Difference between revisions of "User:Shawndouglas/sandbox/sublevel9"

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We continue to look at 20 broad industry categories and the laboratories associated with them. For each you'll find a brief description with common services and how the lab type affects the average person. As discussed previously, using our client type + function model we dig into examples found in the private, government, and academic sectors and then outline function through activities, sciences, test types, equipment, and unique attributes.
<div class="nonumtoc">__TOC__</div>
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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>
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<div align="center">-----Return to [[User:Shawndouglas/sandbox/sublevel4|the beginning]] of this guide-----</div>
==Sandbox begins below==
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{{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      =
|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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==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.


==Labs by industry: Part 2==
==Introduction==
===Clinical and academic research===
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.
[[File:Methoxamine in it's current manufactured form in a solution in both a syringe and vial..jpg|left|400px]]
{{clear}}


Clinical research laboratories provide a regulated environment for the testing of the safety and efficacy of a variety of medical treatments and diagnostic devices, including medications, implants, and physician test kits. These facilities form the backbone of today's effective medical treatments, from cholesterol-lowering medications to pacemakers for the heart. In the U.S., these types of labs are overseen by the Food and Drug Administration, unlike the previously mentioned clinical and public health laboratories. Clinical research labs are found in the private, government, and academic sectors and provide many different services, including (but not limited to)<ref name="FCRDefinition">{{cite web |url=https://firstclinical.com/fda-gcp/?show=2004/Definition+of+Central+Laboratory |title=Definition of Central Laboratory |work=First Clinical Research |publisher=First Clinical Research, LLC |date=19 April 2004 |accessdate=01 June 2017}}</ref><ref name="MinorHandbook06">{{cite web |url=https://books.google.com/books?id=RmrLBQAAQBAJ&printsec=frontcover |title=Handbook of Assay Development in Drug Discovery |editor=Minor, L.K. |publisher=CRC Press |year=2006 |pages=488 |isbn=9781420015706}}</ref>:
==Development of core competencies for bioinformatics==
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.


* clinical studies
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.
* bioequivalence studies
* study design and management
* high-volume specimen testing
* custom assay development
* test kit development and supply


Clinical studies and trials aside, other types of research may require laboratory services as well. (For the purposes of this guide, we refer to it as "academic research," a broad catch-all category for other research involving laboratories that doesn't readily fit into other industry categories.) Take for example the archeology laboratory, which is responsible for cleaning, analyzing, and identifying artifacts and remains from various sites either as part of a greater research effort or as a contract laboratory service.<ref name="AugustanaArchLab">{{cite web |url=http://www.augie.edu/archeology-laboratory |title=Archeology Laboratory |publisher=Augustana University |accessdate=01 June 2017}}</ref><ref name="SLUArchLab">{{cite web |url=http://www.slu.edu/department-of-sociology-and-anthropology/research-labs-and-facilities/archaeology-laboratory |title=Archeology Laboratory |publisher=Saint Louis University |accessdate=01 June 2017}}</ref> Research in information technology and communication also occurs in (dry) laboratories; examples include the privately owned Nokia Bell Laboratory<ref name="NokiaHistoryBell">{{cite web |url=https://www.bell-labs.com/explore/history-bell-labs/ |title=History - Bell Labs |publisher=Nokia Group |accessdate=01 June 2017}}</ref> and the university-affiliated University of New Hampshire InterOperability Laboratory.<ref name="UNH-IOL_FAQ">{{cite web |url=https://www.iol.unh.edu/about/faq |title=UNH-IOL FAQ |publisher=University of New Hampshire InterOperability Laboratory |accessdate=01 June 2017}}</ref>
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.


''How do clinical and academic research laboratories intersect the average person's life on a daily basis?'' If you've had a medical device implanted, taken a prescription medication, visited an archeological exhibit in a museum, or experienced improvements in how you communicate with others, then you've been touched by a clinical or academic research laboratory. Without these facilities we'd have fewer medications and assistive devices, and by extension shorter life spans. We'd know less about humanity's past growth and development, and we'd lack the technology to rapidly disseminate those findings around the globe.  
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.


====Client types====
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.


'''Private''' - Private clinical research labs are most often "central laboratories" (see the end of this section for more on this term) that are contracted by pharmaceutical companies and medical device manufacturers.
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" />


Examples include:
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.
 
* [http://www.acmgloballab.com/Central-Laboratory-Services/Clinical-Trials-Research-Central-Lab-Services-Clinical-Research-Laboratory.aspx ACM Global Central Laboratory]
* [http://www.covance.com/services/clinical-testing/central-laboratory-services.html Covance Central Labs]
* [https://www.jmilabs.com/clinical-trial-support/ JMI Laboratories]
 
'''Government''' - These labs are typically set up by a government agency to perform specific research into medical conditions such as cancer, depression, or HIV infection.
 
Examples include:
 
* [https://frederick.cancer.gov/ Frederick National Laboratory for Cancer Research]
* [https://clinicalcenter.nih.gov/ccc/crc/ NIH Clinical Trial Center]
* [https://www.fda.gov/ScienceResearch/FieldScience/ Office of Regulatory Affairs' Field Laboratories]
 
'''Academic''' - Many academic institutions set up their own clinical research activities, often within an affiliated medical center. These research efforts often serve as training grounds for students to learn more about clinical research and its administration.
 
Examples include:
 
* [http://ictr.johnshopkins.edu/clinical/clinical-resources/human-subjects-research-core/ictr-clinical-research-units-crus/services/clinical-research-unit-core-lab/ Johns Hopkins Clinical Research Unit Core Laboratory]
* [https://careers.insidehighered.com/job/1326323/clinical-research-laboratory-assistant/ University of Colorado Denver Anschutz Medical Campus]
* [https://www.mir.wustl.edu/research/research-support-facilities/clinical-research-lab-crl Washington University Clinical Research Laboratory]
 
====Functions====
 
''What are the most common functions?'' research/design, clinical studies, contract lab work
 
''What materials, technologies, and/or aspects are being analyzed and researched?'' artifacts, biological specimens, communication networks, medical devices, etc. (depending on academic discipline practiced in the lab)
 
''What sciences are being applied in these labs?'' archeology, clinical research, information theory, etc. (depending on academic discipline practiced in the lab)
 
''What are some examples of test types and equipment?''
 
'''Common test types include''':
 
Absorption, Acoustic startle, Acute contact, Acute oral, Acute toxicity, Adhesion, Age determination, Amino acid analysis, Angle of repose, Antimicrobial, Antigen, Behavioral, Blood culture, Blood gases, Bioavailability, Bioburden, Biocompatibility, Bioequivalence, Biomechanical, Biomolecular, Biosafety, Calorimetry, Carcinogenicity, Clinical diagnostic, Colorimetric, Compaction, Compendial, Complete blood count, Cytology, Cytopathology, Cytotoxicity, Detection, Developmental and reproductive toxicology, Dietary exposure, Ecotoxicology, Efficacy, Electrolyte and mineral panel, Electromagnetic compatibility, Electromagnetic interference, Electrophoresis, Endocrine disruptor screening program, Endotoxin, Environmental fate, Environmental metabolism, Extractables and leachables, Feasibility, Fluid dynamics, Functional observational battery, Genetic, Genotoxicity, Hematocrit, Hemoglobin, Hematotoxicity, Human factors, Immunohistochemistry, Impact, Impurity, Inhalation, Irritation, Kidney function, Learning and memory, Lipid profile, Liver function, Locomotor activity, Metabolic, Microfluidics, Minimum bactericidal concentration, Minimum inhibitory concentration, Nanoparticulate, Neurotoxicity, Nutritional, Osmolality, Osmolarity, Oxidation reduction potential, Oxidation stability, Parasitic, Pathogen, Pathogenicity, pH, Pharmacokinetic, Phototoxicity, Protein analysis, Protein characterization, Red blood cell count, Refractive index, Sensitization, Solubility, Specific gravity, Thyroid function, Toxicokinetic, Urine culture, Validation, Verification, Virucidal efficacy, Wildlife toxicology
 
'''Industry-related lab equipment may include''':
 
autoclave, balance, biohazard container, biosafety cabinet, centrifuge, chromatographic, clinical chemistry analyzer, colorimeter, desiccator, dissolved oxygen meter, dry bath, electrophoresis system, ELISA plate reader, fluorometer, freezers, fume hood, genetic analyzer and sequencer, homogenizer, hotplate, incubator, magnetic stirrer, mass spectrometry equipment, microcentrifuge tube, microplate reader, microscope, multi-well plate, orbital shaker, PCR machine, personal protective equipment, pH meter, Petri dish, pipettor, powered air purifying respirators, refractometer, spectrophotometer, syringes, test tube and rack, thermal cycler, thermometer, urinalysis device, water bath
 
''What else, if anything, is unique about the labs in the clinical and academic research fields?'' It's important to note that some clinical research laboratories may be referred to as "central laboratories." Though mentioned occasionally in its regulation and guidance, the U.S. Food and Drug Administration doesn't seem to provide a definition of the term. However, it seems to be used by some in the context of an analytical laboratory that provides analyses of biological specimens associated with clinical and bioequivalence studies (including multi-site studies, prompting the idea of a "central" lab handling sample analysis) performed at medical institutions.<ref name="FCRDefinition" /><ref name="KarelinSelecting13">{{cite web |url=http://www.contractpharma.com/issues/2013-05/view_features/selecting-a-central-laboratory/ |title=Selecting a Central Laboratory |author=Karelin, A.; Belotserkovskiy, M.; Khokhlova, V.; Kumar, A. |work=Contract Pharma |publisher=Rodman Media, Inc |date=06 May 2013 |accessdate=01 June 2017}}</ref>
 
====LIMSwiki resources====
 
* [[Translational research]]
* [[Translational research informatics]]
 
====Further reading====
 
* {{cite book |url=https://books.google.com/books?id=Eu62G5a8oEAC&printsec=frontcover |title=Principles and Practice of Clinical Research |editor=Gallin, J.I.; Ognibene, F.P. |publisher=Academic Press |year=2012 |pages=796 |isbn=9780123821683}}
 
 
<div align="center"><hr width="50%"></div>
 
===Cosmetic===
[[File:Cosmetics-1078712 1280.jpg|left|400px]]
{{clear}}
Cosmetic labs provide research and development as well as quality control functions to the world of cosmetics. From makeups and moisturizers to hair dyes and lipsticks, the cosmetic laboratory is responsible for making safe and effective products of many types. Cosmetic chemists tend to mostly work in private laboratories or as part of a private-public research partnership, though some work in academic labs.<ref name="BrowneTheJob">{{cite web |url=http://work.chron.com/job-description-cosmetic-chemist-17987.html |title=The Job Description of a Cosmetic Chemist |author=Browne, C. |work=Chron |publisher=Hearst Newspapers, LLC |accessdate=01 June 2017}}</ref> Cosmetic labs are found largely in the private sector, though they exist in the government and academic sectors and provide many different services, including (but not limited to):
 
* formulation and development of products<ref name="BrowneTheJob" />
* safety testing of products<ref name="BrowneTheJob" />
* process engineering improvement<ref name="BrowneTheJob" />
* chemical and material research<ref name="BrowneTheJob" />
* substantiation of compatibility and efficacy claims<ref name="NWUCEL">{{cite web |url=http://health-sciences.nwu.ac.za/pharmaceutical-and-biomedical-services/cel |title=CEL |publisher=North-West University |accessdate=01 June 2017}}</ref>
* allergy testing
* contaminate testing
 
''How do cosmetic laboratories intersect the average person's life on a daily basis?'' In private industry, cosmetic scientists are tasked with creating a safe product free from contaminates and allergens that may negatively affect a user. At the higher government level, some labs are responsible for substantiating manufacturer claims, testing cosmetics, and even manufacturing cosmetic components<ref name="NWUCEL" />; the U.S. Food and Drug Administration (FDA), for example, certifies some color additives as safe for consumers in its own lab.<ref name="FDASmallBus16">{{cite web |url=https://www.fda.gov/cosmetics/resourcesforyou/industry/ucm388736.htm |title=Small Businesses & Homemade Cosmetics: Fact Sheet |publisher=Food and Drug Administration |date=05 October 2016 |accessdate=01 June 2017}}</ref> Without these labs, the soaps, shampoos, moisturizers, and makeup on the market wouldn't likely exist, or if they did, they would be of unknown quality, posing a threat to human health. When we use such a product, we are reminded that a laboratory was at some point involved in its creation.
 
====Client types====
 
'''Private''' - Private cosmetic labs are either found as part of a major company initiative (think L’Oréal Group and its laboratories<ref name="LOrealUSAResearch">{{cite web |url=http://www.lorealusa.com/group/discover-l%27or%C3%A9al-usa/l%E2%80%99or%C3%A9al-usa-research-and-innovation |title=L’Oréal USA Research And Innovation |publisher=L’Oréal Group |accessdate=01 June 2017}}</ref>) or as a third-party contract lab that provides development, manufacturing, and consulting services to clients.
 
Examples include:
 
* [http://ariellabs.com/ Ariel Laboratories]
* [http://cosmeticlaboratories.com/ Cosmetic Laboratories]
* [http://cla-cosmeticlabs.com/services/ Cosmetic Laboratories of America]
 
'''Government''' - Governments around the world differ in how they regulate and test cosmetics. Though not common, some governments will dedicate space for laboratory testing, certification of constituents, and testing of efficacy and compatibility claims.<ref name="NWUCEL" /><ref name="FDASmallBus16" />
 
Examples include:
 
* [http://www.fdaghana.gov.gh/index.php?option=com_content&view=article&id=25&Itemid=3 Ghana Food and Drugs Authority, Cosmetic Laboratory]
* [http://www.thehindu.com/news/national/other-states/odisha-government-identifies-land-for-cosmetic-testing-lab/article8514721.ece Government of Odisha's Central Cosmetic Testing Laboratory]
* [http://www.hsa.gov.sg/content/hsa/en/Applied_Sciences/Pharmaceuticals_Cosmetics_Tobacco/Overview/Cosmetics.html Singapore Health Sciences Authority's Cosmetics Laboratory]
 
'''Academic''' - Academic programs in cosmetic science aren't abundant, but they can be found. (The Society of Cosmetic Chemists lists a few U.S.-based programs [http://www.scconline.org/resources/ here].) The laboratories associated with this course of study are presumably similar in makeup to a chemistry teaching laboratory in a typical university, with a few additions, including research facilities.
 
Examples include:
 
* [http://view2.fdu.edu/academics/university-college/school-of-natural-sciences/academic-programs/ms-in-cosmetic-science/ Farleigh Dickinson University Cosmetic Science Programs]
* [http://pharmacy.uc.edu/program-information/graduate/cosmetic/overview University of Cincinnati Cosmetic Science Programs]
* [http://health-sciences.nwu.ac.za/pharmaceutical-and-biomedical-services/cel North-West University Cosmetics Efficacy Laboratory]
 
====Functions====
 
''What are the most common functions?'' analytical, research/design, QA/QC, and teaching
 
''What materials, technologies, and/or aspects are being calibrated, researched, and quality controlled?'' colorants, dyes, emulsions, lacquers, polymers, silicones, surfactants
 
''What sciences are being applied in these labs?'' biochemistry, biology, chemical engineering, chemistry, cosmetic science, macromolecular science, pharmaceutical science, process engineering
 
''What are some examples of test types and equipment?''
 
'''Common test types include''':
 
Absorption, Allergy, Antimicrobial, Bioburden, Biocompatibility, Comparison, Compliance/Conformance, Composition, Contamination, Detection, Efficacy, Expiration dating, Flammability, Fluorescence, Formulation, Fragrance, Impurity, Ingredient, Irritation, Labeling, Oxidation reduction potential, Oxidation stability, Pathogen, Performance, pH, Photostability, Preservative challenge, Proficiency, Purity, Pyrogenicity, Quality control, Safety, Sensitization, Stability, Water activity
 
'''Industry-related lab equipment may include''':
 
autoclave, balance, chromatographic, digital imaging devices, ESR spectroscopy equipment, fluorescent laser scan microscope, Fourier transform infrared spectroscopy equipment, microscope, multiphotone tomography equipment, pH meter, Raman spectroscopy equipment, test tube and rack, thermometer, transepidermal water loss (TEWL) instrumentation
 
''What else, if anything, is unique about the labs in the cosmetic industry?'' In the U.S., whereas the Centers for Medicare & Medicaid Services (CMS) regulates clinical laboratory testing<ref name="CMSCLIA">{{cite web |url=https://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/index.html |title=Clinical Laboratory Improvement Amendments (CLIA) |publisher=Centers for Medicare & Medicaid Services |date=05 April 2017 |accessdate=01 June 2017}}</ref>, the FDA regulates cosmetic laboratories.<ref name="FDAAuthority">{{cite web |url=https://www.fda.gov/cosmetics/guidanceregulation/lawsregulations/ucm074162.htm |title=FDA Authority Over Cosmetics: How Cosmetics Are Not FDA-Approved, but Are FDA-Regulated |publisher=Food and Drug Administration |date=15 November 2016 |accessdate=01 June 2017}}</ref> Regulation of cosmetic laboratories in other countries varies; in Singapore, for example, the Health Sciences Authority helps enforce cosmetic testing of its Health Products Act.<ref name="HSACosmetics">{{cite web |url=http://www.hsa.gov.sg/content/hsa/en/Applied_Sciences/Pharmaceuticals_Cosmetics_Tobacco/Overview/Cosmetics.html |title=Cosmetics |publisher=Health Sciences Authority |date=17 July 2014 |accessdate=01 June 2017}}</ref>
 
====LIMSwiki resources====
 
* None
 
====Further reading====
 
* {{cite book |url=https://books.google.com/books?id=HGp_CwAAQBAJ&printsec=frontcover |title=Cosmetic Science and Technology: Theoretical Principles and Applications |author=Sakamoto, K.; Lochhead, R.; Maibach, H.; Yamashita, Y. |publisher=Elsevier |year=2017 |pages=854 |isbn=9780128020548}}
 
 
<div align="center"><hr width="50%"></div>
 
===Energy===
[[File:Pomiary rezystancji uzwojenia transformatora z rdzeniem amorficznym miernikiem Sonel MMR-6000.jpg|left|400px]]
{{clear}}
The energy laboratory is largely a place for the research and development of energy sources and devices, though it also is a place for researchers to focus on improving energy efficiency in current fuels, systems, and structures. These labs are found in the government and academic sectors, and occasionally in the private sector, providing many different services, including (but not limited to)<ref name="NRELResearch">{{cite web |url=https://www.nrel.gov/research/ |title=Research |work=National Renewable Energy Laboratory |publisher=Alliance for Sustainable Energy, LLC |accessdate=02 June 2017}}</ref>:
 
* chemical and biomolecular engineering
* applied research and development
* analysis and improvement of energy efficiency
* analysis and improvement of transportation systems
* development of energy systems
* discovery and development of materials
* integration of energy systems
 
''How do energy laboratories intersect the average person's life on a daily basis?'' "I want my phone's battery to last longer!" you shout, as you put it on the charger for the second time in a day. The truth is your device probably has a better battery life than the generation before it, and the generation before it, etc., but you're at the same time making it do more demanding tasks than it used to at the same time. Yet advances continue to be made in energy storage.<ref name="ArgonneResearchers16">{{cite web |url=https://phys.org/news/2016-03-pave-battery.html |title=Researchers continue to pave way for improved battery performance testing |author=Argonne National Laboratory |work=Phys.org |publisher=Science X |date=31 March 2016 |accessdate=02 June 2017}}</ref> You can thank an energy laboratory and its scientists for that and similar advances that affect you on a daily basis.
 
====Client types====
 
'''Private''' - Private laboratories tend to focus on a company's R&D or provide third-party analysis of materials used as fuel sources.
 
Examples include:
 
* [http://www.biomassenergylab.com/index.htm Biomass Energy Lab]
* [https://www.energylab.com/ Energy Laboratories]
 
'''Government''' - Along with academic labs, government labs (public and public-private) make up the majority of energy laboratories and typically provide much of the funding for energy research, at least in the United States.<ref name="KotokFinancing06">{{cite web |url=http://www.sciencemag.org/careers/2006/07/financing-your-research-alternative-energy |title=Financing Your Research in Alternative Energy |work=Science |author=Kotok, A. |publisher=American Association for the Advancement of Science |date=14 July 2006 |accessdate=02 June 2017}}</ref>
 
Examples include:
 
* [https://www.netl.doe.gov/ National Energy Technology Laboratory]
* [http://www.nrel.gov/ National Renewable Energy Laboratory]
* [https://energy.usgs.gov/GeochemistryGeophysics/GeochemistryLaboratories.aspx#3898249-overview U.S. Geological Survey's Geochemistry Laboratory]
 
'''Academic''' - Higher education continues to be a major source for the study, research, and application of energy sources and equipment. From the optimization of commercial and industrial buildings to alternative fuels and clean energy systems, the academic-affiliated energy lab is pushing energy science forward at a significant pace.
 
Examples include:
 
* [http://esl.tamu.edu/ Texas A&M's Energy Systems Laboratory]
* [https://rael.berkeley.edu/ University of California - Berkeley's Renewable & Appropriate Energy Laboratory]
* [http://www.hnei.hawaii.edu/ University of Hawaii at Manoa's Hawaii Natural Energy Institute]
 
====Functions====
 
''What are the most common functions?'' analytical, research/design, and QA/QC, and teaching
 
''What materials, technologies, and/or aspects are being calibrated, researched, and quality controlled?'' biomass, emissions, energy efficiency, energy storage and retrieval, hydropower, petrochemicals, solar energy, thermal energy, thin films, wind power
 
''What sciences are being applied in these labs?'' chemical engineering, chemistry, engineering, environmental science, material science, mechanical design, microbiology, thermodynamics
 
''What are some examples of test types and equipment?''
 
'''Common test types include''':
 
Accelerated stress testing, Aging, Calorimetry, Characterization, Climatics, Combustion, Contact mechanics, Contamination, Degredation, Design verification testing, Dielectric withstand, Durability, Efficiency, Electromagnetic compatibility, Electromagnetic interference, Electrostatic discharge, Emissions, Endurance, Flash point, Fluid dynamics, Friction, Geothermal, Hydraulic, Lightning, Mechanical, Mechanical durability, Power quality, Proficiency, Resistance - capacitance - inductance, Solar, Temperature, Thermal, Torque, Validation, Velocity and flow, Voltage
 
'''Industry-related lab equipment may include''':
 
calorimeter, climate test chamber, gas turbine, geothermal energy absorber, hydrogen fuel cell, impulse turbine, light sensor, photovoltaic trainer/system, plasma light system, porosimeter,  reaction turbine, solar thermal system, temperature sensor, viscometer, wind turbine
 
''What else, if anything, is unique about the labs in the energy industry?'' By and far, energy laboratories seem to have the most prominent footprint in the government and academic sectors. Privately run energy laboratories exist but appear to be the minority, appearing as either R&D labs inside a larger manufacturing company or as niche third-party testing facilities for biomass and/or petrochemicals. As an aside, since agriculture and forest biomass<ref name="FSForestBiorefine">{{cite web |url=https://www.fpl.fs.fed.us/research/research_emphasis_areas/introduction.php?rea_id=3 |title=Forest Biorefinery - Introduction |work=Forest Products Laboratory |publisher=U.S. Forest Service |accessdate=02 June 2017}}</ref> as well as petrochemicals can be used as fuel sources, the energy industry has ties to the agriculture, forestry, and petrochemical industries. Of course, the power and utility industry — which focuses on large-scale energy solutions for communities — is closely linked as well.
 
====LIMSwiki resources====
 
* None
 
====Further reading====
 
* {{cite book |url=https://books.google.com/books?id=SFvOBQAAQBAJ&printsec=frontcover |title=Principles of Sustainable Energy Systems |editor=Kreith, F., Krumdieck, S. |edition=2nd |publisher=CRC Press |year=2013 |pages=790 |isbn=9781466556973}}
 
 
<div align="center"><hr width="50%"></div>
 
===Environmental===
[[File:K4641-1rootscientists.jpg|left|300px]]
{{clear}}
Environmental laboratories are responsible for the analysis and research of a wide variety of materials and environments with the purpose of promoting human, animal, and ecosystem health. These labs also act as compliance enforcement entities for regulators. These labs provide services to energy and utility companies, engineering firms, pharmaceutical companies, governments, and other industry forces. These labs are found in the private, government, and academic sectors and provide many different services, including (but not limited to):
 
* exposure testing<ref name="BangertEnviro96">{{cite web |url=https://www.nap.edu/read/9191/chapter/6 |chapter=Chapter 5: Environmental Testing Laboratories and Instruments |title=Risk & Innovation: Small Companies in Six Industries: Background Papers Prepared for the NAE Risk and Innovation Study |author=Bangert, C.E.; Lynch, R.A. |publisher=National Academies Press |date=1996 |pages=83–108 |doi=10.17226/9191}}</ref>
* field testing<ref name="BangertEnviro96" />
* radiological testing<ref name="MNDoHEnviro">{{cite web |url=http://www.health.state.mn.us/divs/phl/environmental/ |title=Environmental Laboratory |publisher=Minnesota Department of Health |accessdate=03 June 2017}}</ref><ref name="STLCoEnviro">{{cite web |url=http://www.stlouisco.com/HealthandWellness/EnvironmentalServices/EnvironmentalLaboratories |title=Environmental Laboratories |publisher=Saint Louis County |accessdate=03 June 2017}}</ref>
* heavy metals testing<ref name="BangertEnviro96" />
* air quality monitoring<ref name="BangertEnviro96" />
* environmental assessments<ref name="BangertEnviro96" />
* environmental engineering<ref name="SarigiannisWelcoming">{{cite web |url=http://www.enve-lab.eu/index.php/about/welcoming-letter/ |title=Welcoming Letter: Message from the director Prof. Dimosthenis A. Sarigiannis |work=EnvE-Lab |publisher=Aristotle University of Thessaloniki |accessdate=03 June 2017}}</ref>
 
''How do environmental laboratories intersect the average person's life on a daily basis?'' The easiest way environmental labs tie into the average person's life is through the potable water supply. Without these labs, more people would become ill or even die due to improperly or non-treated drinking water supplies. We need not look further than the Flint, Michigan water crisis, where improper funding for testing and treatment of contaminated water led to the metal lead leaching into the drinking water.<ref name="CNNFlint17">{{cite web |url=http://www.cnn.com/2016/03/04/us/flint-water-crisis-fast-facts/ |title=Flint Water Crisis Fast Facts |work=CNN |publisher=Turner Broadcasting System, Inc |date=10 April 2017 |accessdate=03 June 2017}}</ref> It may be easy to take clean drinking water for granted, but remember that a lab is most likely in place to ensure it's clean in the first place.
 
====Client types====
 
'''Private''' - Private environmental labs cater to industry and the government, providing third-party testing services, often under contract.
 
Examples include:
 
* [http://aellabs.com/ American Environmental Laboratories]
* [http://www.caduceonlabs.com/ Caduceon Environmental Laboratories]
* [https://www.pacelabs.com/ Pace Analytical Services]
 
'''Government''' - Government-affiliated labs not only provide analytical services for states and municipalities; they also may conduct academic and field research to better guide local, state, and federal environmental policy.
 
Examples include:
 
* [http://www.health.state.mn.us/divs/phl/environmental/ Minnesota Department of Health's Environmental Laboratory]
* [http://www.stlouisco.com/HealthandWellness/EnvironmentalServices/EnvironmentalLaboratories Saint Louis County Environmental Health Laboratories]
* [https://www.epa.gov/aboutepa/about-national-health-and-environmental-effects-research-laboratory-nheerl U.S. Environmental Protection Agency's National Health and Environmental Effects Research Laboratory]
 
'''Academic''' - The environmental labs affiliated with higher education are usually researched-based, though they may occasionally provide third-party analyses. These labs are often directly affiliated with a local or even international watershed or ecosystem, providing valuable field training to students while monitoring changes to the location over time and issuing public reports.
 
Examples include:
 
* [http://www.enve-lab.eu/ Aristotle University of Thessaloniki's Environmental Engineering Laboratory]
* [http://web.plattsburgh.edu/academics/envsci/chemlab.php SUNY Plattsburgh's Lake Champlain Research Institute]
* [http://www.wm.edu/as/kecklab/ William & Mary's Keck Environmental Field Laboratory]
 
====Functions====
 
''What are the most common functions?'' analytical, research/design, QA/QC, and teaching
 
''What materials, technologies, and/or aspects are being analyzed, researched, and quality controlled?'' acoustics, air quality, allergens, biological specimens, contaminates, finished products, hazardous waste, pesticides, raw materials, sediment, soil, solid waste, water quality
 
''What sciences are being applied in these labs?'' chemistry, chemical engineering, environmental engineering, environmental science, microbiology, organic and inorganic chemistry, radiation chemistry
 
''What are some examples of test types and equipment?''
 
'''Common test types include''':
 
Absorption, Acute contact, Acute oral, Acute toxicity, Allergy, Anion, Antimicrobial, Atterberg limits, Bioaccumulation, Bioavailability, Bioburden, Biodegradation, Chemical and biochemical oxygen demand, Colorimetric, Conductivity, Consolidation, Contamination, Decomposition, Degradation, Density, Ecotoxicology, Emissions, Environmental fate, Environmental metabolism, Environmental monitoring, Geochemistry, Geophysics, Humidity, Hydraulic conductivity, Isotope analysis, Leak, Metallurgical analysis, Minimum bactericidal concentration, Minimum inhibitory concentration, Mobility, Organic carbon, Oxidation reduction potential, Permeability, pH, Photostability, Plant metabolism, Pressure, Proficiency, Radioactivity, Radiochemical, Refractive index, Seismic, Sensory, Soil microflora, Specific gravity, Temperature, Terrestrial toxicology, Turbidity, Wildlife toxicology
 
'''Industry-related lab equipment may include''':
 
balance, Bunsen burner, burette, colorimeter, centrifuge, chromatographic, crucible, desiccator, dropper, enzyme immunoassay, Erlenmeyer flask, extractor, Florence flask, flow meter, fume hood, funnel, graduated cylinder, hot plate, moisture analyzer, mortar and pestle, multi-well plate, organic carbon analyzer, oven, particle counter, pH meter, pipestem triangle, reagent dispenser, remote sensors, ring stand, rotary evaporator, sediment analyzer, spectrometer, spectrophotometer, stirring rod, thermometer, viscometer
 
''What else, if anything, is unique about the labs in the environmental industry?'' "The environmental laboratory industry will be undergoing continuous radical change in coming years as environmental markets continue to evolve," stated Bangert and Lynch in a 1996 study for the National Research Council. "The model laboratory of the future, therefore, is likely to be far different from that of today," they added.<ref name="BangertEnviro96" /> Fast forward 20 years, and we see their then vision for the future of environmental testing labs came to fruition: today's environmental testing lab uses a [[laboratory information management system]] (LIMS) to manage data in an automated, innovative lab that provides analytical services as well as research.<ref name="BangertEnviro96" /><ref name="DePalmaInsights13">{{cite web |url=http://www.labmanager.com/insights/2013/09/insights-on-starting-and-running-an-environmental-lab |title=Insights on Starting and Running an Environmental Lab |author=DePalma, A. |work=Lab Manager |publisher=LabX Media Group |date=10 September 2013 |accessdate=03 June 2017}}</ref> And they need to be agile as the concepts of "climate change," "biodiversity," and "sustainable ecosystems" continue to weave their way into the focus of environmental laboratories.<ref name="SimmondsTheImport09">{{cite web |url=http://your.kingcounty.gov/dnrp/library/water-and-land/science/newsletter/2009/june/0906-3-monitoring-import.pdf |title=The Importance of Environmental Monitoring and Analysis |work=King County's SciFYI |author=Simmonds, J. |publisher=King County |date=June 2009 |accessdate=03 June 2017}}</ref><ref name="ERDCEnvironmental">{{cite web |url=http://www.erdc.usace.army.mil/Media/Fact-Sheets/Fact-Sheet-Article-View/Article/476745/environmental-laboratory/ |title=Environmental Laboratory |publisher=U.S. Army Corps of Engineers - Engineer Research & Development Center |accessdate=03 June 2017}}</ref> As such, these labs will play an ever-increasing role in helping scientists better understand how we are impacting our environment.
 
====LIMSwiki resources====
 
* [[Environmental informatics]]
* [[Hydroinformatics]]
 
====Further reading====
 
* {{cite book |url=https://books.google.com/books?id=VUCcAQAAQBAJ&printsec=frontcover |title=Environmental Chemistry: A Global Perspective |author=vanLoon, G.W.; Duffy, S.J. |publisher=Oxford University Press |year=2011 |pages=545 |isbn=9780199228867}}
 
 
<div align="center"><hr width="50%"></div>
 
===Food and beverage===
[[File:Laboratório de Tecnologia de Alimentos.jpg|left|400px]]
{{clear}}
Food and beverage laboratories are responsible for developing, protecting, and supporting the food, beverages, and nutritional supplements humans and animals consume. From creating new flavor enhancers for food to ensuring the quality and safe consumption of a wine, these labs play a vital role in most parts of the world where processed food and agricultural products are produced. These labs are found in the private, government, and academic sectors and provide many different services, including (but not limited to)<ref name="NielsenFood15">{{cite book |title=Food Analysis Laboratory Manual |author=Nielsen, S. |publisher=Springer |pages=177 |edition=2nd |year=2015 |isbn=9781441914620}}</ref>:
 
* reverse engineering
* claims testing
* contaminate testing
* batch variation testing
* extractable and leachable testing
* allergen testing
* shelf life testing
* non-routine quality testing
* packaging testing
 
''How do food and beverage laboratories intersect the average person's life on a daily basis?'' Have you ever enjoyed a candy bar, soda, or snack cake? A laboratory and food scientists were behind its production. Don't care much for processed foods? A laboratory is still involved in the quality and safety testing of raw fruits and vegetables, milk, and nuts. And when food supplies become contaminated, government testing labs are often in the thick of determining the source of the contamination as quickly as possible before more people become ill. Whether it's the unique flavor profile of a potato chip you love or the fact you can reliably acquire safe foods, remember that a laboratory is often behind it.
 
====Client types====
 
'''Private''' - Whether manufacturers seek help with a formulation problem or a government subcontracting contamination analysis, private food and beverage labs are there. These labs may appear within a major food corporation or act as third-party contact labs for work as needed.
 
Examples include:
 
* [https://www.avomeen.com/services/food-and-beverage-testing/ Avomeen Analytical Services]
* [http://www.dtsfoodassurance.com.au/ DTS Food Assurance]
* [http://www.eag.com/food/ EAG Laboratories]
 
'''Government''' - The government-affiliated labs of the food and beverage industry typically act as protectors of the local, regional, or national food supply. Some may be responsible for developing and enforcing regulations as well.
 
Examples include:
 
* [http://www.ava.gov.sg/explore-by-sections/food/laboratory-services/food-testing Agi-Food & Veterinary Authority of Singapore's Food and Food Product Laboratory]
* [http://health.mo.gov/lab/foodbeverageanalysis.php Missouri State Public Health Laboratory, Chemistry Unit]
* [http://www.agriculture.pa.gov/Protect/FoodSafety/Laboratory/Pages/default.aspx Pennsylvania Department of Agriculture Food Safety Laboratory Division]
 
'''Academic''' - Academic food and beverage labs are usually teaching labs, often associated with a university's agriculture department.
 
Examples include:
 
* [http://www.fshn.chhs.colostate.edu/research/BSL/index.aspx Colorado State University Brewing Science and Food Microbiology Laboratory]
* [http://ifstl.jifsan.umd.edu/about/ University of Maryland, Joint Institute for Food Safety and Applied Nutrition's International Food Safety Training Lab]
* [http://www.fst.vt.edu/aboutus/facilities.html VirginiaTech's Food Analysis, Meat Chemistry, and Enology Laboratories]
 
====Functions====
 
''What are the most common functions?'' analytical, research/design, QA/QC, and teaching
 
''What materials, technologies, and/or aspects are being analyzed, researched, and quality controlled?'' candy, dairy, fruits, grains, meats, nuts, oils, proteins, soft drinks, starches, sugars, vegetables, vitamins
 
''What sciences are being applied in these labs?'' biochemistry, chemical engineering, chemistry, fermentation science, microbiology, molecular gastronomy, nutrition and food science
 
''What are some examples of test types, terminology, and equipment?''
 
'''Common test types include''':
 
Absorption, Active ingredient, Alcohol level, Allergy, Altitude, Amino acid analysis, Ash, Bioavailability, Bioburden, Biodegradation, Biomolecular, Boiling - freezing - melting point, Comparison, Compliance/Conformance, Contamination, Density, Detection, Efficacy, Expiration dating, Extractables and leachables, Flavor, Fluid dynamics, Fluorescence, Fragrance, Genotoxicity, GMO detection, HACCP, Hazard analysis, Identification, Ingredient, Iodine value, Isotope analysis, Labeling, Moisture, Mold - fungal - mycotoxin, Mutagenicity, Nutritional, Oxidation reduction potential, Oxidation stability, Pathogen, PDCAAS, Permeability, Peroxide value, pH, Plant metabolism, Polarimetry, Preservative challenge, Proficiency, Purity, Quality control, Radioactivity, Radiochemical, Refractive index, Safety, Sanitation, Saponification value, Sensory, Shelf life, Smoke point, Sulfide, Thermal, Total viable count, Turbidity, Viscosity, Water activity
 
'''Industry-related lab equipment may include''':
 
alcohol analyzer, balance, biosafety cabinet, centrifuge, chiller, chromatographic, colorimeter, ELISA equipment, evaporator, fat analyzer, freezer, fume hood, gravimetric diluter, hot/forced air oven, incubator, Kjeldahl digestion apparatus, laminar airflow workstation, media sterilizer, microscope, moisture analyzer, muffle furnace, Petri dish, photometric analyzer, protein analyzer, refractometer, spectrometer, titrator
 
''What else, if anything, is unique about the labs in the food and beverage industry?'' As previously mentioned in the agriculture section, the food and beverage industry has strong ties to the agriculture industry, though broadly speaking the food and beverage industry is typically dealing with the end products of agriculture.
 
While most industries see global standards coalesce around their industry, this holds especially true for food and beverage laboratories. Given the vital nature of a clean and safe food supply, regulation and global standardization remains a strong goal for the industry.<ref name="NitaGlobal17">{{cite web |url=http://www.foodsafetymagazine.com/signature-series/global-standards-impacting-food-and-beverage-processors/ |title=Global Standards Impacting Food and Beverage Processors |author=Nita, I. |work=Food Safety Magazine |date=18 January 2017 |accessdate=03 June 2017}}</ref>
 
====LIMSwiki resources====
 
* None
 
====Further reading====
 
* {{cite book |url=https://books.google.com/books?id=14VPAwAAQBAJ&printsec=frontcover |title=Practical Food Safety: Contemporary Issues and Future Directions |editor=Bhat, R.; Gomez-Lopez, V.M. |publisher=John Wiley & Sons |year=2014 |pages=632 |isbn=9781118474594}}
 
* {{cite book |url=https://books.google.com/books?id=duFMBgAAQBAJ&printsec=frontcover |title=Microbiological Examination Methods of Food and Water: A Laboratory Manual |author=da Silva, N.; Taniwaki, M.H.; Junqueria, V.C. et al. |publisher=CRC Press |year=2012 |pages=484 |isbn=9780203168394}}
 
 
<div align="center"><hr width="50%"></div>


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


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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]]

Revision as of 16:51, 26 August 2018

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Full article title The development and application of bioinformatics core competencies to improve bioinformatics training and education
Journal PLOS Computational Biology
Author(s) Mulder, Nicola; Schwartz, Russell; Brazas, Michelle, D.; Brooksbank, Carth; Gaeta, Bruno; Morgan, Sarah L.;
Pauley, Mark A.; Rosenwald, Anne; Rustici, Gabriella; Sierk, Michael; Warnow, Tandy; Welch, Lonnie
Author affiliation(s) University of Cape Town, Carnegie Mellon University, Ontario Institute for Cancer Research, Wellcome Genome Campus, University of New South Wales, University
of Nebraska at Omaha, Georgetown University, University of Cambridge, Saint Vincent College, University of Illinois at Urbana-Champaign, Ohio University
Primary contact Email: nicola dot mulder at uct dot ac dot za
Year published 2018
Volume and issue 14(2)
Page(s) e1005772
DOI 10.1371/journal.pcbi.1005772
ISSN 1553-7358
Distribution license Creative Commons Attribution 4.0 International
Website 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 (PDF)

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

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[1], 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.

Development of core competencies for bioinformatics

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[2], 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[3] 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[1] and the competency-use case scoring mechanism.

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.

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.

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[4] 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.

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.[3]

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.

References

  1. 1.0 1.1 Welch, L.; Brooksban, C.; Schwartz, R. et al. (2016). "Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee)". PLOS Computational Biology 12 (5): e1004943. doi:10.1371/journal.pcbi.1004943. PMC PMC4866758. PMID 27175996. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866758. 
  2. Welch, L.R.; Schwartz, R.; Lewitter, F. (2012). "A report of the Curriculum Task Force of the ISCB Education Committee". PLOS Computational Biology 8 (6): e1002570. doi:10.1371/journal.pcbi.1002570. PMC PMC3386154. PMID 22761560. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386154. 
  3. 3.0 3.1 Welch, L.; Lewitter, F; Schwartz, R. et al. (2014). "Bioinformatics curriculum guidelines: toward a definition of core competencies". PLOS Computational Biology 10 (3): e1003496. doi:10.1371/journal.pcbi.1003496. PMC PMC3945096. PMID 24603430. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945096. 
  4. Anderson, L.W.; Krathwohl, D.R., ed. (2001). A Taxonomy for Learning, Teaching, and Assessing: A Revision of Bloom's Taxonomy of Educational Objectives. Pearson. pp. 336. ISBN 9780801319037. 

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.