biovis - vda.univie.ac.atvda.univie.ac.at/teaching/vis/19w/lecturenotes/biovispart1.pdf · lessons...
TRANSCRIPT
![Page 1: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/1.jpg)
BioVisVisualization in Biology
![Page 2: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/2.jpg)
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.
![Page 3: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/3.jpg)
BioVis Fields
Microscopy Next generation Sequencing
![Page 4: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/4.jpg)
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
![Page 5: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/5.jpg)
Existing tools
● Complicated to use● Specialized for own needs● No maintenance● Ressource hungry and high runtime● No documentation --> Provenance Problem
![Page 6: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/6.jpg)
Testing for viable technologies
● Database Approache● Python vs. Rust● Usability Focus● Testing existing tools
Why don’t you use “better” tools?
![Page 7: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/7.jpg)
![Page 8: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/8.jpg)
![Page 9: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/9.jpg)
![Page 10: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/10.jpg)
Lessons learned?
![Page 11: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/11.jpg)
Why does Visualization in Molecular Biology matter?
![Page 12: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/12.jpg)
“It doesn’t”
![Page 13: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/13.jpg)
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
![Page 14: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/14.jpg)
•Data Provenance Problem in molecular biology “All downstream analysis was performed using custom R (v3.3.2) and bash scripts” – Nature 2018
![Page 15: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/15.jpg)
BioOptics
● Image Segmentation for Cells/Nuclei● Cell Tracking● Classification and finding Regions of Interest● Find interactive Visualizations for Statistical Features in
Cells
![Page 16: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/16.jpg)
Ilastik
![Page 17: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/17.jpg)
![Page 18: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/18.jpg)
Cellcognition Explorer
![Page 19: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/19.jpg)
Visual Data Exploration in BioVisResearchers often don't know how to quantify or measure findings
![Page 20: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/20.jpg)
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
![Page 21: BioVis - vda.univie.ac.atvda.univie.ac.at/Teaching/Vis/19w/LectureNotes/BioVisPart1.pdf · Lessons Learned •Tools are not maintained or stable •Bioinformaticians is not a Standard](https://reader035.vdocuments.site/reader035/viewer/2022070719/5edf6210ad6a402d666abb77/html5/thumbnails/21.jpg)