Relaxation Techniques for the Upset Data Scientist

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The document discusses relaxation techniques for data scientists experiencing stress and tension, including letting go of thoughts, stretching, aligning oneself, gathering focus, sorting thoughts, and using visualization to free up cognition. It provides examples of proven visualization techniques and advertises open postdoc positions applying data visualization, analysis, and management to topics like genomics and cancer research.

Science

Relaxation Techniques for the
Upset Data Scientist
Nils Gehlenborg, PhD
http://gehlenborglab.org | @nils_gehlenborg

What are the sources of your
tension and anger?

Xu et al., Nature Communications 3, 1258 (2014)
Where is the biggest intersection?

Rat Genome Sequencing Consortium, Nature 428, 493 (2004)
“Rats,” you’ll say, “I’ll go bananas!”
D’Hont et al., Nature 488, 213 (2012)

This visualization makes you work!
[Good] visualization uses
perception to free up cognition!

What does that mean?
453 x 862 =
906
+ 27,180
+ 362,400
390,486

What are some proven
relaxation techniques?

EGFR
76
PTEN
87
TP53
80
44
22
5
19
43
9
41
Lex & Gehlenborg, Nature Methods 11, 1 (2014)

Lex & Gehlenborg, Nature Methods 11, 1 (2014)

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
1. Let Go!

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
2. Stretch!

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
3. Align!

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
4. Gather!

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
5. Sort!

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
6. Let Go!
(again)

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
IntersectionSize
Set Size

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
Yellow
Red
Blue
44 43
41
22
19
9
5
80
76
87
IntersectionSize
Set Size

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
TP53
EGFR
PTEN
44 43
41
22
19
9
5
80
76
87
IntersectionSize
Set Size

Lex & Gehlenborg, Nature Methods 11, 1 (2014)
TP53
EGFR
PTEN
44 43
41
22
19
9
5
80
76
87
IntersectionSize
Set Size
EGFR
76
PTEN
87
TP53
80
44
22
5
19
43
9
41

Conway, Lex, Gehlenborg, Bioinformatics 2017
Hey! It’s an UpSet Plot!

A ⋂ B A ⋃ B B A
http://en.wikipedia.org/wiki/Venn_diagram
Venn Diagrams are actually very useful!

I am hiring postdocs!
HARVARD MEDICAL SCHOOL
DEPARTMENT OF BIOMEDICAL INFORMATICS
See http://gehlenborglab.org or http://dbmi.med.harvard.edu for details.
Data visualization, analysis, and management for:
• genomic structural variants
• dynamics of the 3D genome
• cancer subtypes in patient cohorts
• exploration tools for data repositories
• provenance graphs

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Relaxation Techniques for the Upset Data Scientist

1. Relaxation Techniques for the Upset Data Scientist Nils Gehlenborg, PhD http://gehlenborglab.org | @nils_gehlenborg

2. What are the sources of your tension and anger?

3. Xu et al., Nature Communications 3, 1258 (2014) Where is the biggest intersection?

4. Rat Genome Sequencing Consortium, Nature 428, 493 (2004) “Rats,” you’ll say, “I’ll go bananas!” D’Hont et al., Nature 488, 213 (2012)

5. Why is this stressful and exhausting?

6. This visualization makes you work!

7. This visualization makes you work! [Good] visualization uses perception to free up cognition!

8. What does that mean? 453 x 862 = ?

9. What does that mean? 453 x 862 = 906 + 27,180 + 362,400 390,486

10. What are some proven relaxation techniques?

11. EGFR 76 PTEN 87 TP53 80 44 22 5 19 43 9 41 Lex & Gehlenborg, Nature Methods 11, 1 (2014)

12. Lex & Gehlenborg, Nature Methods 11, 1 (2014)

13. Lex & Gehlenborg, Nature Methods 11, 1 (2014) 1. Let Go!

14. Lex & Gehlenborg, Nature Methods 11, 1 (2014)

15. Lex & Gehlenborg, Nature Methods 11, 1 (2014) 2. Stretch!

16. Lex & Gehlenborg, Nature Methods 11, 1 (2014)

17. Lex & Gehlenborg, Nature Methods 11, 1 (2014) 3. Align!

18. Lex & Gehlenborg, Nature Methods 11, 1 (2014)

19. Lex & Gehlenborg, Nature Methods 11, 1 (2014) 4. Gather!

20. Lex & Gehlenborg, Nature Methods 11, 1 (2014)

21. Lex & Gehlenborg, Nature Methods 11, 1 (2014) 5. Sort!

22. Lex & Gehlenborg, Nature Methods 11, 1 (2014)

23. Lex & Gehlenborg, Nature Methods 11, 1 (2014) 6. Let Go! (again)

24. Lex & Gehlenborg, Nature Methods 11, 1 (2014) Yellow Red Blue

25. Lex & Gehlenborg, Nature Methods 11, 1 (2014) Yellow Red Blue

26. Lex & Gehlenborg, Nature Methods 11, 1 (2014) Yellow Red Blue

27. Lex & Gehlenborg, Nature Methods 11, 1 (2014) Yellow Red Blue

28. Lex & Gehlenborg, Nature Methods 11, 1 (2014) Yellow Red Blue

29. Lex & Gehlenborg, Nature Methods 11, 1 (2014) Yellow Red Blue IntersectionSize Set Size

30. Lex & Gehlenborg, Nature Methods 11, 1 (2014) Yellow Red Blue 44 43 41 22 19 9 5 80 76 87 IntersectionSize Set Size

31. Lex & Gehlenborg, Nature Methods 11, 1 (2014) Yellow Red Blue 44 43 41 22 19 9 5 80 76 87 IntersectionSize Set Size

32. Lex & Gehlenborg, Nature Methods 11, 1 (2014) TP53 EGFR PTEN 44 43 41 22 19 9 5 80 76 87 IntersectionSize Set Size

33. Lex & Gehlenborg, Nature Methods 11, 1 (2014) TP53 EGFR PTEN 44 43 41 22 19 9 5 80 76 87 IntersectionSize Set Size EGFR 76 PTEN 87 TP53 80 44 22 5 19 43 9 41

34. Conway, Lex, Gehlenborg, Bioinformatics 2017 Hey! It’s an UpSet Plot!

35. Disclaimer

36. A ⋂ B A ⋃ B B A http://en.wikipedia.org/wiki/Venn_diagram Venn Diagrams are actually very useful!

37. I am hiring postdocs! HARVARD MEDICAL SCHOOL DEPARTMENT OF BIOMEDICAL INFORMATICS See http://gehlenborglab.org or http://dbmi.med.harvard.edu for details. Data visualization, analysis, and management for: • genomic structural variants • dynamics of the 3D genome • cancer subtypes in patient cohorts • exploration tools for data repositories • provenance graphs

Relaxation Techniques for the Upset Data Scientist

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