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 Motion

Develop 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/