Impro-Visor

This week we have started to analyze the data Lawrence David has sent from his study and downloaded the Impro-Visor program (http://sourceforge.net/projects/impro-visor/) used in the Microbial bebop study. Impro-Visor will allow us to convert datasets into sheet music which we will need to teach the choir our songs. 

In order to use the data in Impro-Visor we will have to normalize the data points of interest and then assign musical notes to each of the selected data points. The data points will be selected on the basis of what relationships we choose to investigate. 

This coming week each of us will identify one relationship and normalize the data points needed to import into Impro-Visor. 

We have also decided, after another skype meeting with Jack Gilbert and Peter Larsen, that to make the interaction with the school children more educational, we will be making them perform a small play while they are singing. A short interactive story explaining what happened to the subjects in terms of the relationships we have chosen to explore would probably be the most fun and educational for the children. If you have any suggestions or tips for us please feel free to leave a comment below.

We would also like to thank Peter for creating a small musical piece to show us that this project might actually work out in the end! 

Peter created and sent us a short song using Impro-Visor of the data obtained from Lawrence's data sets. Although the song is virtually composed, it demonstrates exactly what we aim to do with our project, but in an acapella fashion.

https://soundcloud.com/carlbruce/testingmicrobiomedata (melody = 6 most abundant orders, notes = caloric intake, chords = fiber)

Do Gut Bacteria Rule Our Minds?

Very interesting article exploring the importance of the role of gastrointestinal microbiota: https://ucsf.box.com/shared/static/pdz2z4b5fdvwlpr9hfdh.pdf 

Meet the team

(From the left): 

Sam Delport

Carl Bruce

Megan Cousins

Heinrich Kreuger

Wildene Le Roux

The Stellenbosch Microbiome Musical

As final year students at Stellenbosch University, we were given the instruction in our last semester as undergrad students to design and carry our own practical for our microbiology module relating to microbial ecology. So as any savvy undergrad students would do, we immediately started scouring through various scientific articles and journals in order to find something we could use as a base for our practicals during the seven week peroid we have to carry out our experiments. 

One article we found online immediately caught our attention: "Microbial Bebop: Creating Music from Complex Dynamics in Microbial Ecology" (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058119). The concept of translating complex data sets into a sonic format in order to involve the non-scientific public seemed to us like an ingenious idea. In order to gain a better comprehension of how the data was converted into music, we emailed one of the authors, associate professor at Chicago University, Jack Gilbert, and set up a skype meeting.

 
During our skype meeting, Jack assisted our group immensely by helping us in formulating exactly what we will be basing our practicals on for the semester. He suggested that we use the data from the paper "Host lifestyle affects human microbiota on daily timescales" (http://genomebiology.com/2014/15/7/R89) in order to generate music from the microbiomes of the two subjects studied in the paper. During our skype meeting with Jack, Peter Larsen (the creator of the microbial bepop sofware) also joined in and further helped guide our group in explaining what would be needed to create the music.

Our next step was to contact one of the authors of "Host lifestyle affects human microbiota on daily timescales" in order to find out if they would be willing for us to use the data they collected in their study in our experient. We contacted one of the authors, an associate professor at Duke University, Lawrence David, to find out. In the skype meeting with Lawrence, we explained to him what we are planning to do and he gave us the go ahead to use the data collected in their study. He also sent us data sets generated for their original study in order to help us with the handling of the data. 

With the data we have assembled we aim to generate sheet music by using Peter Larsen's microbial bebop sofware to sonically explore the unique microbiomes of the subject's involved in Lawrence David's study. 

After the generation of the sheet music, we will be approaching a local primary school choir to convey the differences and similarities of the two individual's microbiomes in an acapella musical. In this manner we hope to involve the local community, the non-scientific public as well as the youth in science. 

The group will be updating this blog weekly in order to track our progress and hopefully generate greater public interest in science.