Yearb Med Inform 2007; 16(01): 149-156
DOI: 10.1055/s-0038-1638539
Research & Education
Georg Thieme Verlag KG Stuttgart

Biomedical Informatics Training at the University of Wisconsin-Madison

D. J. Severtson
1   Computation and Informatics in Biology and Medicine Program, University of Wisconsin-Madison, USA
2   School of Nursing, University of Wisconsin-Madison, USA
,
L. Pape
1   Computation and Informatics in Biology and Medicine Program, University of Wisconsin-Madison, USA
,
C. D. Page Jr.
1   Computation and Informatics in Biology and Medicine Program, University of Wisconsin-Madison, USA
4   Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, USA
6   Computer Sciences Department, University of Wisconsin-Madison, USA
,
J. W. Shavlik
1   Computation and Informatics in Biology and Medicine Program, University of Wisconsin-Madison, USA
4   Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, USA
6   Computer Sciences Department, University of Wisconsin-Madison, USA
,
G. N. Phillips
1   Computation and Informatics in Biology and Medicine Program, University of Wisconsin-Madison, USA
4   Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, USA
6   Computer Sciences Department, University of Wisconsin-Madison, USA
,
P. Flatley Brennan
1   Computation and Informatics in Biology and Medicine Program, University of Wisconsin-Madison, USA
2   School of Nursing, University of Wisconsin-Madison, USA
3   Department of Industrial and Systems Engineering, University of Wisconsin-Madison, USA
4   Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, USA
› Author Affiliations
We thank the NLM for its support of the CIBM Training Program (Grant No. T15LM007359). Additional support to CIBM comes from the Genome Center of Wisconsin, the Department of Biochemistry, the Department of Biosta tistics and Medical Informatics, and the UW-Madison Graduate School.
Further Information

Correspondence to

Dolores J. Severtson
H6/295 CSC
600 Highland Ave. Madison
WI 53575, USA
Phone: +1 608-263-5311   
Fax: +1 08-263-5332   

Publication History

Publication Date:
05 March 2018 (online)

 

Summary

Objectives

The purpose of this paper is to describe biomedical informatics training at the University of Wisconsin-Madison (UW Madison).

Methods

We reviewed biomedical informatics training, research, and faculty/trainee participation at UW-Madison.

Results

There are three primary approaches to training 1) The Computation & Informatics in Biology & Medicine Training Program, 2) formal biomedical informatics offered by various campus departments, and 3) individualized programs. Training at UW-Madison embodies the features of effective biomedical informatics training recommended by the American College of Medical Informatics that were delineated as: 1) curricula that integrate experiences among computational sciences and application domains, 2) individualized and interdisciplinary cross training among adiverse cadre of trainees to develop key competencies that he or she does not initially possess, 3) participation in research and development activities, and 4) exposure to a range of basic informational and computational sciences.

Conclusions

The three biomedical informatics training approaches immerse students in multidisciplinary training and education that is supported by faculty trainers who participate in collaborative research across departments. Training is provided across a range of disciplines and available at different training stages. Biomedical informatics training at UW-Madison illustrates how a large research University, with multiple departments across biological, computational and health fields, can provide effective and productive biomedical informatics training via multiple bioinformatics training approaches.


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  • References

  • 1 Friedman CP, Altman RB, Kohane IS, McCormick KA, Miller PL, Ozbolt JG. et al. Training the next generation of informaticians: the impact of “BISTI” and bioinformatics—A Report from the American College of Medical Informatics. J Am Med Inform Assoc 2004; Jan 11: 167-72.
  • 2 Darling A, Mau B, Blattner F, Perna N. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; Jul 14 (07) 1394-403.
  • 3 Bockhorst J, Qiu Y, Glasner J, Liu M, Blattner F, Craven M. Predicting bacterial transcription units using sequence and expression data. Bioinformatics (special issue: Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology) 2003; 19 Suppl 1: 34i-43i.
  • 4 Molla M, Waddell M, Page D, Shavlik J. Using machine learning to design and interpret gene expression microarrays. AI Magazine 2004; 25: 23-44.
  • 5 Ong J, Glasner J, Page D. Modeling regulatory pathways in E. coli from time series expression profiles. Published in Bioinformatics supplement as Proceedings of the International Conference on Intelligent Systems for Molecular Biology (ISMB-02) 2002; 241-8.
  • 6 Waddell M, Page D, Zhan F, Barlogie B, Shaughnessy J. Predicting cancer susceptibility from single-nucleotide polymorphism data: a case study in multiple myeloma. Appears in the Proceedings of the 5th international workshop on Bioinformatics, Conference on Knowledge Discovery in Data 2005; 21-8.
  • 7 DiMaio F, Shavlik J, Phillips GN. Pictorial structures for molecular modeling. Adv Neural Inf Process Syst (NIPS). MIT Press 2005; 17: 369-76.
  • 8 DiMaio F, Shavlik J, Phillips GN. A probabilistic approach to protein backbone tracing in electron density maps. Bioinformatics 2006; Jul 15; 22 (14) e81-9.
  • 9 Han BW, Bingman CA, Mahnke DK, Bannen RM, Bednarek S, Sabina RL. et al. Membrane association, mechanism of action and structure of Arabidopsis embryonic factor 1 (FAC1). J Biol Chem 2006; May 26; 281 (21) 14939-47.
  • 10 Kondrashov DA, Phillips Jr GN. Molecular mastication mechanics. Structure 2005; Jun 13 836-7.
  • 11 Kondrashov DA, Cui Q, Phillips Jr GN. Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J 2006; Oct 15; 91 (08) 2760-7 Epub 2006 Aug 4..
  • 12 Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips Jr GN. Protein structural variation in computational models and crystallographic data. Structure 2007; Feb; 15 (02) 169-77.
  • 13 Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR 2005; May; 32 (01) 71-81.
  • 14 McCarty CA, Wilke RA, Giampietro PF, Wesbrook SD, Caldwell MD. Marshfield Clinic Personalized Medicine Research Project (PMRP): design, methods and recruitment for a large population-based biobank. Personalized Medicine 2005; 02 (01) 49-79.
  • 15 Greenlee RG. Measuring disease frequency in the Marshfield epidemiologic study area (MESA). Clin Med Res 2003; 01 (04) 273-80.
  • 16 Kossman S, Casper GR, Severtson DJ, Grenier AS, Or C, Carayon P. et al. Designing study nurses’ training to enhance research integrity: A macro ergonomic approach. Proceedings of the 9th Annual meeting of the American Medical Informatics Association. Washington DC. N: November 10 14 2006: 439-43.
  • 17 Carayon P, Schoofs AHundt, Karsh B-T, Gurses AP, Alvarado CJ, Smith M. et al. Work system design for patient safety: The SEIPS Model. Qual Saf Health Care 2006; 15 Suppl 1 i50-i58.

Correspondence to

Dolores J. Severtson
H6/295 CSC
600 Highland Ave. Madison
WI 53575, USA
Phone: +1 608-263-5311   
Fax: +1 08-263-5332   

  • References

  • 1 Friedman CP, Altman RB, Kohane IS, McCormick KA, Miller PL, Ozbolt JG. et al. Training the next generation of informaticians: the impact of “BISTI” and bioinformatics—A Report from the American College of Medical Informatics. J Am Med Inform Assoc 2004; Jan 11: 167-72.
  • 2 Darling A, Mau B, Blattner F, Perna N. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; Jul 14 (07) 1394-403.
  • 3 Bockhorst J, Qiu Y, Glasner J, Liu M, Blattner F, Craven M. Predicting bacterial transcription units using sequence and expression data. Bioinformatics (special issue: Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology) 2003; 19 Suppl 1: 34i-43i.
  • 4 Molla M, Waddell M, Page D, Shavlik J. Using machine learning to design and interpret gene expression microarrays. AI Magazine 2004; 25: 23-44.
  • 5 Ong J, Glasner J, Page D. Modeling regulatory pathways in E. coli from time series expression profiles. Published in Bioinformatics supplement as Proceedings of the International Conference on Intelligent Systems for Molecular Biology (ISMB-02) 2002; 241-8.
  • 6 Waddell M, Page D, Zhan F, Barlogie B, Shaughnessy J. Predicting cancer susceptibility from single-nucleotide polymorphism data: a case study in multiple myeloma. Appears in the Proceedings of the 5th international workshop on Bioinformatics, Conference on Knowledge Discovery in Data 2005; 21-8.
  • 7 DiMaio F, Shavlik J, Phillips GN. Pictorial structures for molecular modeling. Adv Neural Inf Process Syst (NIPS). MIT Press 2005; 17: 369-76.
  • 8 DiMaio F, Shavlik J, Phillips GN. A probabilistic approach to protein backbone tracing in electron density maps. Bioinformatics 2006; Jul 15; 22 (14) e81-9.
  • 9 Han BW, Bingman CA, Mahnke DK, Bannen RM, Bednarek S, Sabina RL. et al. Membrane association, mechanism of action and structure of Arabidopsis embryonic factor 1 (FAC1). J Biol Chem 2006; May 26; 281 (21) 14939-47.
  • 10 Kondrashov DA, Phillips Jr GN. Molecular mastication mechanics. Structure 2005; Jun 13 836-7.
  • 11 Kondrashov DA, Cui Q, Phillips Jr GN. Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J 2006; Oct 15; 91 (08) 2760-7 Epub 2006 Aug 4..
  • 12 Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips Jr GN. Protein structural variation in computational models and crystallographic data. Structure 2007; Feb; 15 (02) 169-77.
  • 13 Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR 2005; May; 32 (01) 71-81.
  • 14 McCarty CA, Wilke RA, Giampietro PF, Wesbrook SD, Caldwell MD. Marshfield Clinic Personalized Medicine Research Project (PMRP): design, methods and recruitment for a large population-based biobank. Personalized Medicine 2005; 02 (01) 49-79.
  • 15 Greenlee RG. Measuring disease frequency in the Marshfield epidemiologic study area (MESA). Clin Med Res 2003; 01 (04) 273-80.
  • 16 Kossman S, Casper GR, Severtson DJ, Grenier AS, Or C, Carayon P. et al. Designing study nurses’ training to enhance research integrity: A macro ergonomic approach. Proceedings of the 9th Annual meeting of the American Medical Informatics Association. Washington DC. N: November 10 14 2006: 439-43.
  • 17 Carayon P, Schoofs AHundt, Karsh B-T, Gurses AP, Alvarado CJ, Smith M. et al. Work system design for patient safety: The SEIPS Model. Qual Saf Health Care 2006; 15 Suppl 1 i50-i58.