Science needs software. In the past two decades, since the human genome was sequenced, the amount of data that has been generated related to biology and genetics is staggering. Genomes and accompanying functional data have been generated for hundreds of species of interest. The pace is not slowing. Benchtop and wetlab technologies have come through on their end of the bargain -- scientists are now capable of generating terabytes of data from a single experiment. The bottleneck is now analysis.
Linkage is a suite of open source software packages for analyzing biological data. Linkage software is written with biologists in mind. Packages interact with biological data using a biological vocabulary keeping the interpretation of data in the biological realm as much as possible. Linkage aims to write software at just the right level of abstraction. Units are in SNPs and Genes, software functions incorporate options for upstream and downstream. To us, polymorphism isn't less about software development and more about DNA. Methods are not overly fancy for the sake of being fancy. The goal is to provide powerful and interpretable analyses. Behind the scenes these biological objects are stored as computationally efficient tuples and records, etc. Your data is powered by databases. The software libraries are influenced by data science standards. This isn't hidden from you (nothing is, its all open source!), it's handled for you.
Linkage is an experiment in development. Our core mission is simple:
To develop useful, sustainable, free and open source software tools for the biological sciences. We aim to work closely with scientists who generate data in order to create code using the best and most computationally effective methods possible. We believe that code thrives in an open source environment and are committed to releasing our work under FOSS guidelines.
Our goal is to occupy the interface between biology and computer science. We believe that collaborative and interdisciplinary science is the future. We are actively seeking out and building collaborations in order to make an impact and help be the changers in the world.
Stayed tuned for more updates!