group, CRC Press is an imprint of the Taylor & Francis Group, an informa business |place=Boca Raton |pages=382 |isbn=978-1-4987-4954-1}}</ref><ref name=":1">{{Cite book |date=2022 |editor-last=Wang |editor-first=Lawrence K. |editor2-last=Wang |editor2-first=Mu-Hao Sung |editor3-last=Hung |editor3-first=Yung-Tse |title=Waste Treatment in the Biotechnology, Agricultural and Food Industries: Volume 1 |url=https://books.google.com/books?id=JxaIEAAAQBAJ&pg=PA108 |series=Handbook of Environmental Engineering |language=en |publisher=Springer International Publishing |place=Cham |volume=26 |pages=108–9 |doi=10.1007/978-3-031-03591-3 |isbn=978-3-031-03589-0}}</ref><ref name=":2">{{Cite web |last=Committee on Environment and Public Works |date=28 September 2000 |title=Federal Formulated Fuels Act of 2000: Report of the Committee on Environment and Public Works, United States Senate |url=https://books.google.com/books?id=dk-gi6ZZ_KsC&pg=PA1 |publisher=U.S. Government Printing Office |accessdate=13 April 2023}}</ref> and improving the overall healthiness of the product<ref name=":3">{{Cite book |last=World Health Organization |date=2022 |title=Reformulation of food and beverage products for healthier diets: policy brief |url=https://apps.who.int/iris/handle/10665/355755 |language=en |publisher=World Health Organization |place=Geneva |isbn=978-92-4-003991-9}}</ref><ref name=":4">{{Cite book |date=2019 |editor-last=Raikos |editor-first=Vassilios |editor2-last=Ranawana |editor2-first=Viren |title=Reformulation as a Strategy for Developing Healthier Food Products: Challenges, Recent Developments and Future Prospects |url=https://books.google.com/books?id=zkG1DwAAQBAJ&pg=PA1 |language=en |publisher=Springer International Publishing |place=Cham |doi=10.1007/978-3-030-23621-2 |isbn=978-3-030-23620-5}}</ref>, to transitioning from traditional holistic medicine approaches to more modern biomedical approaches.<ref name=":5">{{Cite book |date=2019 |editor-last=Lechevalier |editor-first=Sébastien |title=Innovation Beyond Technology: Science for Society and Interdisciplinary Approaches |url=https://books.google.com/books?id=Sx2nDwAAQBAJ&pg=PA133 |series=Creative Economy |language=en |publisher=Springer Singapore |place=Singapore |pages=133–7 |doi=10.1007/978-981-13-9053-1 |isbn=978-981-13-9052-4}}</ref> Examples of products that have seen reformulation by manufacturers include:
The University of New South Wales (UNSW) (Sydney, Australia) offers a Bachelor of Engineering (Bioinformatics Engineering) program, which aims to empower graduates to design and implement computing systems for bioinformatics, including software algorithms as well as data management and analysis infrastructures. The BE (Bioinformatics Engineering) degree started in 2001 and is the longest-running undergraduate bioinformatics program in Australia. It is fully accredited as an engineering degree by Engineers Australia: graduates are recognized as entry-level engineers in all the countries that are signatories of the Washington Accord, an international agreement among bodies responsible for accrediting engineering degree programs.<ref name="IEAWashington">{{cite web |url=http://www.ieagreements.org/accords/washington/ |title=Washington Accord |publisher=International Engineering Alliance |accessdate=26 March 2017}}</ref> The program is revised periodically to keep it relevant and is reviewed every five years by an external panel of engineers to ensure that accreditation criteria are met. Curriculum mapping of the program content to the ISCB and Engineers Australia core competencies as well as to the university’s Graduate Attributes is a crucial step in that process.


The process starts at the whole program level, by identifying which courses in the program significantly address specific core competencies. Then, for each core competency, the learning outcomes of the relevant courses are examined and refined to address this competency. Assessment activities are tailored with the core competency in mind to ensure that at the conclusion of the course, students are able to demonstrate that they have achieved sufficient levels of proficiency. The process is repeated for each core competency, resulting in a matrix mapping competencies to curricula. The matrix may reveal weaknesses, which can be addressed by modifying or substituting courses. For example, in the most recent revision, the program was modified to replace generic elective courses with additional design project courses and software engineering workshops. To facilitate the evaluation of a program relative to core competencies and graduate attributes, the university’s Academic Information Management System requires each course description to include a mapping of the course’s learning outcomes to both assessment tasks and core competencies. The competency mapping matrix can then be generated automatically for each course and at a whole program level. Expanding the ISCB curriculum guidelines by including examples of learning outcomes for each core competency would facilitate this kind of analysis and increase the usefulness of the competencies in curriculum design and evaluation
*Paints and other coatings<ref name=":0" />,
*Fuels such as gasoline<ref name=":2" />,
*Foods and beverages<ref name=":3" /><ref name=":4" />, and
*Pharmaceuticals and cosmetics.<ref name=":1" /><ref name=":5" />


In addition to its long-standing bachelor of engineering in bioinformatics, UNSW recently introduced a bachelor of science in bioinformatics major emphasizing the use of existing bioinformatics methods for biological discovery rather than the design of new bioinformatics methods. The core competencies were used to guide the design of the program by identifying the competencies to emphasize relative to the engineering program (B, C, and D) and those for which a lower level of achievement was acceptable (G, H, J, K, M, O). This in turn guided the choice of courses for the bachelor of science major.
In the end, reformulation is a means for improving impacts on the end user, the environment, or even the long-term budget of the manufacturer. The type of lab activities associated with reformulation largely varies by product; the laboratory methods used to reformulate gasoline may be quite different from those in a food and beverage lab. Reformulation can also be a complicated process, as found with pharmaceutical products. The reformulated product "must have the same therapeutic effect, stability, and purity profile" as the original, while maintaining pleasing aesthetic qualities to the end user. Adding to the problem is regulatory approval times of such pharmaceutical reformulations.<ref name=":1" />


====Undergraduate degrees in bioinformatics at a small liberal arts college: Saint Vincent college====
'''Nondestructive testing and materials characterization''': Raj ''et al.'' describe nondestructive testing (NDT) as "techniques that are based on the application of physical principles employed for the purpose of determining the characteristics of materials or components or systems and for detecting and assessing the inhomogeneities and harmful defects without impairing the usefulness of such materials or components or systems."<ref name=":7">{{Cite book |last=Raj, B.; Jayakumar, T.; Thavasimuthu, M. |year=2014 |title=Practical Non-Destructive Testing |url=https://archive.org/details/practicalnondest0000rajb |edition=Ninth Reprint, 3rd |publisher=Narosa Publishing House Pvt. Ltd |isbn=9788173197970}}</ref> NDT has many applications, including with food, steel, petroleum, medical devices, transportation, and utilities manufacturing, as well as electronics manufacturing.<ref>{{Cite book |last=Huang |first=Songling |last2=Wang |first2=Shen |date=2016 |title=New Technologies in Electromagnetic Non-destructive Testing |url=https://books.google.com/books?id=YuCvCwAAQBAJ&printsec=frontcover |chapter=Chapter 1: The Electromagnetic Ultrasonic Guided Wave Testing |series=Springer Series in Measurement Science and Technology |language=en |publisher=Springer Singapore |place=Singapore |pages=1 |doi=10.1007/978-981-10-0578-7 |isbn=978-981-10-0577-0}}</ref><ref>{{Cite book |date=2020-09-29 |editor-last=Tian |editor-first=Guiyun |editor2-last=Gao |editor2-first=Bin |title=Electromagnetic Non-Destructive Evaluation (XXIII) |url=https://books.google.com/books?id=by4NEAAAQBAJ&printsec=frontcover |series=Studies in Applied Electromagnetics and Mechanics |publisher=IOS Press |volume=45 |doi=10.3233/saem45 |isbn=978-1-64368-118-4}}</ref><ref>{{Cite book |date=2010 |editor-last=Jha |editor-first=Shyam N. |title=Nondestructive Evaluation of Food Quality: Theory and Practice |url=https://books.google.com/books?id=RXIJu3TRPWEC&printsec=frontcover |language=en |publisher=Springer Berlin Heidelberg |place=Berlin, Heidelberg |doi=10.1007/978-3-642-15796-7 |isbn=978-3-642-15795-0}}</ref> It also plays an important role in materials testing and characterization.<ref>{{Cite book |date=2016 |editor-last=Huebschen |editor-first=Gerhard |title=Materials characterization using nondestructive evaluation (NDE) methods |url=https://books.google.com/books?id=ZR1rBgAAQBAJ&printsec=frontcover |series=Woodhead Publishing series in electronic and optical materials |publisher=Elsevier/Woodhead Publishing |place=Amsterdam ; Boston |isbn=978-0-08-100040-3 |oclc=932174125}}</ref> NDT and materials testing is often used as a quality control mechanism during manufacturing (see the next subsection), but it can also be used during the initial R&D process to determine if a prototype is functioning as intended or a material is satisfactory for a given application.<ref name=":7" />
The bioinformatics program at Saint Vincent College, a small liberal arts college in western Pennsylvania, was started in 2005. The program is small, with less than 20 students in the major, but it has graduated at least one student each year from 2009 to the present. Initially, there was only one set of required courses for the BS degree, which included courses covering programming (in C++), data structures, discrete structures, introduction to databases, biostatistics, cell biology, molecular genetics, genomics, and [[Health |informatics|biomedical informatics]]. There was also a capstone three-semester research project. Roughly speaking, three types of students entered the program: (1) students who enjoyed both biology and computation and were good at both; (2) students who enjoyed biology but struggled with the programming courses; and (3) students who enjoyed programming but struggled in the upper biology courses, particularly labs. The program tended to lose students in the latter two groups from the program to biology or computer science. As a result, in 2013 they split the curriculum into two tracks—biology and computation—to try to accommodate students in these groups and keep them in the major. About two-thirds of the courses are common between the two tracks, but, for example, the biology track only requires one semester of C++ programming rather than three for the computation track.


In 2015, the program underwent a comprehensive program review, including both internal reviewers and an external reviewer. As part of the initial report on the program, the ISCB Core Competencies were used as a standard against which to evaluate the curriculum and student training, which was very valuable as without them, it would have been difficult to find a way to evaluate strengths and weaknesses of the curriculum against an external standard. One of the issues raised in the review was the learning goals for the major and how those relate to the two tracks, since the learning goals had not been revised when the two tracks were implemented. Roughly speaking, the two tracks correspond with the ISCB roles of bioinformatics users and bioinformatics scientists. These issues, examined in light of the competencies, highlight a principal challenge for smaller programs: how to accommodate both types of students given limitations on number of faculty, types of courses available from different departments, enrollment, etc.
'''Stability, cycle, and challenge testing''': Multiple deteriorative catalysts can influence the shelf life of a manufactured product, from microbiological contaminants and chemical deterioration to storage conditions and the packaging itself. As such, there are multiple approaches to taming the effects of those catalysts, from introducing additives to improving the packaging.<ref name="SubramaniamTheStab16">{{Cite book |date=2016 |editor-last=Subramaniam |editor-first=Persis |title=The stability and shelf life of food |url=https://www.worldcat.org/title/mediawiki/oclc/956922925 |series=Woodhead Publishing Series in Food Science, Technology and Nutrition |edition=Second edition |publisher=Elsevier/WP, Woodhead Publishing |place=Amsterdam |isbn=978-0-08-100436-4 |oclc=956922925}}</ref> However, stability, cycle, and challenge testing must be conducted on many products to determine what deleterious factors are in play. The analytical techniques applied in stability, cycle, and challenge testing will vary based on, to a large degree, the product matrix and its chemical composition.<ref name="SubramaniamTheStab16" /> Microbiological testing is sure to be involved, particularly in challenge testing, which simulates what could happen to a product if contaminated by a microorganism and placed in a representative storage condition.<ref>{{Cite book |last=Komitopoulou, E. |date=2011 |editor-last=Kilcast |editor-first=David |editor2-last=Subramaniam |editor2-first=Persis |title=Food and beverage stability and shelf life |url=https://www.worldcat.org/title/mediawiki/oclc/838321011 |chapter=Microbiological challenge testing of food |series=Woodhead Publishing Series in Food Science, Technology and Nutrition |publisher=WP, Woodhead Publ |place=Oxford |pages=507–526 |isbn=978-0-85709-254-0 |oclc=838321011}}</ref><ref name=":6">{{Cite book |last=Chen, S.-C. |date=2018 |editor-last=Warne |editor-first=Nicholas W. |editor2-last=Mahler |editor2-first=Hanns-Christian |title=Challenges in Protein Product Development |url=https://books.google.com/books?id=LyVhDwAAQBAJ&pg=PA264&dq=Stability,+cycle,+and+challenge+testing |chapter=Chapter 12: Container Closure Integrity Testing of Primary Containers for Parenteral Products |series=AAPS Advances in the Pharmaceutical Sciences Series |language=en |publisher=Springer International Publishing |place=Cham |volume=38 |pages=257–290 |doi=10.1007/978-3-319-90603-4 |isbn=978-3-319-90601-0}}</ref> Calorimetry, spectrophotometry, spectroscopy, and hyperspectral imaging may be used to properly assess color, particularly when gauging food quality.<ref name="SubramaniamTheStab16" /> Other test types that may be used include water content, texture, viscosity, dispersibility, glass transition, and gas chromatography.<ref name="SubramaniamTheStab16" /> In the end, the substrate being examined will be a major determiner of what kind of lab methods are used. The lab method chosen for stability, cycle, and challenge testing should optimally be one that errs on the side of caution and is appropriate to the test, even if it takes longer. As Chen notes: "A longer test cycle is less a concern for stability protocol as the study typically has a limited number of samples. Applying a less reliable method to the limited number of samples in a stability study can be problematic."<ref name=":6" />


===Certifications, tracks, and specializations===
'''Packaging analysis and extractable and leachable testing''': Materials that contact pharmaceuticals, foods and beverages, cosmetics, and more receive special regulatory consideration in various parts of the world. This includes alloys, bioplastics, can coatings, glass, metals, regenerated cellulose materials, paper, paperboard, plastics, printing inks, rubber, textiles, waxes, and woods.<ref>{{Cite book |date=2021 |editor-last=Baughan |editor-first=Joan Sylvain |title=Global Legislation for Food Contact Materials |url=https://www.worldcat.org/title/mediawiki/oclc/on1272898230 |series=Woodhead Publishing Series in Food Science, Technology and Nutrition |edition=Second edition |publisher=Woodhead Publishing |place=Oxford |isbn=978-0-12-821181-6 |oclc=on1272898230}}</ref> As such, meeting regulatory requirements and making inroads with packaging development can be a complicated process. Concerns of chemicals and elements that can be extracted or leach into sensitive products add another layer of complexity to developing and choosing packaging materials for many manufactured goods. This requires extractable and leachable testing at various phases of product development to ensure the packaging selected during formulation is safe and effective.<ref name=":6" /><ref name="BaloghTesting11">{{cite journal |url=https://www.chromatographyonline.com/view/testing-critical-interface-leachables-and-extractables |title=Testing the Critical Interface: Leachables and Extractables |author=Balogh, M.P. |journal=LCGC North America |volume=29 |issue=6 |pages=492–501 |year=2011}}</ref> Extractable and leachable testing for packaging could involve a number of techniques ranging from gas and liquid chromatography to ion chromatography and inductively coupled plasma mass spectrometry.<ref name="LAExtract">{{cite web |url=https://leeder-analytical.com/extractables-and-leachables-testing/ |title=Extractables and leachables testing (E&Ls) |publisher=Leeder Analytical |accessdate=14 April 2023}}</ref>
====Certificate programs and specializations: Ohio University====
Ohio University offers bioinformatics certificates at both the undergraduate and graduate levels. Additionally, computer science students at the BS, MS, and PhD degree levels may specialize in bioinformatics by selecting degree tracks that contain appropriate biology and bioinformatics courses. To complete an undergraduate bioinformatics certificate, trainees take courses in the following: statistics, discrete mathematics, data structures, genetics, [[laboratory]] biology, cell biology, one elective course in biology, bioinformatics tools, and data mining. A graduate certificate in bioinformatics is earned by completing graduate level courses in biochemistry, two elective courses in genetics/molecular biology/systematics, laboratory biology, bioinformatics tools, computational genomics, data mining, or statistical foundations for bioinformatics. Similarly, explicit biomedical informatics tracks within the computer science degree programs allow students to elect a structured training program.


The elucidation of the training categories of bioinformatics engineer, scientist, and user necessitates a review of Ohio’s programs. While the bioinformatics specializations within the computer science degree programs provide adequate training for bioinformatics engineers, it would be beneficial to migrate from one-size-fits-all bioinformatics certificate programs to multi-track programs for training bioinformatics users, scientists, and engineers. The certificate programs are currently being broadened to allow customization for training in each different bioinformatics role. As an initial step, the biology elective course requirement is being changed to a role-specific elective course requirement. This will allow bioinformatics engineers to select elective courses in algorithm analysis, data science, database design, machine learning, artificial intelligence, software engineering, computer security, and parallel computing. Additionally, the bioinformatics certificate program requirements are being redesigned to feature specific tracks for users, scientists, and engineers. This redesign process would be aided by having the ISCB competencies for bioinformatics engineers detailed, perhaps in the form of sample programs (e.g., an aggregation from the survey of bioinformatics programs discussed by Welch ''et al.''<ref name="WelchApplying16" />), or by mapping each competency to suggested courses and/or course topics (e.g., from the controlled vocabulary defined by Welch ''et al.''<ref name="WelchApplying16" />).
====1.2.2 Pre-manufacturing and manufacturing roles and activities====
The laboratory participating in these roles is performing one or more tasks that relate to the preparative (i.e., pre-manufacturing) or [[quality control]] (QC; i.e., manufacturing) activities of production. An example of preparative work is conducting allergen, calorie, and nutrition testing for a formulated food and beverage product. Calorie and nutrition testing—conducted in part as a means of meeting regulation-driven labeling requirements—lands firmly in the role of pre-manufacturing activity, most certainly after commercial formulation and packing requirements have been finalized but before the formal manufacturing process has begun.<ref name="BSNutTest">{{cite web |url=https://www.bevsource.com/news/what-do-i-need-know-about-nutrition-testing-my-beverage-brand |title=What Do I Need To Know About Nutrition Testing for My Beverage Brand? |publisher=BevSource |date=14 April 2023}}</ref> Allergen testing works in a similar fashion, though the manufacturer ideally uses a full set of best practices for food allergen management and testing, from confirming allergens (and correct labeling) from ingredients ordered to performing final production line cleanup (e.g., when a new allergen-free commercial formulation is being made or an unintended contamination has occurred).<ref name="CA80-2020">{{cite web |url=https://www.fao.org/fao-who-codexalimentarius/sh-proxy/en/?lnk=1&url=https%253A%252F%252Fworkspace.fao.org%252Fsites%252Fcodex%252FStandards%252FCXC%2B80-2020%252FCXC_080e.pdf |format=PDF |title=Code of Practice on Food Allergen Management for Food Business Operators, CXC 80-2020 |work=Codex Alimentarius |date=2020 |accessdate=14 April 2023}}</ref> These types of pre-production analyses aren't uncommon to other types of manufacturing, discussed below.


====Specialist track in an undergraduate bioengineering program: The University of Illinois====
As for in-process manufacturing QC, some QC and [[quality assurance]] (QA) methods may already be built into the manufacturing process in-line, not requiring a lab. For example, poka-yokes—mechanisms that inhibit, correct, or highlight errors as they occur, as close to the source as possible—may be built in-line to a manufacturing process to prevent a process from continuing should a detectable error occur, or until a certain condition has been reached.<ref name="DanielPoka21">{{cite web |url=https://www.techtarget.com/searcherp/definition/poka-yoke |title=poka-yoke |author=Daniel, D. |work=TechTarget ERP - Definition |date=October 2021 |accessdate=14 April 2023}}</ref><ref>{{Cite book |last=Dogan, O.; Cebeci, U. |date=2021 |editor-last=García Alcaraz |editor-first=Jorge Luis |editor2-last=Sánchez-Ramírez |editor2-first=Cuauhtémoc |editor3-last=Gil López |editor3-first=Alfonso Jesús |title=Techniques, Tools and Methodologies Applied to Quality Assurance in Manufacturing |url=https://link.springer.com/10.1007/978-3-030-69314-5 |chapter=Chapter 1: An Integrated Quality Tools Approach for New Product Development |language=en |publisher=Springer International Publishing |place=Cham |pages=3–22 |doi=10.1007/978-3-030-69314-5 |isbn=978-3-030-69313-8}}</ref> However, despite the value of inline QC/QA, these activities also happen beyond the production line, in the laboratory (discussed further, below).  
At the University of Illinois, undergraduate bioengineering majors select a track, one of which is computational and systems biology (CSB). Students not in the CSB track get a small amount of programming experience, but do take a non-majors CS course in their sophomore year that exposes them to MATLAB and C programming. They also take a junior-level course, Computational Tools for Biological Data, that covers basic probability and statistics; hypothesis testing; modelling and simulation; and experimental design and applies these concepts and techniques to human genomic variation; sequence alignment; Hidden Markov Models and gene finding; cancer genomics; and gene regulatory networks. Students in the CSB track take the Computational Tools for Biological Data course described above but have a more rigorous training in mathematics and computer science. Specifically, CSB students take courses for CS majors, including introductory programming, discrete mathematics, data structures, data mining and bioinformatics. Overall, CSB students have a rigorous training in mathematics, probability, statistics, and computer science, and take at least two senior-level courses in which techniques from these disciplines are applied in bioinformatics analyses. Experience with this population highlights a gap remaining in the competencies, with a population not currently well represented in their use. It suggests a possible direction for future work, as the Bioinformatics Engineer Curriculum Working Group might extend its guidelines to better encompass the field of bioengineering.


===Other training guidelines and resources===
The following types of lab-related activities may be associated with the pre-manufacturing and manufacturing role:
====Bioinformatics short courses: European Bioinformatics Institute (EMBL-EBI) and University of Cambridge====
Both EMBL-EBI (www.ebi.ac.uk/training) and the University of Cambridge (UCAM, http://bioinfotraining.bio.cam.ac.uk/) offer extensive programs of short courses that enable the research community to gain competency in bioinformatics. These programs differ from the full-time curricula described above in that they are aimed at individuals already pursuing a research career. Most of the scientists attending these courses are PhD students, postdoctoral researchers, or more senior researchers (in academia or in industry), who are performing data-intensive experiments and need guidance on experimental design, data analysis, and interpretation. As a proof of principle for ELIXIR, Europe’s distributed infrastructure for biological data with nodes in 20 countries, EMBL-EBI and UCAM recently performed an exercise to map their course programs to the ISCB competency framework. The goal was to identify any gaps in training provision and also to rapidly check the robustness of the competency profile; in total they looked at 50 short courses offered by UCAM and 21 at EMBL-EBI, covering a wide range of topics aimed primarily at bioinformatics scientists and bioinformatics users. Both programs included coverage of all the competency areas, with only a very small number of courses increasing competence in A, general biology (this is already well developed in the target audience, many of whom have postgraduate degrees in the biological sciences) and a high proportion of the courses increasing competence in F, bioinformatics tools and their usage (48 courses from UCAM; 20 courses from EMBL-EBI); D, details of the scientific discovery process and the role of bioinformatics in it (34 courses from UCAM; 20 courses from EMBL-EBI); and N, effective communication of bioinformatics problems, issues and topics (28 courses from UCAM; 20 from EMBL-EBI). Two competency areas were identified that they felt were not adequately covered by the existing framework and that they would like to propose adding: Data curation for dissemination of research data (for example, the annotation of data required when submitting data sets to public databases, and the annotation of data performed by professional biocurators who add value to these resources) and data curation for analysis of research data (for example, annotation of a newly sequenced genome to find orthologues/paralogues or to gain a functional overview of the genome). This exercise, if performed across all of the ELIXIR nodes, will help to understand the impact of ELIXIR’s training portfolio for different target audiences and will enable them to shape our offering accordingly. Mapping existing short courses to bioinformatics core competencies could also be used to help individuals along a learning path, taking them from one competency level to the next.


====Clinical bioinformatics: The United Kingdom 100,000 genomes project====
'''Various pre-manufacturing analyses''': Also known as pre-production, some level of laboratory activity takes place here. Like the previously mentioned food and beverage industry, the garment manufacturing industry will have its own laboratory-based pre-production activities, including testing various raw material samples for potential use and quality testing pre-production samples before deciding to go into full production.<ref name="BaukhPreprod20">{{cite web |url=https://techpacker.com/blog/manufacturing/pre-production-processes-in-garment-manufacturing/ |title=Pre-production processes in garment manufacturing |author=Baukh, O. |work=Techpacker |date=14 October 2020 |accessdate=14 April 2023}}</ref> In another example, a manufacturer intending to produce "a new chemical substance for a non-exempt commercial purpose" in the U.S. must submit a pre-manufacture notice to the Environmental Protection Agency (EPA), which must include "test data on the effect to human health or the environment."<ref name="EPAFiling22">{{cite web |url=https://www.epa.gov/reviewing-new-chemicals-under-toxic-substances-control-act-tsca/filing-pre-manufacture-notice-epa |title=Filing a Pre-manufacture Notice with EPA |work=Reviewing New Chemicals under the Toxic Substances Control Act (TSCA) |publisher=U.S. Environmental Protection Agency |date=26 October 2022 |accessdate=14 April 2023}}</ref>
The need for bioinformatics to infiltrate current clinical practice is urgent, expedited by programs such as the 100,000 Genomes Project in the U.K. (https://www.genomicsengland.co.uk/the-100000-genomes-project/), which will sequence 100,000 patient genomes with the goal of using the genomic data to inform clinical decision-making. Many different types of healthcare professionals will be impacted by this project. For example, specialist healthcare scientists require training to handle and interpret genomic data; clinical staff involved in recruiting patients to the 100,000 Genomes Project require training to understand the results of genome sequencing and to counsel patients (and their relatives); and the general workforce requires training to provide awareness of genomic medicine and how it can improve patient care. To this aim, in 2014 Health Education England convened a “Task and Finish Group” in clinical bioinformatics to provide recommendations on training requirements arising not only as an immediate consequence of the 100,000 Genomes Project but also from the increasing use of biomolecular data in medical practice as a whole. The group decided to tackle the immediate problem by defining the competencies needed by healthcare professionals to enable them to use data emerging from the 100,000 Genomes Project to inform clinical decision-making. As a proof of principle, the group also mapped these competencies to existing or newly designed training programs commissioned by Health Education England, to inform the design of future training programs for healthcare professionals.


As a starting point, the group used the ISCB core competencies and a policy paper that defined the role of clinical bioinformaticians to draft a rough list of competencies. The group also created a list of different types of healthcare professionals likely to be impacted by the 100,000 Genomes Project. Each member of the group then consulted with colleagues and the wider community, asking them to provide information on which competencies were required to make use of the 100,000 genomes data, and requesting participants to think about whether any additional competencies are required. At least five representatives of each profession were consulted, and all input was combined to create a consensus competency profile. This consensus view, published in the white paper ''Developing clinical bioinformatics training in the NHS''<ref name="NHSDeveloping15">{{cite web |url=https://www.genomicseducation.hee.nhs.uk/images/publications/Developing_NHS_Clinical_Bioinformatics_Training.pdf |format=PDF |title=Developing clinical bioinformatics training in the NHS - A timeline for action |author=Clinical Bioinformatics Task & Finish Group |publisher=NHS |date=February 2015}}</ref> captures not only which competencies are required by the professions listed but also an indication of the level of expertise required, from no knowledge through general awareness and working knowledge to specialist expertise. The profile does not provide guidance on the evidence required to assess whether an individual has gained each of the required competencies, but this would be an obvious next step.
'''Quality control testing''': While QC testing can appear in multiple manufacturing laboratory roles, it's most noticeable in the pre-manufacturing and manufacturing role. Manufacturers in many industries have set up formal testing laboratories to better ensure that their products conform to a determined set of accepted standards, whether those standards come from a standards-setting organization


====Learning framework for a metacurricular resource: The CourseSource bioinformatics learning framework====
CourseSource (http://www.coursesource.org) is “an open-access journal of peer-reviewed teaching resources for undergraduate biological sciences.”<ref name="RosenwaldTheCourse16">{{cite journal |title=The CourseSource Bioinformatics Learning Framework |author=Rosenwald, A.G.; Pauley, M.A.; Welch, L. et al. |volume=15 |issue=1 |page=le2 |doi=10.1187/cbe.15-10-0217 |pmid=27290739 |pmc=PMC4803100}}</ref> CourseSource organizes its resources by biological disciplines (e.g., evolution, genetics, molecular biology, and bioinformatics) that play integral roles in biology. Each discipline has an associated framework of learning goals and objectives that undergraduate students in the biological sciences should have reached by the time they have completed their degree. The ISCB curriculum and competency guidelines were used as a model to develop the Bioinformatics Learning Framework. The framework can be viewed at http://www.coursesource.org/courses/bioinformatics. It represents a practical application of the guidelines and provides an elaboration of the guidelines to a level appropriate for implementation in classroom settings.


==Discussion and conclusions==
NDT and materials testing, discussed in the prior subsection about R&D, can also occur during the various phases of manufacturing, as part of an overall quality control effort.<ref name=":7" />
The work of the Task Force identified a pressing need for bioinformatics education but also tremendous variability in the details of this need and widespread confusion about how to meet it for diverse target user populations and training contexts. The effort to develop and successively refine a set of core competencies for bioinformatics training has sought to assist educators in this domain by providing a conceptual framework in which the field can more productively share experiences and pool our efforts in identifying best practices for bioinformatics education in the face of divergent needs and expectations. Several years of community engagement efforts and subsequent refinements have brought us ever closer to that goal, leading to a broader appreciation of the range of user personas in need of bioinformatics education and a more productive language through which to identify and discuss shared needs and training mechanisms. As the use cases presented here illustrate, the core competencies that arose from this process provide a basis for the community of bioinformatics educators, despite widely divergent goals and student populations, to draw upon their common experiences in designing, refining, and evaluating their own training programs.


We caution that these core competencies are not, and are not intended to be, a prescription for a specific set of curricula or curricular standards. While the competencies highlight common points of focus across training scenarios, few points escape dissent. The field is still figuring out what it means to be trained in bioinformatics or how best to provide that training. We do not expect that state of affairs to end in the near future. Nonetheless, we hope that having a framework in which we can evaluate how different programs define and service their training needs will prove valuable in the maturation of bioinformatics as a discipline.
====1.2.3 Post-production regulation and security roles and activities====
The laboratory participating in these roles is performing one or more tasks that relate to the post-production examination of products for regulatory, security, or accreditation purposes. Labs are often third parties accrediting a producer to a set of standards, ensuring regulatory compliance, conducting authenticity and adulteration testing, conducting security checks at borders, and applying contamination testing as part of an overall effort to track down contamination sources. In addition to ensuring a safer product, society also benefits from these and similar labs by better holding producers legally accountable for their production methods and obligations.


In the future, the Task Force plans to detail its guidelines in a manner similar to the CourseSource framework. Specifically, the plan is to provide an explicit mapping between the competencies and the CourseSource framework, which is tailored for life scientists. The taskforce's ultimate goal is to have explicit mappings of courses to competencies for each of the personas in the ISCB competency framework. This is already underway for life scientists (with the CourseSource framework) and clinical practitioners (with the NHS clinical bioinformatics framework). Where there are synergies with other frameworks, we see potential to map these to curricula for other personas; for example, the Edison framework for data science has many elements relevant to bioinformatics engineers; the ABET framework was indeed used as a basis to develop the ISCB competency framework; and the curricula described in this manuscript also provide specific examples that can be generalized into a framework for bioinformatics engineers.
The following types of lab-related activities may be associated with the post-production regulation and security role:


==Acknowledgements==
'''Authenticity and adulteration testing''':
===Funding===
NM is supported by the National Human Genome Research Institute (NHGRI) and the Office of The Director (OD), National Institutes of Health under award number U41HG006941. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. RS is supported by U.S. National Institutes of Health awards R21CA216452 and R01GM117425 and Pennsylvania Dept. of Health Grant GBMF4554 #4100070287. The Pennsylvania Department of Health specifically disclaims responsibility for any analyses, interpretations or conclusions. For portions of this work, MAP and AR were supported by the National Science Foundation under Grants #7368644 and #1539900. MDB is supported by the Ontario Institute for Cancer Research, with funding from the Government of Ontario. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


===Competing interests===
'''Accreditation-led testing''':
The authors have declared that no competing interests exist.


==References==
==References==
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==Notes==
This presentation is faithful to the original, with only a few minor changes to presentation, spelling, and grammar. PMCID and DOI were added when they were missing from the original reference. The link to the ''Developing clinical bioinformatics training in the NHS'' was turned into a citation.
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[[Category:LIMSwiki journal articles (added in 2018)‎]]
[[Category:LIMSwiki journal articles (all)‎]]
[[Category:LIMSwiki journal articles on bioinformatics]]
[[Category:LIMSwiki journal articles on education]]

Latest revision as of 23:30, 14 April 2023

Sandbox begins below

1. Introduction to manufacturing laboratories

According to McKinsey & Company, the U.S. manufacturing industry represents only 11 percent of U.S. gross domestic product (GDP) and eight percent of direct employment, yet it "makes a disproportionate economic contribution, including 20 percent of the nation’s capital investment, 35 percent of productivity growth, 60 percent of exports, and 70 percent of business R&D spending."[1] These categories of economic contribution are important as many of them indirectly point to how the work of laboratories is interwoven within the manufacturing industry. As we'll discuss later in this chapter, manufacturing-based laboratories primarily serve three roles: research and development (R&D), pre-manufacturing and manufacturing, and post-production regulation and security (e.g., through exports and trade). We can be sure that if U.S. manufacturers' efforts represent huge chunks of total business R&D spending, trade, and capital expenditure (capex), a non-trivial amount of laboratory effort is associated with that spending. Why? Because R&D, trade, and manufacturing quality control (QC) activities rarely can occur without laboratories backing up their work.[2][3][4][5]

Labs in the manufacturing sector provide vital services, including but not limited to quality assurance (QA), QC, production control, regulatory trade control (e.g., authenticity and adulteration), safety management, label claim testing, and packaging analysis. These activities occur in a wide array of manufacturing industries. Looking to the North American Industry Classification System (NAICS), employed by the U.S. Bureau of Labor Statistics (BLS), manufacturing industries and sub-industries include[6]:

  • apparel (e.g., knitted goods, cut-and-sew clothing, buttons and clasps)
  • chemical (e.g., pesticides, fertilizers, paints, cleaning products, adhesives, electroplating solutions)
  • electric power (e.g., light bulbs, household appliances, energy storage cells, transformers)
  • electronics (e.g., sensors, semiconductors, electrodes, mobile phones, computers)
  • food and beverage (e.g., baked goods, probiotics, preservatives, wine)
  • furniture (e.g., mattresses, sofas, window blinds, light fixtures)
  • leather (e.g., purses, saddles, footwear, bookbinding hides)
  • machinery (e.g., mining augers, air conditioning units, turbines, lathes)
  • materials (e.g., ceramics, cements, glass, nanomaterials)
  • medical equipment and supplies (e.g., ventilators, implants, lab equipment, prosthetics, surgical equipment)
  • metal forming and casting (e.g., steel beams, aluminum ingots, shipping containers, hand tools, wire)
  • paper and printing (e.g., cardboard, sanitary items, stationery, books, bookbinding papers)
  • petrochemical (e.g., solvents, fuel additives, biofuels, lubricants)
  • pharmaceutical and medicine (e.g., antivenom, vaccines, lab-on-a-chip diagnostic tests, cannabis products, nutraceuticals)
  • plastics and rubbers (e.g., dinnerware, tires, storage and shelving, outdoor furniture)
  • textiles (e.g., carpeting, upholstery, bulk fabric, yarn)
  • vehicular and aerospace (e.g., electric vehicles, reusable rocketry, railroad rolling stock, OEM auto parts)
  • wood (e.g., plywood, flooring, lumber, handrails)

If you've ever used a sophisticated two-part epoxy adhesive to repair a pipe crack, used an indoor sun lamp, gotten a lot of mileage out of a pair of leather gloves, received a medical implant, taken a medication, eaten a Twinkie, or ridden on Amtrak, one or more laboratories were involved somewhere in the manufacturing process before using that item. From endless research and testing of prototypes to various phases of quality and safety testing, laboratory science was involved. The importance of the laboratory in manufacturing processes can't be understated.

But what of the history of the manufacturing-focused lab? What of the roles played and testing conducted in them? What do they owe to safety and quality? This chapter more closely examines these questions and more.


1.1 Manufacturing labs, then and now

In 1852, the Putnam's Home Cyclopedia: Hand-Book of the Useful Arts was published as a dictionary-like source of scientific terms. Its definition of a laboratory at that time in U.S. history is revealing (for more on the equipment typically described with a laboratory of that time period, see the full definition)[7]:

Laboratory. The workshop of a chemist. Some laboratories are intended for private research, and some for the manufacture of chemicals on the large scale. Hence it is almost impossible to give a description of the apparatus and disposition of a laboratory which would be generally true of all. A manufacturing laboratory necessarily occupies a large space, while that of the scientific man is necessarily limited to a peculiar line of research. Those who study in organic chemistry have different arrangements than that of the mineral analyst.

This definition highlights the state of laboratories at the time: typically you either had a small private laboratory for experiments in the name of research and development (R&D) and producing prototype solutions, or you had a slightly larger "manufacturing laboratory" that was responsible for the creation of chemicals, reagents, or other substances for a wider customer base.[7][8][9] These laboratory types date back further than the mid-1800s, to be sure, though they also saw great change leading up to and after this time period. This is best characterized by the transition from the humble apothecary lab to the small-scale manufacturing laboratory before the mid-1800s, to the full-scale pharmaceutical manufacturing lab and facility well beyond the mid-1800s.

1.1.1 From apothecary to small-scale manufacturing laboratory

A critical area to examine in relation to the evolution of manufacturing laboratories involves pharmaceuticals and the apothecary, which is steeped in the tradition of making pharmaceutical preparations, as well as prescribing and dispensing them to customers. The idea of an individual who attempted to make medical treatments dates back to at least to 2000 BC, from which Sumerian documents reveal compounding formulas for various medicinal dosage types.[10] By 1540, Swiss physician and chemist Paracelsus made a significant contribution to the early apothecary, influencing "the transformation of pharmacy from a profession based primarily on botanic science to one based on chemical science."[10] Thanks to Paracelsus and other sixteenth century practitioners, the concept of the apothecary became more formalized and chemistry-based in the early seventeenth century. With this formalization came the need for the regulation of apothecaries to better ensure the integrity of the profession. For example, the Master, Wardens and Society of the Art and Mystery of Pharmacopolites of the City of London was founded in 1617 through the Royal Charter of James the First, requiring an aspiring apothecary to conduct an apprenticeship or pay a fee, followed by taking an examination proving the individual's knowledge, skill, and science in the art.[10][11]

However, despite this sort of early regulation, medical practitioners took exception to apothecaries encroaching upon the medical practitioners' own services, and apothecaries took exception to the untrained and uncertified druggists who were still performing the work of pharmacists. (As it turns out, these sorts of recriminations would continue on in some form or another into the beginning of the twenty-first century, discussed later.) But as an 1897 article from The Pharmaceutical Journal portrayed, the apothecaries likely wanted to have their cake and eat it too. "[W]hile the apothecaries urged, in the interest of the public, the desirability of a guarantee for the the competences of every person authorised to practise pharmacy," the journal noted, "they also sought, in their own interest, to extend the scope of their medical practice."[11] This led to further debate and changes over time, including British Parliament declaring medicinal preparations as "very proper objects for taxation" in 1783, while at the same time requiring non-apprenticed apothecaries to apply annually for a license. By this time, most apprenticed apothecaries ceased being perceived as mere pharmacists and more as medical practitioners, though the Society's power of conferring medical qualifications, given to them in 1617, were by this point largely lost.[11]

By the end of the eighteenth century, apothecaries and druggists were setting up their own manufacturing laboratories to make chemical and pharmaceutical products. However, these labs were likely still limited in scope. In 1897, The Pharmaceutical Journal portrayed manufacturing labs as such, in the scope of the growing Plough Court Pharmacy run by William Allen and Luke Howard[11]:

It is, however, difficult to at the present time to realise what must have been the position of a manufacturing chemist in 1797, or to comprehend, without some reflection, how limited was the range of his operations and how much his work was beset with difficulties which are now scarecely conceivable. At that time chemical industry was confined to the production of soap, the mineral acids, and some saline compounds then used in medicine. Among the latter, mercurial preperations held an important place, and some of these appear to have first received attention by the firm of Allen and Howard. The early laboratory account books of the firm mention ammoniacals, caustic potash, borax, argentic nitrate, and cream of tartar, as well as ether, benzoic acid, and refine camphor, which were then articles of the materia medics, citric, tartatic and oxalic acids, etc.

To be sure, other types of manufacturing were occurring during the rise and dominance of the apothecary, not just pharmaceutical manufacture. But, retrospectively, the pharmaceutical manufacturing lab in general was likely not in the best of shape as the nineteenth century approached. With several changes in Europe and United States in the early 1800s, the apothecary's manufacturing lab arguably saw more formalized and regulated activity, through various releases of pharmacopoeias[10][12], openings of new pharmacy schools (though still limited in scope)[13], publishing of books[13], and additional formalization of regulating legislation (such as Britain's Apothecaries Act of 1815).[11] By the time the United States Pharmacopeia came upon the scene in 1820, the apothecary was viewed as "competent at collecting and identifying botanic drugs and preparing from them the mixtures and preparations required by the physician."[10] Pharmaceutical historian Loyd Allen, Jr. refers to this time period as "a time that would never be seen again," a sort of Golden Age of the apothecary, given the increasingly rapid rate that scientific and technological discoveries were being made soon after, particularly in synthetic organic chemistry.[10]

Of course, the manufacturing lab—pharmaceutical and otherwise—had other issues as well. For example, just because a small-scale experimental R&D process yielded a positive result didn't mean that process was scalable to large-scale manufacturing. "Frequently, things work well on a small scale, and failure results when mass action comes into effect," noted Armour Fertilizer Company's president Charles McDowell in April 1917, while discussing American research methods.[14] Sometimes a process was sufficiently simple that switching to more robust and appropriate apparatuses was all that was needed to scale up from experiment to full production.[15] In other cases, a full-scale manufacturing laboratory process had yet to be developed, let alone the experiments conducted to develop a proof-of-concept solution in the experimental lab.[16]

Another challenge the manufacturing lab had was in ensuring the stability of any laboratory manufactured solution. Discussing the British Pharmacopoeia-introduced substance of sulphurous acid for afflictions of the throat, Fellow of the Chemical Society Charles Umney noted the stability considerations of the substance when made in the manufacturing laboratory[17]:

Now the Pharmacopoeia solution (which is about 37 volumes) was designedly made nearly one of saturation at the average summer temperature of this country, and, if one may be excused for making a guess, we described from calculations made from the above data of Bunsen's, and not practically worked out to see whether such a solution could be ordinarily obtained in the manufacturing laboratory without chance of failure, and, when made, be kept without great alteration in the various stages it would have to pass through, even if only from the manufacturer to the wholesale druggist, then to the pharmacists, in whose store it might retain for a year or more, being perhaps placed in a temperature many degrees above the point at which it was saturated, thereby causing expansion, liberation of gas, and inconvenience.

Difficulties aside, as the 1800s progressed, the resources of a collaboratory manufacturing laboratory were often greater than those of the individual private laboratory, with enterprising businesses increasingly turning to larger labs for greater and more high-quality quantities of materials. For example, in a letter from the Royal Institution of Great Britain, editor William Crookes discussed the discovery of thallium, noting that the manufacturing lab of noted manufacturing chemists Hopkin and Williams were able to prepare chloride of thallium for him from two hundredweight (cwt) in less time than it took Crookes to make 10 pounds of sulfur in his private laboratory.[18] This trend would continue into the late 1800s, for pharmaceutical and other manufactured goods.

1.1.2 From small-scale private manufacturing lab to larger-scale industrial manufacturing lab

By the 1860s, numerous changes to the paradigm of the manufacturing lab were beginning to take shape, with noticeable momentum away from the small-scale private manufacturing labs to those larger in scope and output, putting competitive pressures on the smaller manufacturing labs.[19] Take, for example, one of the largest U.S.-based enameled brick factories for its time, in 1896, which "[i]n addition to their manufacturing laboratory for slips, enamels and glazes, they maintain an analytical chemical laboratory, and have two chemists in their employ."[20] Ten years prior, a report on the visit to the experimental and manufacturing laboratories of Louis Pasteur highlights the need for a more sizeable facility for meeting demand for the anthrax vaccine[21]:

To meet the demands upon the laboratory work for the supply of anthrax vaccine, the preparation of this is now carried out in an establishment apart from the experimental laboratory in connection with the Ecole Normale, where it was originally started. In the Rue Vaquelin, under the charge of educated assistants, M. Chamberland carries out the preparation on a large scale—the necessity for this being apparent when regard is had to the statement of the quantity demanded for France and other countries.

The author, William Robertson, then goes into greater detail of the many rooms and floors of the building housing the manufacturing laboratory and its apparatuses, highlighting the grandness of the lab's efforts.

The change from small-scale private to larger-scale industrial manufacturing labs—in turn seemingly being supplanted by analytical laboratories[22]—is arguably best seen in the transition from the apothecary and pharmacist to the large-scale pharmaceutical manufacturer. During this time of change in the late 1800s, laws dictating higher manufacturing quality, educational requirements, and restrictions on who can sell medicines were derided, debated, or cheered, depending on who was involved.[23][24]

Reading for a meeting at the Kings County Pharmaceutical Society of Ohio, Charles E. Parker had the following to say about the state of the apothecary-turned-pharmacist in 1896, which fully highlights the transition from small-scale private to larger-scale industrial manufacturing of pharmaceuticals[24]:

The modern pharmacist succeeds to all the responsibilities and obligations of the ancient apothecary without opposition, but his utmost efforts have not preserved to him his inheritance of former privileges and emoluments ... Technical skill is of no use to the professional side of pharmacy unless it is used, and used for the public welfare as well as that of its possessor. The dispenser is the typical pharmacist. But where in former years his sphere included many activities and much manipulative expertness in the preparation of drugs, and even the production of many of them, the midern tendancy is for him to become a mere compounder and dispenser. Of course he is expected to know how, but actually is seldom required to perform the operations once a matter of constant routine. Step by step the productive processes of his little laboratory have been transferred to the works of large manufacturers. Year by year the pharmaceutical improvements and useful inventions which would once have conferred reputation and profit upon the dispensing pharmacies where they originated, have found a better market through these same manufacturers ... In addition, it is to be considered that some of the requisites of modern pharmacy are of a nature involving the use of expensive machinery and large plant, which places their production quite beyond the reach of the pharmacy.

Writing for the Pharmaceutical Review in 1897, editor Dr. Edward Kremers penned an editorial on the role of the manufacturing laboratory in the growing pharmaceutical industry, noting that "[d]uring the past hundred years a most remarkable industrial revolution has taken place," and that pharmacy was also victim to that, lamenting that the apothecaries of the beginning of the century—along with the druggists of 1897—had largely become "relics of the past."[25] Kremers also touched upon another complaint popular at the time: that of pharmacy as a money-making venture.[22][25] In his editorial, Kremers says:

It is a hope cherished by some that higher education will revolutionize pharmacy of today and lift her out of her present unenviable situation. The manufacturing industries, however, have revolutionized pharmacy of fifty years ago and are to no small extent coresponsible for the present state of affairs. The pharmaceutical profession as a whole is justified in asking what a particular branch is doing for the general good. Is the pharmaceutical manufacturer in the erection of his buildings, in the equipment of his laboratories and in the selection of his working force simply bent upon making so many thousands of dollars a paying investment, viewed from a merely commercial standpoint, or are his doings influenced to some extent to at least by higher than purely necessary motives.

By the early years of 1900, recognition of the sea-level change to the apothecary, pharmacist, and manufacturing laboratory had arguably gained traction, and by 1920 it was largely accepted[26]. Writing for The Rocky Mountain Druggist in 1908, pharmaceutical doctor Geo H. Meeker laid it out in no uncertain terms:

Large manufacturing establishments can, for the most part, furnish the druggist at lower prices, with better authentic goods than he himself could produce, assay and guarantee. The inevitable result is that the druggist of today purchases finished products rather than raw materials as did the apothecary of yesterday. It is obvious that a large manufacturing establishment, conducted on ethical lines, employing a complete corps of specialists, buying raw materials to the best advantage and by assay only, making preparations on a large and intelligent technical scale and testing and assying the finished products, does a work that is too immense in its scope for the individual apothecary ... Our present remnant of the drug store laboratory is, as in the past, essentially a manufacturing laboratory. It is of limited and rapidly vanishing scope because the small local laboratory man cannot successfully compete with his rivals, the great and highly-organized factories.

Similar comments were being made by Pearson in 1911[19], Thiesing in 1915[27], and Beal in 1919.[26] Beal in particular spoke solemnly of the transition, largely complete by the time of his acceptance of the Joseph P. Remington Honor Medal in 1919. Speaking of Remington and his experiences in pharmacy, until his death in 1918, Beal said[26]:

Professor Remington's professional experience bridged the space between two distinct periods of pharmaceutical development. When he began his apprenticeship the apothecary, as he was then commonly called, was the principal manufacturer as well as the purveyor of medical supplies ... He lived to see the period when the apothecary ceased to be the principal producer of medicinal compounds and became mainly the purveyor of preparations manufactured by others, and when the medicinal agents in most common use assumed a character that required for the successful production the resources of establishments maintained by large aggregations of capital and employing large numbers of specially trained workers. To those who knew him intimately it was evident that although Professor Remington did not welcome the passing of the manufacturing functions of the apothecary to the large laboratory, he at length came to realize that such a change was inevitable, that it was but a natural step in the process of social evolution, and that the logical action of the apothecary was not to resist that which he could neither prevent nor change, but to readjust himself to the new conditions.

Of course, by then, the rise of the industrial research lab within large-scale manufacturing enterprises was in full swing.

1.1.3 The rise of the industrial research lab within large-scale manufacturing, and today's manufacturing landscape

Like the small, privately owned manufacturing labs evolving to large-scale company-run manufacturing labs, so did the research processes of prior days. The individual tinkering with research in their private laboratory and making small batches of product gave way to a collective of individuals with more specialized talents cooperatively working in a large industrial manufacturing center towards a common, often complex research goal, i.e., within the industrial research laboratory.[28][29] Those larger manufacturing entities that didn't have an industrial research lab were beginning to assess the value of adding one, while smaller enterprises that didn't have the resources to support an extensive collection of manufacturing and research labs were increasingly joining forces "to maintain laboratories doing work for the whole industry."[28]

But what drove the advance of the industrial research lab? As the National Research Council pointed out in 1940, "individuals working independently could not, for very long, provide the technical and scientific knowledge essential to a rapidly developing industrial nation."[30] Newly emerging industries had a need for new knowledge to feed their growth, and they proved to be the early adopters of establishing separate research departments or divisions in their businesses, unlike businesses in long-established industries. The First World War was also responsible for driving organized research efforts in various industries to solve not only wartime problems but also plant the seed of development in peacetime industries. By 1920, two-thirds of all research workers surveyed by the National Research Council were employed in the emerging electrical, chemical, and rubber industries, though the overall adoption of industrial research approaches was still limited across all companies.[30]

In 1917, the previously mentioned Charles McDowell presented his view of American research and manufacturing methods of his time, referring to research as "diligent inquiry."[14] In his work, McDowell stated three types of research that leads up to the manufacturing process: pure scientific inquiry, industrial research, and factory research. He noted that of pure scientific inquiry, little thought is typically given to whether the research—often conducted by university professors—will have any real commercial value, though such value is able to emerge from this fundamental research. As for factory research, McDowell characterized it as full-scale factory-level operations that range from haphazard approaches to well-calculated contingency planning, all of which could make or break the manufacturing business.

In regards to the middle category of industrial research, McDowell made several observations that aptly described the state of manufacturing research in the early 1900s. He noted that unlike pure scientific inquiry, industrial research had commercial practicality as a goal, often beginning with small-scale experiments while later seeking how to reproduce those theoretical results into large-scale manufacturing. He also reiterated his point about needing to "have good backing" financially. "The larger manufacturer maintains his own staff and equipment to carry out investigations along any line that may seem desirable," he said, "but the smaller industries are not able to support an establishment and must rely on either consulting engineers or turn their problems over to some equipped public or private laboratory to solve."[14]

In his 1920 book The Organization of Industrial Scientific Research, Mees presented these three types of research somewhat similarly, though in the context of the industrial laboratory and its operations. Mees argued that industrial laboratories could be classified into three divisions[28]:

  • Laboratories "working on pure theory and the fundamental sciences associated with the industry," aligning in part with McDowell's "pure scientific inquiry";
  • Work laboratories "exerting analytical control over materials, processes and product," aligning slightly with McDowell's "factory research" but more akin to the modern quality control lab; and
  • Industrial laboratories "working on improvements in product and in processes," aligning with McDowell's "industrial research."

Mees argued in particular that those industrial research laboratories that simply improve products and processes were not doing enough; they should, necessarily, also direct some of their goals towards more fully understanding the fundamental and underlying theory of the topic of research.[28] In other words, Mees suggested that those labs simply working on theoretical and fundamental science research, as well as those labs conducting industrial research to improve products and processes, shouldn't necessarily function in separate vacuums. "Research work of this fundamental kind involves a laboratory very different from the usual works laboratory and also investigators of a different type from those employed in a purely industrial laboratory," he noted. Of course, this hybrid approach to fundamental and industrial research was largely reserved for the largest of manufacturers, and solutions were needed for smaller manufacturing endeavors. Here, like McDowell in 1917, Mees argued for smaller businesses with limited resources adopting both cooperative laboratory (those businesses that pool resources together for a fully supported research laboratory) and consulting laboratory (a third-party lab with the resources to fully study a problem, undertake investigations, model a manufacturing process, and implement that process into its client's factory, all for a fee) approaches.[28] With such solutions, the industrial research laboratory continued to take on a new level of complexity to address emerging industry needs, far from the humble origins of an early nineteenth-century manufacturing laboratory.

This growth or industrial research would continue onward from the twentieth century into the twenty-first century. In 1921, some 15 companies maintained research groups of more than 50 people; by 1938, there were 120 such businesses.[30] By the 1990s, "the share of funding for basic research provided by industry actually grew from 10 percent to 25 percent of the national total, even though basic research accounted for just 5-7 percent of total R&D expenditures by industry."[31] This trend of large research groups continues today, though with the recognition that smaller teams may still have advantages. In a 2019 article in the Harvard Business Review, Wang and Evans recognize "large teams as optimal engines for tomorrow’s largest advances," while smaller research teams are better poised to ask disruptive questions and make innovative discoveries.[32]


1.2 Laboratory roles and activities in the industry

Today, the "manufacturing laboratory" is a complex entity that goes beyond the general idea of a lab making or researching things. Many of the historical aspects discussed prior still hold today, but other aspects have changed. As indicated in the introduction, the world of manufacturing encompasses a wide swath of industries and sub-industries, each with their own nuances. Given the nuances of pharmaceutical manufacturing, food and beverage development, petrochemical extraction and use, and other industries, it's difficult to make broad statements about manufacturing laboratories in general. However, the rest of this guide will attempt to do just that, while at times pointing out a few of those nuances found in specific industries.

The biggest area of commonality is found, unsurprisingly, in the roles manufacturing-based labs play today, as well as the types of lab activities they're conducting within those roles. These roles prove to be important in the greater scheme of industry activities, in turn providing a number of benefits to society. As gleaned from prior discussion, as well as other sources, these laboratory roles can be broadly broken into three categories: research and development (R&D), pre-manufacturing and manufacturing, and post-production regulation and security. Additionally, each of these categories has its own types of laboratory activities.

The scientific disciplines that go into these laboratory roles and activities is as diverse as the manufacturing industries and sub-industries that make up the manufacturing world. For example, the food and beverage laboratory taps into disciplines such as biochemistry, biotechnology, chemical engineering, chemistry, fermentation science, materials science, microbiology, molecular gastronomy, and nutrition.[33][34][35][36] However, the paper and printing industry taps into disciplines such as biochemistry, biology, chemistry, environmental science, engineering, forestry, and physics.[37][38] By extension, the reader can imagine that these and other industries also have a wide variety of laboratory techniques associated with their R&D, manufacturing, and post-production activities.

The following subsections more closely examine the three roles manufacturing-based labs can play, as well as a few examples of lab-related activities found within those roles.

1.2.1 R&D roles and activities

The National Institute of Standards and Technology (NIST) and its Technology Partnerships Office offer a detailed definition of manufacturing-related R&D as an activity "aimed at increasing the competitive capability of manufacturing concerns," and that "encompasses improvements in existing methods or processes, or wholly new processes, machines or system."[39] They break this down into four different technology levels[39]:

  • Unit process-level technologies that create or improve manufacturing processes,
  • Machine-level technologies that create or improve manufacturing equipment,
  • Systems-level technologies for innovation in the manufacturing enterprise, and
  • Environment- or societal-level technologies that improve workforce abilities and manufacturing competitiveness.

Obviously, this definition applies to actual development of and innovation towards methods of improving and streamlining manufacturing processes. However, this same concept can, in part, can be applied to the actual products made in a manufacturing plant. Not only does product-based R&D focus on improving "existing methods and processes," but it also focuses on "manufacturing competitiveness" by developing new and innovating existing products that meet end users' needs. Laboratories play an manufacturing-based R&D laboratories play an important role in this regard.

The laboratory participating in this role is performing one or more tasks that relate to the development or improvement of a manufactured good. This often leads to a commercial formulation, process, or promising insight into a product. The R&D lab may appear outside the manufacturing facility proper, but not necessarily always. Some manufacturing companies may have an entire research complex dedicated to creating and improving some aspect of their products.[40] Other companies may take their R&D to a third-party consulting lab dedicated to conducting development and formulation activities for manufacturers.[41][42] Industrial research activities aren't confined to manufacturers, however. Some higher education institutions provide laboratory-based research and development opportunities to students engaging in work-study programs, often in partnership with some other commercial enterprise.[43]

The following types of lab-related activities may be associated with the R&D role:

Overall product development and innovation: Jain et al. noted in their book on managing R&D activities that in 2010, 60 percent of U.S. R&D was focused on product development, while 22 percent focused on applied research and 18 percent on basic research. However, they also argue that any R&D lab worth its weight should have a mix of these activities, while also including customer participation in the needs assessment and innovation activities that take place in product development and other research activities. Jain et al. define a manufacturer's innovation activities as "combining understanding and invention in the form of socially useful and affordable products and processes."[44] As the definition denotes, newly developed products ("offerings") and processes (usually which improve some level of efficiency and effectiveness) come out of innovation activities. Additionally, platforms that turn existing components or building blocks into a new derivative offering (e.g., a new model or "generation" of product), as well as "solutions that solve end-to-end customer problems," can be derived from innovation. Those activities can focus on more risky radical innovation to a new product or take a more cautious incremental approach to improvements on existing products.[45]

Reformulation: Reformulation involves the material substitution of one or more raw materials used in the production of a product to accomplish some stated goal. That goal may be anything from reducing the toxicity or volume of wastes generated[46][47][48] and improving the overall healthiness of the product[49][50], to transitioning from traditional holistic medicine approaches to more modern biomedical approaches.[51] Examples of products that have seen reformulation by manufacturers include:

  • Paints and other coatings[46],
  • Fuels such as gasoline[48],
  • Foods and beverages[49][50], and
  • Pharmaceuticals and cosmetics.[47][51]

In the end, reformulation is a means for improving impacts on the end user, the environment, or even the long-term budget of the manufacturer. The type of lab activities associated with reformulation largely varies by product; the laboratory methods used to reformulate gasoline may be quite different from those in a food and beverage lab. Reformulation can also be a complicated process, as found with pharmaceutical products. The reformulated product "must have the same therapeutic effect, stability, and purity profile" as the original, while maintaining pleasing aesthetic qualities to the end user. Adding to the problem is regulatory approval times of such pharmaceutical reformulations.[47]

Nondestructive testing and materials characterization: Raj et al. describe nondestructive testing (NDT) as "techniques that are based on the application of physical principles employed for the purpose of determining the characteristics of materials or components or systems and for detecting and assessing the inhomogeneities and harmful defects without impairing the usefulness of such materials or components or systems."[52] NDT has many applications, including with food, steel, petroleum, medical devices, transportation, and utilities manufacturing, as well as electronics manufacturing.[53][54][55] It also plays an important role in materials testing and characterization.[56] NDT and materials testing is often used as a quality control mechanism during manufacturing (see the next subsection), but it can also be used during the initial R&D process to determine if a prototype is functioning as intended or a material is satisfactory for a given application.[52]

Stability, cycle, and challenge testing: Multiple deteriorative catalysts can influence the shelf life of a manufactured product, from microbiological contaminants and chemical deterioration to storage conditions and the packaging itself. As such, there are multiple approaches to taming the effects of those catalysts, from introducing additives to improving the packaging.[57] However, stability, cycle, and challenge testing must be conducted on many products to determine what deleterious factors are in play. The analytical techniques applied in stability, cycle, and challenge testing will vary based on, to a large degree, the product matrix and its chemical composition.[57] Microbiological testing is sure to be involved, particularly in challenge testing, which simulates what could happen to a product if contaminated by a microorganism and placed in a representative storage condition.[58][59] Calorimetry, spectrophotometry, spectroscopy, and hyperspectral imaging may be used to properly assess color, particularly when gauging food quality.[57] Other test types that may be used include water content, texture, viscosity, dispersibility, glass transition, and gas chromatography.[57] In the end, the substrate being examined will be a major determiner of what kind of lab methods are used. The lab method chosen for stability, cycle, and challenge testing should optimally be one that errs on the side of caution and is appropriate to the test, even if it takes longer. As Chen notes: "A longer test cycle is less a concern for stability protocol as the study typically has a limited number of samples. Applying a less reliable method to the limited number of samples in a stability study can be problematic."[59]

Packaging analysis and extractable and leachable testing: Materials that contact pharmaceuticals, foods and beverages, cosmetics, and more receive special regulatory consideration in various parts of the world. This includes alloys, bioplastics, can coatings, glass, metals, regenerated cellulose materials, paper, paperboard, plastics, printing inks, rubber, textiles, waxes, and woods.[60] As such, meeting regulatory requirements and making inroads with packaging development can be a complicated process. Concerns of chemicals and elements that can be extracted or leach into sensitive products add another layer of complexity to developing and choosing packaging materials for many manufactured goods. This requires extractable and leachable testing at various phases of product development to ensure the packaging selected during formulation is safe and effective.[59][61] Extractable and leachable testing for packaging could involve a number of techniques ranging from gas and liquid chromatography to ion chromatography and inductively coupled plasma mass spectrometry.[62]

1.2.2 Pre-manufacturing and manufacturing roles and activities

The laboratory participating in these roles is performing one or more tasks that relate to the preparative (i.e., pre-manufacturing) or quality control (QC; i.e., manufacturing) activities of production. An example of preparative work is conducting allergen, calorie, and nutrition testing for a formulated food and beverage product. Calorie and nutrition testing—conducted in part as a means of meeting regulation-driven labeling requirements—lands firmly in the role of pre-manufacturing activity, most certainly after commercial formulation and packing requirements have been finalized but before the formal manufacturing process has begun.[63] Allergen testing works in a similar fashion, though the manufacturer ideally uses a full set of best practices for food allergen management and testing, from confirming allergens (and correct labeling) from ingredients ordered to performing final production line cleanup (e.g., when a new allergen-free commercial formulation is being made or an unintended contamination has occurred).[64] These types of pre-production analyses aren't uncommon to other types of manufacturing, discussed below.

As for in-process manufacturing QC, some QC and quality assurance (QA) methods may already be built into the manufacturing process in-line, not requiring a lab. For example, poka-yokes—mechanisms that inhibit, correct, or highlight errors as they occur, as close to the source as possible—may be built in-line to a manufacturing process to prevent a process from continuing should a detectable error occur, or until a certain condition has been reached.[65][66] However, despite the value of inline QC/QA, these activities also happen beyond the production line, in the laboratory (discussed further, below).

The following types of lab-related activities may be associated with the pre-manufacturing and manufacturing role:

Various pre-manufacturing analyses: Also known as pre-production, some level of laboratory activity takes place here. Like the previously mentioned food and beverage industry, the garment manufacturing industry will have its own laboratory-based pre-production activities, including testing various raw material samples for potential use and quality testing pre-production samples before deciding to go into full production.[67] In another example, a manufacturer intending to produce "a new chemical substance for a non-exempt commercial purpose" in the U.S. must submit a pre-manufacture notice to the Environmental Protection Agency (EPA), which must include "test data on the effect to human health or the environment."[68]

Quality control testing: While QC testing can appear in multiple manufacturing laboratory roles, it's most noticeable in the pre-manufacturing and manufacturing role. Manufacturers in many industries have set up formal testing laboratories to better ensure that their products conform to a determined set of accepted standards, whether those standards come from a standards-setting organization


NDT and materials testing, discussed in the prior subsection about R&D, can also occur during the various phases of manufacturing, as part of an overall quality control effort.[52]

1.2.3 Post-production regulation and security roles and activities

The laboratory participating in these roles is performing one or more tasks that relate to the post-production examination of products for regulatory, security, or accreditation purposes. Labs are often third parties accrediting a producer to a set of standards, ensuring regulatory compliance, conducting authenticity and adulteration testing, conducting security checks at borders, and applying contamination testing as part of an overall effort to track down contamination sources. In addition to ensuring a safer product, society also benefits from these and similar labs by better holding producers legally accountable for their production methods and obligations.

The following types of lab-related activities may be associated with the post-production regulation and security role:

Authenticity and adulteration testing:

Accreditation-led testing:

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