Bioinformatics in Motion

Steffen Heber, NCSULeif Saul, CU-Boulder

Overview• Background about Animations

• The Bioinformatics in Motion Project

• Conclusions and Future Developments

Educational Animations are Popular!

Algorithm animation in Computer Science

Other Life Science Animations• Biology in motion [http://biologyinmotion.com/]• Biology Animation Library

[http://www.dnalc.org/ddnalc/resources/animations.html]• HHMI’s Biointeractive – Virtual Labs

[http://www.hhmi.org/biointeractive/vlabs/]• Science Animations, Movies & Interactive Tutorial Links

[http://science.nhmccd.edu/BioL/animatio.htm]• Geospiza, Inc. Education [http://www.geospiza.com/outreach/]• Virtual Cell Animation Collection

[http://vcell.ndsu.nodak.edu/animations/]• DNA Microarray Methodology – Flash Animation

[http://www.bio.davidson.edu/Courses/genomics/chip/chip.html]

• Also, often used in software demos, tutorials, and webinars

Common Knowledge?Educational Animations can …

• directly show changes in form, position, and time

• increase student interest and motivation

• help students to understand and remember information

Student Response

• “I used them to study for the final”• “yes, to practice how the algorithm

works”• “it helped me to understand, and

stay awake”• “they helped to make the lecture

interesting”• “fun stuff!”• “probably not, too time consuming”

2Did not respond

1Negative answer

1Indifferent

25Positive answer

Do you feel that algorithm visualization/animationhelped you to learn how algorithms work?

Are Animations Effective?

Just watching does not improve learning

How We Learn from Animations

• Two main information processing channels:visual and auditory

• Learning = active processing in memory

• Limited capacity for info processing

What Makes a “Good” Animation?

Use research based design principles:

• Present animation and narration simultaneously

• Avoid identical streams of printed and spoken words

• Use narration in conversational style • Focus on interactive activities

Bioinformatics in MotionDevelop Flash Animation Modules for

undergraduate students. Topics:• Sequence Alignment• Motif Finding/Discovery• Database Search: BLAST• Genome Rearrangements• Fragment Assembly • Hidden Markov Models

Animations: http://statgen.ncsu.edu/slse/animations/

Workflow

1. Text storyboard– Illustrated with static Flash images– Images developed into animations

A similar approach as used by PIXAR

Why Flash?• Flash - Benefits include:

– Small file size– Plug-in widely distributed– Object-oriented programming

(Actionscript 3)– Visual authoring tools

• Animated programmatically– Static images placed on stage– Transitions encoded in XML– Animations generated at runtime

Project Features• Static images• Cartoons / metaphors• Animations• Spoken narration• Interactivity• User controls delivery• Instructor controls delivery

Project Features• Static images• Cartoons / metaphors• Animations• Spoken narration• Interactivity• User controls delivery• Instructor controls delivery• Other resources

User Controls Delivery• Playback controls• Voice vs. text narration• “Liquid” interface adjusts to

screen size• User feedback

Please send us feedback!

Types of Animation Used• Changes in size, position,

etc.• Cartoons / metaphors• Visual effects /

enhancements• Computed

Types of Interactivity Used• Quiz• Exploration / experiment• Game-like (user seeks an optimum)

Some Design Dilemmas

• Continuous “movie” vs. chunks?– Movie: Inviting, easy experience– Chunks: User can choose

• How much narration per step?– Too much: User less in control– Too little: User gets “click” fatigue

Conclusions: Animations …• are fun!

– they increase attention and enthusiasm• address different learning styles• support teachers, distance education

& independent student learning• work best if interactive• in Flash are time-consuming to

develop

Future Areas of Development

• What material is best taught via animations?

• How to package and integrate animations into class/html documents?

• Can animations adapt to different student needs?

Acknowledgments

Benjamin Wheeler, NCSU

Questions?

Animations: http://statgen.ncsu.edu/slse/animations/