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lunch break
Distractions and amusements, with a sandwich and coffee.
data visualization + celebration
Genome Sciences Center 20th Anniversary Clothing, Music, Drinks and Art
On 15 November 2019, the Genome Sciences Center held its 20th anniversary celebration.
Here you can read about the design of the evening's clothing, music, drinks and other art.
After silence, that which comes nearest to expressing the inexpressible is music.
— Aldous Huxley
Music
We commissioned Segue to create a unique ambient music landscape for the celebration.
Segue is the name used by Jordan Sauer, an electronic music producer from Vancouver, BC. He creates ambient electronic music with layers of field recordings, acoustic and electronic sounds, creating sonic soundscapes that conjure images of nature and emotions of peace and introspection. He has release numerous solo albums and collaborations with artists from around the world, and recently released a solo album “The Island” on the Silent Season record label in summer 2019. Jordan is thrilled to partner with the GSC in the production of “Gene Machines”.
gene machines
Gene machines will be available as a digital download soon. We are also planning to have a vinyl release.
An assembly of shifting soundscapes, textures and rhythmic loops produced by the laboratory machines.
In commemoration of the 20th anniversary of Canada’s Michael Smith Genome Sciences Centre, Segue was comissioned to create an original composition based on audio recordings from the GSC’s laboratory equipment, robots and computers—to make “music” from the noise they produce.
Machine noise is a challenging palette of musical ingredients—sharp, abrasive and whirring sounds are typically unpleasant. For one night, these machines are repurposed as acoustical performers.
In the process of creating “Gene Machines”, recordings were analyzed for their specific frequency profiles and then used to generate melodic or percussive sounds. Together with bass from a Moog synthesizer, the sounds were then stretched, manipulated and sequenced into a series of compositions. Each composition is based on the recording from one specific laboratory machine, emphasizing its tone and timbre quality.
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news + thoughts
The Outbreak Poems
I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.
Panic can wait for tomorrow.
Regrets live on curves not tangents.
Small chances are never zero.
Month's last day waits for another year.
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses
A poster full of epidemiological worry and statistics. Now updated with the genome of SARS-CoV-2 and COVID-19 case statistics as of 3 March 2020.
Bacterial and viral genomes of various diseases are drawn as paths with color encoding local GC content and curvature encoding local repeat content. Position of the genome encodes prevalence and mortality rate.
The deadly genomes collection has been updated with a posters of the genomes of SARS-CoV-2, the novel coronavirus that causes COVID-19.
Using Circos in Galaxy Australia Workshop
A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. 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.
