resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
communication + science
Nature Methods: Points of View
Bang Wong is the creative director of the Broad Institute and an adjunct assistant professor in the Department of Art as Applied to Medicine at The Johns Hopkins University School of Medicine.
Nils Gehlenborg is a research associate at Harvard Medical School.
Martin Krzywinski is a staff scientist at Canada’s Michael Smith Genome Sciences Centre.
Marc Streit is an assistant professor of computer science at Johannes Kepler University Linz.
Cydney Nielsen is a Research Associate at the BC Cancer Research Center.
Rikke Schmidt Kjærgaard is an assistant professor in the Interdisciplinary Nanoscience Center at Aarhus University.
Noam Shoresh is a senior computational biologist at the Broad Institute
Erica Savig is a PhD candidate in Cancer Biology at Stanford University.
Alberto Cairo is a Professor of Professional Practice at the School of Communication of the University of Miami.
Alexander Lex is a postdoctoral fellow in computer science at Harvard University.
Gregor McInerny is a Senior Research Fellow at the Department of Computer Science, University of Oxford.
Barbara J. Hunnicutt is a research assistant at Oregon Health and Science University.
news + thoughts
Using Circos in Galaxy Australia Workshop
A workshop in using the Circos Galaxy wrapper by Rasche and Hiltemann. Event organized by Australian Biocommons.
Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).
Essence of Data Visualization in Bioinformatics Webinar
My webinar on fundamental concepts in data visualization and visual communication of scientific data and concepts. Event organized by Australian Biocommons.
Markov models — training and evaluation of hidden Markov models
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.
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
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.
As part of the celebration and with the help of our engineering team, we framed 48 flow cells from the lab.
Each flow cell was accompanied by an interpretive plaque explaining the technology behind the flow cell and the sample information and sequence content.
Scientific data visualization: Aesthetic for diagrammatic clarity
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.