Write up short 1-page report for ICAD

[ihh]

Key points for introduction:

• What are genome annotations? What type of features are included in genome annotations (protein-coding genes, pseudogenes, RNAs etc)? What sorts of things do biologists use these for (genome analysis, studying genetic disease, bioengineering)?
• Traditionally biologists have used genome browsers, which visualize genome annotations. We hypothesized that auditory display of these annotations would provide additional immersion and navigational orientation
• Previous attempts to implement auditory display of biological sequences have focused on sonification of the sequence itself e.g. amino acid sequence of proteins (cite Protein Music paper) or nucleic acid sequence of genomes (cite recent coronavirus genome paper). To our knowledge there has been no previous attempt to sonify the annotations themselves - despite the fact that these annotations are relatively stable digital objects that can be traced directly to materially tangible evidence
• In this paper we demonstrate a simple system for converting a genome annotation database into a sequence of MIDI notes which yield an audible signal

Methods...

• goal: unique audio signature for any region
• describe your scripts (including your Sequence Ontology mapping to particular notes, based on frequency of different SO terms)

Demonstration

• we picked a region (which was an interesting region.... explain why)
• we made some sounds

[ihh]

I would suggest picking somewhere that has biological relevance e.g. somewhere in the MHC region on chromosome 6 http://hg38.jbrowse.org/?loc=chr6%3A30486501..31238500&tracks=DNA%2CHomo_sapiens.GRCh38.93_ncRNA_gene.gff3.gz%2CHomo_sapiens.GRCh38.93_lnc_RNA.gff3.gz%2CHomo_sapiens.GRCh38.93_ncRNA.gff3.gz%2CHomo_sapiens.GRCh38.93_pseudogene.gff3.gz&highlight=

[ihh]

Goal is to submit as one-page Installation/Demonstration to https://icad2022.icad.org/

[ihh]

Try pasting their LaTeX template into Overleaf... or just do it in Google Docs

[ihh]

See also #13