Packaging and containerization of computational methods.

Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.

Comparison of Marbling Fleck Characteristics and Objective Tenderness Parameters with Different Marbling Coarseness within Longissimus thoracis Muscle of High-marbled Hanwoo Steer.

It is important to understand how marbling traits and tenderness differ among beef steaks from the carcass grading site and other regions within the longissimus thoracis (LT) muscle, as these characteristics are closely associated with consumer acceptability and willingness to purchase. Thus, the aim of this study was to compare the marbling fleck traits and objective tenderness parameters in the groups classified by the coarseness index (CI) of marbling fleck (high and low groups) at the carcass grading site (13th thoracic vertebra; 13T) and three different locations (13T, 9T, and 6T) within the LT muscle from well-marbled (marbling score 7 to 9) Hanwoo steer. Image analysis showed that the longitudinal locations had a significant effect on marbling fleck traits. The total area of large marbling fleck divided by the total marbling area (coarseness) was higher at the central region (13T to 12T) compared to the front thoracic region (6T to 5T) in the high CI group (0.23 vs. 0.17, p<0.05), whereas no significant differences were observed in the total number of marbling fleck within the LT muscle in the high or low CI groups (p>0.05). Location effect on objective tenderness parameters within the LT muscle was somewhat limited, although the high CI group had a lower Warner-Bratzler shear force (WBS) value than did the low group (p<0.05). Taken together, the degree of coarseness of marbling fleck decreased from the carcass grading site to the front thoracic site, whereas the objective tenderness parameters, including WBS and hardness, of the grading site did not differ from the other regions within the LT muscle.