Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - contact me Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
Here we are now at the middle of the fourth large part of this talk.Pepe Deluxeget nowheremore quotes

art: fun



See you at Shonan Meeting 167 — Formalizing Biomedical Visualization


communication + science

Nature Methods: Points of View

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Points of View column in Nature Methods. (Points of View)
1 | Krzywinski M 2016 Intuitive design Nat Methods 13:895.
2 | Krzywinski M 2016 Binning high-resolution data Nat Methods 13:463.
3 | Hunnicutt BJ & Krzywinski M 2016 Neural circuit diagrams Nat Methods 13:189.
4 | Hunnicutt BJ & Krzywinski M 2016 Pathways Nat Methods 13:5.
5 | McInerny G & Krzywinski M 2015 Unentangling complex plots Nat Methods 12:591.
6 | Streit M & Gehlenborg N 2015 Temporal Data Nat Methods 12:97.
7 | Lex A & Gehlenborg N 2014 Sets and Intersections Nat Methods 11:778.
8 | Streit M & Gehlenborg N 2014 Bar charts and box plots Nat Methods 11:117.
9 | Krzywinski M & Cairo A 2013 Storytelling Nat Methods 10:687.
10 | Krzywinski M & Savig E 2013 Multidimensional Data Nat Methods 10:595.
11 | Krzywinski M & Wong B 2013 Plotting symbols Nat Methods 10:451.
12 | Krzywinski M 2013 Elements of visual style Nat Methods 10:371.
13 | Krzywinski M 2013 Labels and callouts Nat Methods 10:275.
14 | Krzywinski M 2013 Axes, ticks and grids Nat Methods 10:183.
15 | Wong B 2012 Visualizing biological data Nat Methods 9:1131.
16 | Wong B & Kjaegaard RS 2012 Pencil and paper Nat Methods 9:1037.
17 | Gehlenborg N & Wong B 2012 Power of the plane Nat Methods 9:935.
18 | Gehlenborg N & Wong B 2012 Into the third dimension Nat Methods 9:851.
19 | Gehlenborg N & Wong B 2012 Mapping quantitative data to color Nat Methods 9:769.
20 | Nielsen C & Wong B 2012 Representing genomic structural variation Nat Methods 9:631.
21 | Nielsen C & Wong B 2012 Managing deep data in genome browsers Nat Methods 9:521.
22 | Nielsen C & Wong B 2012 Representing the genome Nat Methods 9:423.
23 | Gehlenborg N & Wong B 2012 Integrating data Nat Methods 9:315.
24 | Gehlenborg N & Wong B 2012 Heat maps Nat Methods 9:213.
25 | Gehlenborg N & Wong B 2012 Networks Nat Methods 9:115.
26 | Shoresh N & Wong B 2012 Data exploration Nat Methods 9:5.
27 | Wong B 2011 The design process Nat Methods 8:987.
28 | Wong B 2011 Salience to relevance Nat Methods 8:889.
29 | Wong B 2011 Layout Nat Methods 8:783.
30 | Wong B 2011 Arrows Nat Methods 8:701.
31 | Wong B 2011 Simplify to clarify Nat Methods 8:611.
32 | Wong B 2011 Avoiding color Nat Methods 8:525.
33 | Wong B 2011 Color blindness Nat Methods 8:441.
34 | Wong B 2011 The overview figure Nat Methods 8:365.
35 | Wong B 2011 Typography Nat Methods 8:277.
36 | Wong B 2011 Points of review (part 2) Nat Methods 8:189.
37 | Wong B 2011 Points of review (part 1) Nat Methods 8:101.
38 | Wong B 2011 Negative space Nat Methods 8:5.
39 | Wong B 2010 Gestalt principles (part 2) Nat Methods 7:941.
40 | Wong B 2010 Gestalt principles (part 1) Nat Methods 7:863.
41 | Wong B 2010 Salience Nat Methods 7:773.
42 | Wong B 2010 Design of data figures Nat Methods 7:665.
43 | Wong B 2010 Color coding Nat Methods 7:573.
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news + thoughts

Using Circos in Galaxy Australia Workshop

Thu 20-02-2020

A workshop in using the Circos Galaxy wrapper by Rasche and Hiltemann. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Using Circos in Galaxy Australia workshop. (zoom)

Download workshop slides.

Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).

Essence of Data Visualization in Bioinformatics Webinar

Thu 20-02-2020

My webinar on fundamental concepts in data visualization and visual communication of scientific data and concepts. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Essence of Data Visualization in Bioinformatics webinar. (zoom)

Download webinar slides.

Markov models — training and evaluation of hidden Markov models

Thu 20-02-2020

With one eye you are looking at the outside world, while with the other you are looking within yourself.
—Amedeo Modigliani

Following up with our Markov Chain column and Hidden Markov model column, this month we look at how Markov models are trained using the example of biased coin.

We introduce the concepts of forward and backward probabilities and explicitly show how they are calculated in the training process using the Baum-Welch algorithm. We also discuss the value of ensemble models and the use of pseudocounts for cases where rare observations are expected but not necessarily seen.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Markov models — training and evaluation of hidden Markov models. (read)

Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of significance: Markov models — training and evaluation of hidden Markov models. Nature Methods 17:121–122.

Background reading

Altman, N. & Krzywinski, M. (2019) Points of significance: Hidden Markov models. Nature Methods 16:795–796.

Altman, N. & Krzywinski, M. (2019) Points of significance: Markov Chains. Nature Methods 16:663–664.

Genome Sciences Center 20th Anniversary Clothing, Music, Drinks and Art

Tue 28-01-2020

Science. Timeliness. Respect.

Read about the design of the clothing, music, drinks and art for the Genome Sciences Center 20th Anniversary Celebration, held on 15 November 2019.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Luke and Mayia wearing limited edition volunteer t-shirts. The pattern reproduces the human genome with chromosomes as spirals. (zoom)

As part of the celebration and with the help of our engineering team, we framed 48 flow cells from the lab.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Precisely engineered frame mounts of flow cells used to sequence genomes in our laboratory. (zoom)

Each flow cell was accompanied by an interpretive plaque explaining the technology behind the flow cell and the sample information and sequence content.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The plaque at the back of one of the framed Illumina flow cell. This one has sequence from a patient's lymph node diagnosed with Burkitt's lymphoma. (zoom)

Scientific data visualization: Aesthetic for diagrammatic clarity

Mon 13-01-2020

The scientific process works because all its output is empirically constrained.

My chapter from The Aesthetics of Scientific Data Representation, More than Pretty Pictures, in which I discuss the principles of data visualization and connect them to the concept of "quality" introduced by Robert Pirsig in Zen and the Art of Motorcycle Maintenance.