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BioVisVisualization in Biology
What is BioVis
Biological Data Visualization helps researchers in life sciences to gain insight from their data by extracting different features out of their data as well as helping them asking the right questions and guide them to the right conclusions.
BioVis Fields
Microscopy Next generation Sequencing
Visualization and Data Analysis in Molekular Biology
● Data Analysis in Next Generation Sequencing● Usability of existing tools● Workflow optimization and customizability● Usable Image Segmentation and Classification● Visualization of statistical features in cell cultures
Existing tools
● Complicated to use● Specialized for own needs● No maintenance● Ressource hungry and high runtime● No documentation --> Provenance Problem
Testing for viable technologies
● Database Approache● Python vs. Rust● Usability Focus● Testing existing tools
Why don’t you use “better” tools?
Lessons learned?
Why does Visualization in Molecular Biology matter?
“It doesn’t”
Lessons Learned
•Tools are not maintained or stable•Bioinformaticians is not a Standard•Misunderstanding of what Visualization is•Developing with Usability in Mind•Containers to avoid environment issues•Not only “one purpose” tools
•Data Provenance Problem in molecular biology “All downstream analysis was performed using custom R (v3.3.2) and bash scripts” – Nature 2018
BioOptics
● Image Segmentation for Cells/Nuclei● Cell Tracking● Classification and finding Regions of Interest● Find interactive Visualizations for Statistical Features in
Cells
Ilastik
Cellcognition Explorer
Visual Data Exploration in BioVisResearchers often don't know how to quantify or measure findings
Outlook: Automated Microscopy
● Let the microscope do all the work● Only help it in defining Regions of Interest● Provide Visualizations for the statistical Features of Cells
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