1. Integrating Bioinformatics into the Life Sciences – Phase 2 Mark Pauley and Bill Tapprich Group #2: Integration

2. Integrating Bioinformatics into the Life Sciences – Phase 2 NSF TUES Phase 2 Award (#1122971; 2011 - 2015) Goals: 1.Permanently modify the biology curriculum at three diverse institutions; 2.Develop a repository of curated “student-friendly” data and computational tools; 3.Vertically integrate the bioinformatics-focused laboratories through several levels of complexity; and 4.Disseminate the bioinformatics-focused laboratories through publisher’s resources. Participating Institutions: 1.University of Nebraska at Omaha: Large (> 15,000), public, metropolitan, Doctoral/Research (Carnegie classification) 2.University of Nebraska at Kearney: Mid-sized (5,000 – 15,000), public, rural, Master’s Large 3.Nebraska Wesleyan University (Lincoln, NE): Small (< 5,000), private, Baccalaureate/A&S

3. Bioinformatics-focused Laboratories Have a narrative that presents the problem and introduces the topic; Structured exercises that sequentially address questions posed by the laboratory. Make use of publicly available bioinformatics tools as well as curated data sets. Implementation Laboratory NameUNOUNKNWU Genomes and Bioinformatics*  Invasive Plants*  BRCA1  Dotplots  Dinosaur DNA  Enolase  Mystery Protein*  Additional labs under development: Dotplots, Paralogs and Orthologs Exploring Ancient Genomes Phylogenetic Analysis of Microorganisms Tetrapod Evolution *To be presented on 18 June at ABLE 2014.

4. Assessment Expert review Student focus groups Pre/posttest developed by the project team and validated by experts on the evaluation team. UNO Spring 2012 – Pre/Posttest Results Laboratory: Genomes and Bioinformatics N = 126Mean ScoreStd. Dev.Std. Error Pretest5.231.5960.142 Posttest5.811.4070.125 Mean Gain0.58*** ***p < 0.001; df = 125; t = 3.579; Effect size = 0.385 NWU Spring 2012 – Pre/Posttest Results Laboratory: Genomes and Bioinformatics N =6Mean ScoreStd. Dev.Std. Error Pretest6.832.1370.872 Posttest7.171.1690.477 Mean Gain0.34*** ***p < 0.611; df = 5; t = 0.542; Effect size = 0.197 UNK Spring 2012 – Pre/Posttest Results Laboratory: Genomes and Bioinformatics N = 132Mean ScoreStd. Dev.Std. Error Pretest4.771.5960.142 Posttest5.771.4070.125 Mean Gain1.00*** ***p < 0.021; df = 131; t = 6.105; Effect size = 0.664

5. Project Website: http://ccli.ist.unomaha.edu 1.Lecture Modules (from CCLI Type 1) 2.Laboratories (current project) 3.Curated tools (linked and mirrored) 4.Curated data

6. UNO Undergraduate Bioinformatics (BIOI) Major Established 2004; first graduate in 2005 Offered simultaneously by the College of Arts and Sciences (A&S) and the College of Information Science & Technology (IS&T) 55 current majors. Graduates: 50% med. school/40% grad. school/10% work Curriculum (other requirements depend on college) Computer Science (24) CIST 1400Introduction to Computer Programming (3) CSCI 1620Introduction to Computer Science II (3) CSCI 2030Discrete Mathematics (IS&T) (3) CIST 2500Introduction to Applied Statistics (3) CSCI 3320Data Structures (3) CSCI 4830Introduction to Software Engineering (3) CSCI 4850Database Management Systems (3) CSCI 4890Data Ware. & Data Mining (3) or CSCI 4150Graph Theory & Applications (3) Mathematics (5) MATH 1950Calculus I (5) Biology (16) BIOL 1450Biology I (5) BIOL 2140Genetics (4) BIOL 3020Molecular Biology of the Cell (3) BIOL 4130Molecular Genetics (4) or BIOL 4140 Cellular Biology (4) Chemistry (17) CHEM 1180General Chemistry I (3) CHEM 1184General Chemistry I Laboratory (1) CHEM 1190 General Chemistry II (3) CHEM 1194General Chemistry II Laboratory (1) CHEM 2210Fund. of Organic Chemistry (4) CHEM 2214Fund. of Organic Chemistry Lab (1) CHEM 3650Fund. of Biochemistry (3) CHEM 3654Fund. of Biochemistry Lab (1) Bioinformatics (27) BIOI 1000Introduction to Bioinformatics (3) BIOI 2000Bioinformatics Foundations BIOI 3000Applied Bioinformatics (3) BIOI 3500Advanced Bioinformatics Programming (3) BIOI 4150Advanced Statistical Methods (3) BIOI 4860Bioinformatics Algorithms (3) BIOI 4870DBase Search & Pattern Disc. (3) BIOI 4890Comp. Genetic Sequence Analysis (3) BIOI 4970Senior Proj. in Bioinformatics I (1) BIOI 4980Senior Proj. in Bioinformatics II (2)I