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Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)

  • Lonnie Welch ,

    welch@ohio.edu

    Affiliation School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, United States of America

  • Cath Brooksbank,

    Affiliation European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom

  • Russell Schwartz,

    Affiliation Department of Biological Sciences and Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America

  • Sarah L. Morgan,

    Affiliation European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom

    ORCID http://orcid.org/0000-0001-9528-8323

  • Bruno Gaeta,

    Affiliation School of Computer Science and Engineering, UNSW, Sydney, New South Wales, Australia

  • Alastair M. Kilpatrick,

    Affiliation Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America

    ORCID http://orcid.org/0000-0002-4795-8799

  • Daniel Mietchen,

    Affiliation National Institutes of Health, Bethesda, Maryland, United States of America

  • Benjamin L. Moore,

    Affiliation MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom

  • Nicola Mulder,

    Affiliation Computational Biology group, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa

  • Mark Pauley,

    Affiliation School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, United States of America

  • William Pearson,

    Affiliation Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America

  • Predrag Radivojac,

    Affiliation School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America

  • Naomi Rosenberg,

    Affiliation Tufts University School of Medicine, Boston, Massachusetts, United States of America

  • Anne Rosenwald,

    Affiliation Department of Biology, Georgetown University, Washington, D.C., United States of America

  • Gabriella Rustici,

    Affiliation School of the Biological Sciences, University of Cambridge, Cambridge Systems Biology Centre, Cambridge, United Kingdom

    ORCID http://orcid.org/0000-0003-3085-1271

  •  [ ... ],
  • Tandy Warnow

    Affiliation Departments of Computer Science and Bioengineering, University of Illinois, Urbana, Illinois, United States of America

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  • [ view less ]

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)

  • Lonnie Welch, 
  • Cath Brooksbank, 
  • Russell Schwartz, 
  • Sarah L. Morgan, 
  • Bruno Gaeta, 
  • Alastair M. Kilpatrick, 
  • Daniel Mietchen, 
  • Benjamin L. Moore, 
  • Nicola Mulder, 
  • Mark Pauley
PLOS
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The Curriculum Task Force (CTF) of ISCB’s Education Committee seeks to define curricular guidelines for those who educate or train bioinformatics professionals at all career stages. A recent report of the CTF [1] presented a draft set of bioinformatics core competencies, derived from the results of surveys of (1) core facility directors, (2) career opportunities, and (3) existing curricula.

Since the publication of its 2014 report, the CTF has focused on the application of the guidelines in varied contexts to identify areas where refinement is needed. As a first step, the task force held an open meeting at the ISMB conference in July 2014. The ideas discussed at the meeting spawned four working groups (WGs), which focus on (i) defining core competencies for specific types and levels of bioinformatics training, (ii) mapping the curriculum guidelines and competencies to existing materials in order to identify the need for development of new materials, and (iii) identifying where revision of the guidelines may be valuable. The CTF is engaging the ISCB community through open WG meetings at ISCB’s official conferences. Thus far, the WGs have convened at the ISCB Great Lakes Bioinformatics Conference (Purdue University, May 2015) and at the ISMB/ECCB Conference (Dublin, Ireland, July 2015). Additionally, the CTF held a workshop at the Annual General Meeting of the Global Organization of Bioinformatics Learning, Education and Training (Cape Town, South Africa, November 2015). Specifically, the draft competencies have been employed in a wide range of activities and contexts (see Table 1 and [211]), including the development of new curricula, the analysis of existing curricula, and the creation of new roles involving bioinformatics. These activities have resulted in the identification of several areas where refinement would be useful:

  • Identify different levels or phases of competency. It would be helpful to define different phases of competency development, or different levels of competency appropriate for distinct roles.
  • Define competency profiles for disciplines that don’t fit into our current silos. Bioengineering provides an illustrative example of a discipline that requires core competency in bioinformatics but does not fit into our current categories. There are almost certainly others. It would be helpful if we could provide some guidance on how to produce ‘hybrid’ competency profiles, perhaps borrowing some competencies from the TF’s core set and others from different disciplines. The LifeTrain initiative (www.lifetrain.eu) [2, 3] is collecting competency profiles for a range of disciplines of relevance to the biomedical sciences and may provide a useful resource kit for this.
  • Broaden the scope of the competency profiles in response to cutting-edge and emerging research. Current areas requiring improvement include incorporating competencies that capture a fundamental understanding of the biological principles central to analyzing biomolecular data, and broadening the user WG to include applications beyond medicine.
  • Provide guidance on the evidence required to assess whether someone has acquired each competency. For undergraduate, Master’s and PhD programs, learning outcomes for each competency, perhaps with examples of appropriate means of assessment, would be valuable. For established professionals who need to assimilate competencies into their working lives, a different approach may be required (such as keeping a portfolio to capture evidence of competency); the CTF should seek guidance from relevant professional bodies, especially in regulated professions such as healthcare.
  • Provide indicative course content or examples of programs that map to the competency requirements. We do not wish to prescribe what course providers should teach or how they should teach it; however, if a course provider is designing a course to meet a specific competency requirement, it may be helpful to find examples of other programs that do this successfully. One way of achieving this is by mapping existing training content to the TF’s competencies. Another way might be to provide an indication, perhaps based on several courses, of the course content that would meet the competency requirements. This would give course providers the freedom to build their own course syllabi without having to reinvent the wheel. Initiatives to collect examples of Creative Commons (or otherwise reusable) course materials will provide an extremely valuable bank of training materials that could be mapped to the core competencies.

References

  1. 1. Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, et al. (2014) Bioinformatics curriculum guidelines: toward a definition of core competencies. PLoS Computational Biology 10: e1003496. pmid:24603430
  2. 2. Brooksbank C, Johnson C (2015) Lifelong learning for all in biomedicine. Nature 524: 415.
  3. 3. Hardman M, Brooksbank C, Johnson C, Janko C, See W, et al. (2013) LifeTrain: towards a European framework for continuing professional development in biomedical sciences. Nature Reviews Drug Discovery 12: 407–408.
  4. 4. Dinsdale E, Elgin SC, Grandgenett N, Morgan W, Rosenwald A, Tapprich W, Triplett EW, Pauley MA. NIBLSE: A Network for Integrating Bioinformatics into Life Sciences Education. CBE Life Sci Educ. 2015 Winter;14(4):le3. pmid:26466989
  5. 5. Tastan Bishop Ö, Adebiyi EF, Alzohairy AM, Everett D, Ghedira K, Ghouila A, Kumuthini J, Mulder NJ, Panji S, Patterton HG; H3ABioNet Consortium; H3Africa Consortium. Bioinformatics education—perspectives and challenges out of Africa. Brief Bioinform. 2015 Mar;16(2):355–64. pmid:24990350
  6. 6. Machanick P, Tastan Bishop Ö. How to establish a bioinformatics postgraduate degree programme—a case study from South Africa. Brief Bioinform. 2015 Mar;16(2):346–54. pmid:24794523
  7. 7. Goodman AL, Dekhtyar A. Teaching bioinformatics in concert. PLoS Comput Biol. 2014 Nov 20;10(11):e1003896. pmid:25411792
  8. 8. Geskin A, Legowski E, Chakka A, Chandran UR, Barmada MM, LaFramboise WA, Berg J, Jacobson RS. Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center. PLoS One. 2015 Jun 26;10(6):e0131166. pmid:26115441
  9. 9. Chimusa ER, Mbiyavanga M, Masilela V, Kumuthini J. "Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development. PLoS Comput Biol. 2015 Nov 19;11(11):e1004512. pmid:26583922
  10. 10. Rosenwald Anne G., Pauley Mark A., Welch Lonnie, Elgin Sarah C. R., Wright Robin, and Blum Jessamina. The CourseSource Bioinformatics Learning Framework. CBE Life Sci Educ. March 1, 2016. 15:le2.
  11. 11. Ned-Sykes R, Johnson C, Ridderhof JC, Perlman E, Pollock A, DeBoy JM; Centers for Disease Control and Prevention (CDC). Competency Guidelines for Public Health Laboratory Professionals: CDC and the Association of Public Health Laboratories. MMWR Surveill Summ. 2015 May 15;64 Suppl 1:1–81.