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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
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| |title_full = The development and application of bioinformatics core competencies to improve bioinformatics training and education
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| |journal = ''PLOS Computational Biology''
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| |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
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| |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
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| |contact = Email: nicola dot mulder at uct dot ac dot za
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| |editors =
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| |pub_year = 2018
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| |vol_iss = '''14'''(2)
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| |pages = e1005772
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| |doi = [http://10.1371/journal.pcbi.1005772 10.1371/journal.pcbi.1005772]
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| |issn = 1553-7358
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| |license = [http://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International]
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| |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]
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| |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.
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| ==Abstract==
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| [[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.
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| ==Introduction==
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| 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.
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| | '''Title''': ''LIMS Selection Guide for Materials Testing Laboratories'' |
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| | '''Edition''': First Edition |
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| | '''Author for citation''': Shawn E. Douglas |
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| | '''License for content''': [https://creativecommons.org/licenses/by-sa/4.0/ Creative Commons Attribution-ShareAlike 4.0 International] |
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| | '''Publication date''': ??? 2023 |
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| ==Development of core competencies for bioinformatics==
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| 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.
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| 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.
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| 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.
| | The table of contents for ''LIMS Selection Guide for Materials Testing Laboratories'' is as follows: |
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| 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.
| | :[[User:Shawndouglas/sandbox/sublevel10|1. Introduction to materials and materials testing laboratories]] |
| | ::1.1 Materials testing labs, then and now |
| | :::1.1.1 Materials testing 2.0 |
| | ::1.2 Industries, products, and raw materials |
| | ::1.3 Laboratory roles and activities in the industry |
| | :::1.3.1 R&D roles and activities |
| | :::1.3.2 Pre-manufacturing and manufacturing roles and activities |
| | :::1.3.3 Post-production quality control and regulatory roles and activities |
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| 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.
| | :[[User:Shawndouglas/sandbox/sublevel11|2. Standards, regulations, and test methods affecting materials testing labs]] |
| | ::2.1 Globally recognized materials manufacturing standards |
| | :::2.1.1 American Society of Civil Engineers (ASCE) materials standards |
| | :::2.1.2 ASTM International Volume 15.04 |
| | :::2.1.3 Canadian Standards Association (CSA) A3000 series |
| | :::2.1.4 International Organization for Standardization (ISO) 10993 |
| | :::2.1.5 Metal Powder Industries Federation (MPIF) Standard 35 family |
| | ::2.2 Regulations and laws around the world |
| | :::2.2.1 21 CFR Part 175 and 176 - United States |
| | :::2.2.2 Building Standard Law - Japan |
| | :::2.2.3 The Furniture and Furnishings (Fire) (Safety) Regulations 1988 - United Kingdom |
| | :::2.2.4 National Environment Protection (Used Packaging Materials) Measure 2011 - Australia |
| | :::2.2.5 Surface Coating Materials Regulations (SOR/2016-193) - Canada |
| | ::2.3 Standardized test methods for materials |
| | ::2.4 Materials laboratory accreditation |
| | :::2.4.1 A note about engineering and construction materials testing |
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| 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" />
| | :[[User:Shawndouglas/sandbox/sublevel12|3. Choosing laboratory informatics software for your materials testing lab]] |
| | ::3.1 Evaluation and selection |
| | :::3.1.1 Technology considerations |
| | ::::3.1.1.1 Laboratory informatics options |
| | :::3.1.2 Features and functions |
| | ::::3.1.2.1 Base features |
| | ::::3.1.2.2 Specialty features |
| | :::3.1.3 Cybersecurity considerations |
| | :::3.1.4 Regulatory compliance considerations |
| | :::3.1.5 System flexibility |
| | :::3.1.6 Cost considerations |
| | ::3.2 Implementation |
| | :::3.2.1 Internal and external integrations |
| | ::3.3 MSW, updates, and other contracted services |
| | ::3.4 How a user requirements specification fits into the entire process (LIMSpec) |
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| 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.
| | :[[User:Shawndouglas/sandbox/sublevel13|4. Resources for selecting and implementing informatics solutions]] |
| | ::4.1 LIMS vendors |
| | ::4.2 Consultants |
| | ::4.3 Professional |
| | :::4.3.1 Trade organizations |
| | :::4.3.2 Conferences and trade shows |
| | ::4.4 LIMSpec |
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| ==References==
| | :[[User:Shawndouglas/sandbox/sublevel14|5. Taking the next step]] |
| {{Reflist|colwidth=30em}}
| | ::5.1 Conduct initial research into a specification document tailored to your lab's needs |
| | ::5.2 Issue some of the specification as part of a request for information (RFI) |
| | ::5.3 Respond to or open dialogue with vendors |
| | :::5.3.1 The value of demonstrations |
| | ::5.4 Finalize the requirements specification and choose a vendor |
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| ==Notes==
| | :[[User:Shawndouglas/sandbox/sublevel15|6. Closing remarks]] |
| 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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| <!--Place all category tags here-->
| | :[[User:Shawndouglas/sandbox/sublevel16|Appendix 1. Blank LIMSpec template for manufacturing labs]] |
| [[Category:LIMSwiki journal articles (added in 2018)]] | | ::A1. Introduction and methodology |
| [[Category:LIMSwiki journal articles (all)]]
| | ::A2. Primary laboratory workflow |
| [[Category:LIMSwiki journal articles on bioinformatics]]
| | ::A3. Maintaining laboratory workflow and operations |
| [[Category:LIMSwiki journal articles on education]]
| | ::A4. Specialty laboratory functions |
| | ::A5. Technology and performance improvements |
| | ::A6. Security and integrity of systems and operations |
| | ::A7. Putting those requirements to practical use and caveats |
| | ::A8. LIMSpec in Microsoft Word format |
