Fundamentals of Visualizing Biological Data Marc Streit marc.streit@jku.at Marc Streit, Johannes Kepler University Linz
Marc Streit, Johannes Kepler University Linz Presentation 2
Interactive Marc Streit, Johannes Kepler University Linz Exploration 3
Marc Streit, Johannes Kepler University Linz Task: Communication of known facts about data Presentation 4
Henry Gray, 1918 Anatomy of the Human Body Drawing of a female body Leonardo da Vinci, ~ 1510 5
hrp://gdac.broadinsutute.org/ Heterogeneous Heatmap TCGA Paper, Nature 2012 Marc Streit, Johannes Kepler University Linz 6
Interactive Task: Generate new hypotheses Exploration 7 Marc Streit, Johannes Kepler University Linz
Detect the expected discover the unexpected John Snow (1813 1858) Wikimedia Commons Marc Streit, Johannes Kepler University Linz 8
WHY IS EXPLORATORY DATA ANALYSIS HARD? 9
http://detroitdataguru.wordpress.com/2010/02/17/driving-decisions-with-data/pile-of-documents/ Big Data? Marc Streit, Johannes Kepler University Linz 10
Big Data is like teenage sex: everyone talks about it, nobody really knows how to do it, everyone thinks everyone else is doing it, so everyone claims they are doing it. Dan Ariely Marc Streit, Johannes Kepler University Linz 11
4 Vs of Big Data as defined by Gartner Group Marc Streit, Johannes Kepler University Linz 12
Data Volume Data Veracity EB TB GB Uncertain Certain MB Homogeneous Static Data Velocity Real Time Heterogeneous Data Variety Marc Streit, Johannes Kepler University Linz 13
14 [Michal 2000]
Giant Hairball Marc Streit, Johannes Kepler University Linz [van Ham et al. 2009] 15
hrp://gdac.broadinsutute.org/ #data_points > #pixels Marc Streit, Johannes Kepler University Linz 16
Get more pixels?! [Samsung - 250 large format displays] Marc Streit, Johannes Kepler University Linz 17
What else can we do? Get even more pixels? well, not really. BeCer: Don t show all informagon Pragmatic Natural display limitations: size, weight, cost Technological Resolution of eye better than of display Human Not able to perceive all information at once Marc Streit, Johannes Kepler University Linz 18
Ways to deal with too much informauon Temporal ParGGoning NavigaUon: Pan, Rotate Geometric/SemanUc Zooming SpaGal ParGGoning MulUple Coordinated Views Marc Streit, Johannes Kepler University Linz 19
Temporal ParUUoning: Panning Marc Streit, Johannes Kepler University Linz 20
Example: Human Protein Atlas Project http://www.proteinatlas.org/ Marc Streit, Johannes Kepler University Linz 21
Temporal ParUUoning: RotaGon Marc Streit, Johannes Kepler University Linz 22
Temporal ParUUoning: Zooming Geometric Zooming Marc Streit, Johannes Kepler University Linz Semantic Zooming 23
AbstracUon 30k nodes 750 nodes 18 nodes Marc Streit, Johannes Kepler University Linz 90 nodes cytoscape.org 24
Example: ConUnuous AbstracUon [Zwan et al. 2011, BioVis best abstract award] Marc Streit, Johannes Kepler University Linz 25
SpaUal ParUUoning: MulGple Coordinated Views (MCV) [Colins and Carpendale 2007] Marc Streit, Johannes Kepler University Linz 26
MCV Type 1: Different vis. techniques showing the same data Marc Streit, Johannes Kepler University Linz 27
MCV Type 2: Same vis. technique showing different data Marc Streit, Johannes Kepler University Linz Cerebral [Barsky et al. 2008] 28
MCV Type 3: Overview + Detail Marc Streit, Johannes [Lex et Kepler al. 2010] University Linz 29
Example: Human Protein Atlas Project http://www.proteinatlas.org/ Marc Streit, Johannes Kepler University Linz 30
SelecUon / Filtering Marc Streit, Johannes Kepler University Linz 31
Example: MizBee [Meyer et al. 2009] Marc Streit, Johannes Kepler University Linz 32
Example: Caleydo Stratomex http://stratomex.caleydo.org Marc Streit, Johannes Kepler University Linz 33
irishfairytrails.com Spot the difference! Marc Streit, Johannes Kepler University Linz 34
stratomex.caleydo.org Spot the difference! Marc Streit, Johannes Kepler University Linz 35
Single Complex VisualizaUon MulUple Simple VisualizaUons Marc Streit, Johannes Kepler University Linz 36
Summary: Key Concepts NavigaUon AbstracUon SemanUc/Geometric Zooming MulUple Coordinated views Marc Streit, Johannes Kepler University Linz 37
Highly Interdisciplinary! Biology, BioinformaUcs + [Keim et al. 2010] Why is Biological Data VisualizaUon hard? Marc Streit, Johannes Kepler University Linz 38
? Marc Streit marc.streit@jku.at! Institute of Computer Graphics Johannes Kepler University Linz, Austria