How do biologists find meaning in their
(large, messy, nuanced) data?

Sidney Bell (@sidneymbell)

Chan Zuckerberg Initiative, BioVis 2020


Data exploration
requires
shifting your
field of
view
 

Bedford

Static views lose information and context

Computational skills

Domain knowledge

(Most important tool in science)

"Thanks. But can you remake the figure in
blue and green, add another variable and
put it all on a log scale?"

The goal: work
ourselves (mostly)
out of a job

Single cell biology

Generalizable

Large matrices

Genomic epidemiology

Domain specific

Medium trees

Helping scientists get hands on with their data

with Colin Megill, Bruce Martin, Charlotte Weaver 
Ambrose Carr, Lia Prins, Seve Badajoz, Brian McCandless, Angela Pisco, Marcus Kinsella, Genevieve Haliburton, Paolo, Justin Kiggins, Fiona Griffin, Arathi Mani, Matthew Weiden, Madison Dunitz, Signe Chambers, Timmy Huang, Trent Smith, Brian Raymore, Jeremy Freeman, Jonah Cool

 

An interactive data explorer for

single-cell transcriptomics datasets

Ratios of gene usage determine cell type

bc open textbooks

Cellxgene matrices

bc open textbooks

cells

genes

metadata

Cellxgene demo

SARS-CoV-2 infection & immune cells

Open-source project for genomic epidemiology of pathogens

Viruses evolve and spread on similar timescales

Grubaugh, Nature Micro, 2019

ACTT

ACTT

ACGT

ACGT

ACGA

Shared mutations indicate shared transmission history

A

C

D

E

B

Shared mutations indicate shared transmission history

Shared mutations indicate shared transmission history

Change

Order

Hierarchy

Nextstrain demo

SARS-CoV-2 in the U.S.

 COVIDTracker

with Josh Batson, David Dynerman, Amy Kistler, Shannon Axelrod, Jack Kamm, Aaron McGeever, Tony Tung, TJ Chen, James Webber, Angela Pisco, and many others

 COVIDTracker

Empowering California counties' Departments of Public Health to use
genomic epidemiology in routine practice

  • Tracking introductions
    Are these all travel-related, or is there community circulation?
     

  • Ambiguous contact tracing
    Is this new workplace infection related to the previous outbreak, or is it coincident?
     

  • Related outbreaks
    Is there transmission between neighboring towns?

Making epidemiology visual

Shared patterns

Information-dense
Shared state across panes
Iterative cross-sectioning of data

Shared challenge: precision vs interpretability

Current viz-related challenges

  • Building baseline understanding and confidence

  • Handling private, sensitive metadata is hard

  • Trees are pretty terrible

    • [WIP] Break out information encodings into separate, paired visualization

Shared challenge:
​generalizability vs tailored use cases

Shared challenge:
Exploration vs formal analysis

Takeaways

  • Meaning-making requires iterative shifting of your field of vision
     
  • Interactive explorers can help empower all researchers to get "hands-on" with their data
     
  • Close partnership between scientists and information designers is key. Special thanks to Colin Megill!

Questions?

@sidneymbell

Many thanks to the CZI cellxgene team,
Nextstrain team, and Biohub Data Science.