Building a cohesive bioinformatics classroom: implementation of wireless sharing technology in a large scale-up of SEA-PHAGES introductory biology lab

Transcription

1 Building a cohesive bioinformatics classroom: implementation of wireless sharing technology in a large scale-up of SEA-PHAGES introductory biology lab Welkin Pope Biological Sciences July

2 Seaphages.org

3 Brussow and Hendrix, 2002

4 Phagesdb.org

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6 Fall semester: Phage Discovery Find phage purify amplify extract DNA characterize (2x per week, 2 hour classes) Design an experiment with hypothesis, controls, etc Keep lab notebooks Scientific notation Serial dilutions Use micropipettors Sterile technique Scientific presentation (Poster, Figures)

7 Spring semester: Bioinformatics Annotate genome comparative genomics further explorations (2x per week, 2 hour classes) Design experiments in bioinformatics (computer programs as experiments) Keep electronic lab notebook Further develop presentation skills Read and write primary literature (genome announcements) Generate, plan and execute multi-experiment project in phage biology using what they have learned.

8 >Anaya Complete Sequence, bp, including 11 bp 3' overhang (CTCGTAGGCAT), Cluster K1 AGGCACCTTTCTCTCCCCAGCATTTTTTTCCAAGCCGATTCAGCGTTTTT CCACGCCCGACCAGCACAGGAGCAACCAATGCACATGACCGAATCCGAAC CGACTGCGCGCGTGTGGGCGTTCGAGGATCAGCGCGACCGCGCGGTGCGC GAGCAATCAATGCACATCGCGTTGAAGGCCGCCGACATCGTGGGTCTCGG CGACGTGACGCTGATCGAGGCGGCCGACAAGATCGCCGATTTCATCCTCG ACGGCAAGGTCGACCGGCGCCCCGACGCTGAGCGGAGCCCCGAATGATGA CGCCCGCCGAGCGTCTCGCCGCGCAGCGCGAGGCCCTCGACAAGCACGAG TGGACCGAGGTCGAGGGCGACCTCACGCCGATCACGCTGCACTGTCTGGT CGCTATTGGCGAGGTGCTCGTCGAGCTGAACGCCCGGCAGGCCCGCCAGG AGGCCGCAGCGATGGGCGCCCCGTCGTGAGCCCGGTCGTCGGCGTCGTGT CGCGCACGCTCGACAGCGCGGCCCGGCTCGCCCGCGCGCTGAACGTGGCT CGCACCGTTCCAATGAGCGTGCCGTCGATCAAGCAGGGGCACGGCCGCGG GTTCAGTTTCGACGCCGTGATCGTCGACGACGAGGTGATGCCGCTCGATG ACTGTGTGCTCGGCACGTTGGCCCCGGCGATGCACGCTCACGGCGGAAAG ATGTACGCGGTTCGGGAGGTTGAGCTGTGACCCCGACTGTCGGCCGCATC GTTCATTACCAGTCTTACGGCACGCCCGGCGGCGAGCACCTGCCTGAGCC CCGCGCCGCGATCGTCACGGCCGTGCTCGGCGGTGGCGTCGTGAGCCTGT GTGTGCTCAACCCGTCGGGGCTGTTTTTCAACGAGTCCGTGCGCCAGGCC GACGAGCCGACGCCGGGCCGCTGGAATTGGCCGCCCCGCAACTGATCTAG CGCGCGTAGCCCAACCGACGGATAGAGGCGGCTGGTAATTCGGCGTCAAC GTGCCGGGCCTCGTCAGCCCGGCCGCGCGCAAATGGGTGTGTAGCTCAAT TGGCAGAGCAGCGGTCTCCAAAGCCGCCGGTTGCACGTTCGAGTCGTGCC GCGCCCGCTTCCACACCGGCTAACCGCCGGCGATCCGCATTCCCGCACGT CAACGCCACGAAAGGCCGTTTTGAGCTAACACGGCACCTCAACACACCAG GAGATATGACCATGCGCGCACCCGCTACCGCCGAGGTTCCTTGCCCGGCC TGCGGCGAGCCGATCACGCTCGCCCTTGGCTTTGAGCTGGCCGAGCCTGA GCCCGGCGCCACGACTGCCCCAATGTTCGTGAGGCCGCTCGACATTGCAG AGCGCGCGCAGGAGCACGGCGAGGTGTGCCCGGTGTGGTCAGGCGGTGGC CGCGATGACTGACGGCAAGCTCGACCGGCTCGGCGAGCTGCGACGGTTGC ACGAGCGCATCTCGT..

9 R H L S L P S I F F Q A I S A F F H T R P A Q E Q P M D M T E S A P G T F L S P A F F S K P F Q R F S T P D Q H R S N Q W T * P N P H A P F S P Q H F F P S H F S V F P H P T S T G A T N G H D R I R T 1 AGGCACCTTTCTCTCCCCAGCATTTTTTTCCAAGCCATTTCAGCGTTTTTCCACACCCGACCAGCACAGGAGCAACCAATGGACATGACCGAATCCGCAC...:......:......:......:......:......:......:......:......:......:... TCCGTGGAAAGAGAGGGGTCGTAAAAAAAGGTTCGGTAAAGTCGCAAAAAGGTGTGGGCTGGTCGTGTCCTCGTTGGTTACCTGTACTGGCTTAGGCGTG Y A G K E G W C K K G L W K L T K G C G V L V P A V L P C S R I R V L C R E R G L M K K W A M E A N K W V R G A C S C G I S M V S D A P V K R E G A N K E L G N * R K E V G S W C L L L W H V H G F G C T A R V W A F E D Q R D R A V R E Q S M H I A L R Q A D S V G I G R L R A C G R S R I S A T A R C A S N Q C T S R C A R P T A W V S A D C A R V G V R G S A R P R G A R A I N A H R A A P G R Q R G Y R 101 CGACTGCGCGCGTGTGGGCGTTCGAGGATCAGCGCGACCGCGCGGTGCGCGAGCAATCAATGCACATCGCGCTGCGCCAGGCCGACAGCGTGGGTATCGG...:......:......:......:......:......:......:......:......:......:... GCTGACGCGCGCACACCCGCAAGCTCCTAGTCGCGCTGGCGCGCCACGCGCTCGTTAGTTACGTGTAGCGCGACGCGGTCCGGCTGTCGCACCCATAGCC S Q A R T P T R P D A R G R P A R A I L A C R A A G P R C R P Y R G V A R T H A N S S * R S R A T R S C D I C M A S R W A S L T P I P R S R A H P R E L I L A V A R H A L L * H V D R Q A L G V A H T D D L T V I E A A D K I A A F I L D G K V D R R P D A E R S P E * * T * P * S R R P T R S P L S S S T A R S T G A P T L S G A P N D D R L D R D R G G R Q D R R F H P R R Q G R P A P R R * A E P R M M T 201 CGACTTGACCGTGATCGAGGCGGCCGACAAGATCGCCGCTTTCATCCTCGACGGCAAGGTCGACCGGCGCCCCGACGCTGAGCGGAGCCCCGAATGATGA...:......:......:......:......:......:......:......:......:......:... GCTGAACTGGCACTAGCTCCGCCGGCTGTTCTAGCGGCGAAAGTAGGAGCTGCCGTTCCAGCTGGCCGCGGGGCTGCGACTCGCCTCGGGGCTTACTACT R S S R S R P P R C S R R K * G R R C P R G A G R R Q A S G R I I S K V T I S A A S L I A A K M R S P L T S R R G S A S R L G S H H A V Q G H D L R G V L D G S E D E V A L D V P A G V S L P A G F S S

10 Inaugural SEA-PHAGES class at Pitt,

11 Challenges: Multi-year large scale-up from 1 section to 15(?) Maintain the quality of the student experience and the scientific research with non-expert instructors and many many MANY more students! Maintain the sense of community in the course Logistics: how do we fit all those lab sections into the space available?

12 Last year s solutions (increased from 1 to 5 sections) Added 1 lecture per week, all students attend. Increased number of UTAs (used alumni) Decreased length of lab classes (1hr 20min each; still 2x per week) Students used own laptops for bioinformatics

13 Bioinformatics Challenges Students work in groups to annotate different bacteriophage genomes. Concepts are more abstract than in fall semester More room for interpretation in making final decisions Genomes are all different May or may not be similar to previously annotated genomes May or may not be similar to others in class

14 Annotation requires application of guiding principles of bacteriophage annotation and careful analysis of (sometimes conflicting) data from multiple computer programs: DNA Master, Phamerator, Starterator, GeneMark, Glimmer, BLAST, HHPred, and others.

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18 Goals for Course Transformation: *Decrease amount of course time spent doing annotations *Expose more students to genomes and genome features *Build sense of cross-section community Problem: How to share data live during class for discussion/demonstration? Tried: Box, Power Point, Google Slides, . All of these require either forethought or wasting class time for file transfers.

19 Solution: ClickShares! Wireless receiver connected to projector; can connect any computer via USB; or can connect tablet/smart phone Can show up to four screens at once.

20 Assessment Pre- and post- survey Student interviews during implementation Pre- and post- measurement of time on task Survey designed with the assistance of Dr David Hanuaer, IUP, and lead SEA-PHAGES assessment coordinator; uses validated tools.

21 Pre-survey Administered spring 2015, voluntary 38 out of 82 students answered Three questions: Where did students get help/feedback on annotations? How familiar did they feel with other groups annotations? How comfortable were they with the annotation process, including genome features that were not present in all genomes?

22 1. To what degree did you receive feedback on your annotations from: # Question Not At All Occasionally Frequently Total Responses 1 Your course instructor Mean Your TAs Students in your group 4 Other students in your lab section section 5 Students that are in the SEA-PHAGES but not in your lab section

23 1. To what degree did you receive feedback on your annotations from: Statistic Your course instructor Your TAs Students in your group Other students in your lab section section Min Value Max Value Mean Variance Standard Deviation Total Responses Students that are in the SEA- PHAGES but not in your lab section

24 2. Please rate your familiarity with other student groups annotations # Question I know nothing about the annotation s of other students 1 To what degree are you familiar with the annotations of other groups of students I have seen some of the annotation s but I am not familiar with them I have seen some of the annotation s but I am not really sure I am familiar with them I have seen the annotatio ns of other students and have some familiarit y with them I am completely familiar with other students annotations Total Response s Mean

25 2. Please rate your familiarity with other student groups annotations Statistic Min Value 1 Max Value 5 Mean 3.24 Variance 0.78 Standard Deviation 0.88 Total Responses 38 To what degree are you familiar with the annotations of other groups of students

26 3. Rate the degree to which you agree or disagree with the followingstatements Question I feel confident that I know how to apply the guiding principles to my phage genome annotation I feel comfortable assigning functions to phage genes I feel comfortable annotating a trna I feel comfortable annotating a programmed translational frame shift I can easily describe what is specific about my phage genome that isn't found in other phage genomes in this course Strongly Disagree Disagree Neither Agree nor Disagree Agree Strongly Agree Total Responses Mean

27 3. Rate the degree to which you agree or disagree with the followingstatements Statistic I feel confident that I know how to apply the guiding principles to my phage genome annotation I feel comfortable assigning functions to phage genes I feel comfortable annotating a trna I feel comfortable annotating a programmed translational frame shift Min Value Max Value Mean Variance Standard Deviation Total Responses I can easily describe what is specific about my phage genome that isn't found in other phage genomes in this course

28 Additional thoughts? Incorporate grades? Adjunct instructors and expert UTAs Replace lecture with online modules? Open lab hours?