Recent advances in omics technologies have led to the broad applicability of computational techniques across various domains of life science and medical research. These technologies provide an unprecedented opportunity to collect the omics data from hundreds of thousands of individuals and to study the gene–disease association without the aid of prior assumptions about the trait biology. Despite the many advantages of modern omics technologies, interpretations of big data produced by such technologies require advanced computational algorithms. I outline key challenges that biomedical researches are facing when interpreting and integrating big omics data. I discuss the reproducibility aspect of big data analysis in the life sciences and review current practices in reproducible research. Finally, I explain the skills that biomedical researchers need to acquire to independently analyze big omics data.