Integrating Bioinformatics into the Life Sciences – Phase 2

Mark Pauley and Bill Tapprich

Group #2: Integration

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; and4. 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

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 Name UNO UNK NWUGenomes 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.

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 = 126 Mean Score Std. Dev. Std. Error

Pretest 5.23 1.596 0.142

Posttest 5.81 1.407 0.125

Mean Gain 0.58***

***p < 0.001; df = 125; t = 3.579; Effect size = 0.385

NWU Spring 2012 – Pre/Posttest Results Laboratory: Genomes and Bioinformatics

N =6 Mean Score Std. Dev. Std. Error

Pretest 6.83 2.137 0.872

Posttest 7.17 1.169 0.477

Mean Gain 0.34***

***p < 0.611; df = 5; t = 0.542; Effect size = 0.197

UNK Spring 2012 – Pre/Posttest Results Laboratory: Genomes and Bioinformatics

N = 132 Mean Score Std. Dev. Std. Error

Pretest 4.77 1.596 0.142

Posttest 5.77 1.407 0.125

Mean Gain 1.00***

***p < 0.021; df = 131; t = 6.105; Effect size = 0.664

Project Website: http://ccli.ist.unomaha.edu1. Lecture Modules (from CCLI Type 1)2. Laboratories (current project)3. Curated tools (linked and mirrored)4. Curated data

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 1400 Introduction to Computer Programming (3)CSCI 1620 Introduction to Computer Science II (3)CSCI 2030 Discrete Mathematics (IS&T) (3)CIST 2500 Introduction to Applied Statistics (3)CSCI 3320 Data Structures (3)CSCI 4830 Introduction to Software Engineering (3)CSCI 4850 Database Management Systems (3)CSCI 4890 Data Ware. & Data Mining (3)orCSCI 4150 Graph Theory & Applications (3)

Mathematics (5)MATH 1950 Calculus I (5)

Biology (16)BIOL 1450 Biology I (5)BIOL 2140 Genetics (4)BIOL 3020 Molecular Biology of the Cell (3)BIOL 4130 Molecular Genetics (4)orBIOL 4140 Cellular Biology (4)

Chemistry (17)CHEM 1180 General Chemistry I (3)CHEM 1184 General Chemistry I Laboratory (1)CHEM 1190 General Chemistry II (3)CHEM 1194 General Chemistry II Laboratory (1)CHEM 2210 Fund. of Organic Chemistry (4)CHEM 2214 Fund. of Organic Chemistry Lab (1)CHEM 3650 Fund. of Biochemistry (3)CHEM 3654 Fund. of Biochemistry Lab (1)

Bioinformatics (27)BIOI 1000 Introduction to Bioinformatics (3)BIOI 2000 Bioinformatics FoundationsBIOI 3000 Applied Bioinformatics (3)BIOI 3500 Advanced Bioinformatics Programming (3)BIOI 4150 Advanced Statistical Methods (3)BIOI 4860 Bioinformatics Algorithms (3)BIOI 4870 DBase Search & Pattern Disc. (3)BIOI 4890 Comp. Genetic Sequence Analysis (3)BIOI 4970 Senior Proj. in Bioinformatics I (1)BIOI 4980 Senior Proj. in Bioinformatics II (2)I