title: Language-Agnostic Reproducible Data Analysis Using Literate Programming.
abstract: A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir.
authors.affiliation: Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
authors.forename: Boris
authors.initials: B
authors.lastname: Vassilev
authors.affiliation: Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.
authors.forename: Riku
authors.initials: R
authors.lastname: Louhimo
authors.affiliation: Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland.|Minerva Foundation Institute for Medical Research, Helsinki, Finland.
authors.forename: Elina
authors.initials: E
authors.lastname: Ikonen
authors.affiliation: Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.
authors.forename: Sampsa
authors.initials: S
authors.lastname: Hautaniemi
mesh_terms: D001692:Biological Transport; D001943:Breast Neoplasms / Q000235:genetics / Q000473:pathology; D018797:Cell Cycle Proteins / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D011992:Endosomes / Q000378:metabolism; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D050356:Lipid Metabolism; D008565:Membrane Proteins / Q000235:genetics; D015513:Oncogene Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012984:Software; D000099259:N-myc Downstream-Regulated Gene 1 Protein
chemical_list: D018797:Cell Cycle Proteins; D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D015513:Oncogene Proteins; D012333:RNA, Messenger; D000099259:N-myc Downstream-Regulated Gene 1 Protein; C477083:LAPTM4B protein, human