Simplifying the development of portable, scalable, and reproducible workflows

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used primarily for batch processing of large datasets, especially in genomics. But it can also be used for analytical steps of a study. This article explains key concepts about CWL and software containers and provides examples for using CWL in biology research. CWL documents are text-based, so they can be created manually, without computer programming. However, ensuring that these documents conform to the CWL specification may prevent some users from adopting it. To address this gap, we created ToolJig, a Web application that enables researchers to create CWL documents interactively. ToolJig validates information provided by the user to ensure it is complete and valid. After creating a CWL tool or workflow, the user can create ‘input-object’ files, which store values for a particular invocation of a tool or workflow. In addition, ToolJig provides examples of how to execute the tool or workflow via a workflow engine. ToolJig and our examples are available at https://github.com/srp33/ToolJig.

Kidney Disease among People Who Are Incarcerated

Chronic kidney disease (CKD) affects 15% of US adults and is associated with increased morbidity and mortality. CKD disproportionately impacts certain populations, including racial and ethnic minorities and individuals from disadvantaged socioeconomic backgrounds. These groups are also disproportionately impacted by incarceration and barriers to accessing health services. Incarceration represents an opportunity to link marginalized individuals to CKD care. Despite a legal obligation to provide a community standard of care including the screening and treatment of individuals with CKD, there is little evidence to suggest systematic efforts are in place to address this prevalent, costly, and ultimately fatal condition. This review highlights unrealized opportunities to connect individuals with CKD to care within the criminal justice system and as they transition to the community, while underscoring the need for more evidence-based strategies to address the health impact of CKD on over-represented communities in the criminal justice system.

Simplifying the development of portable, scalable, and reproducible workflows

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool's inputs, outputs, and other execution details in a manner that fosters use of shared computational methods and reproducibility of complex analyses. CWL documents can include instructions for executing tools inside software containers-isolated, operating-system environments. Accordingly, CWL tools are portable-they can be executed on diverse computers-including personal workstations, high-performance clusters, or the cloud. This portability enables easier adoption of bioinformatics pipelines. CWL supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used primarily for batch processing of large datasets, especially in genomics. But it can also be used for analytical steps of a study. This article explains key concepts about CWL and software containers and provides examples for using CWL in biology research. CWL documents are text-based, so they can be created manually, without computer programming. However, ensuring that these documents confirm to the CWL specification may prevent some users from adopting it. To address this gap, we created ToolJig, a Web application that enables researchers to create CWL documents interactively. ToolJig validates information provided by the user to ensure it is complete and valid. After creating a CWL tool or workflow, the user can create "input-object" files, which store values for a particular invocation of a tool or workflow. In addition, ToolJig provides examples of how to execute the tool or workflow via a workflow engine.

Allotetraploidization in Brachypodium May Have Led to the Dominance of One Parent’s Metabolome in Germinating Seeds

Seed germination is a complex process during which a mature seed resumes metabolic activity to prepare for seedling growth. In this study, we performed a comparative metabolomic analysis of the embryo and endosperm using the community standard lines of three annual Brachypodium species, i.e., B. distachyon (Bd) and B. stacei (Bs) and their natural allotetraploid B. hybridum (BdBs) that has wider ecological range than the other two species. We explored how far the metabolomic impact of allotetraploidization would be observable as over-lapping changes at 4, 12, and 24 h after imbibition (HAI) with water when germination was initiated. Metabolic changes during germination were more prominent in Brachypodium embryos than in the endosperm. The embryo and endosperm metabolomes of Bs and BdBs were similar, and those of Bd were distinctive. The Bs and BdBs embryos showed increased levels of sugars and the tricarboxylic acid cycle compared to Bd, which could have been indicative of better nutrient mobilization from the endosperm. Bs and BdBs also showed higher oxalate levels that could aid nutrient transfer through altered cellular events. In Brachypodium endosperm, the thick cell wall, in addition to starch, has been suggested to be a source of nutrients to the embryo. Metabolites indicative of sugar metabolism in the endosperm of all three species were not prominent, suggesting that mobilization mostly occurred prior to 4 HAI. Hydroxycinnamic and monolignol changes in Bs and BdBs were consistent with cell wall remodeling that arose following the release of nutrients to the respective embryos. Amino acid changes in both the embryo and endosperm were broadly consistent across the species. Taking our data together, the formation of BdBs may have maintained much of the Bs metabolome in both the embryo and endosperm during the early stages of germination. In the embryo, this conserved Bs metabolome appeared to include an elevated sugar metabolism that played a vital role in germination. If these observations are confirmed in the future with more Brachypodium accessions, it would substantiate the dominance of the Bs metabolome in BdBs allotetraploidization and the use of metabolomics to suggest important adaptive changes.

The openCARP Simulation Environment for Cardiac Electrophysiology

Background and ObjectiveCardiac electrophysiology is a medical specialty with a long and rich tradition of computational modeling. Nevertheless, no community standard for cardiac electrophysiology simulation software has evolved yet. Here, we present the openCARP simulation environment as one solution that could foster the needs of large parts of this community.Methods and ResultsopenCARP and the Python-based carputils framework allow developing and sharing simulation pipelines which automate in silico experiments including all modeling and simulation steps to increase reproducibility and productivity. The continuously expanding openCARP user community is supported by tailored infrastructure. Documentation and training material facilitate access to this complementary research tool for new users. After a brief historic review, this paper summarizes requirements for a high-usability electrophysiology simulator and describes how openCARP fulfills them. We introduce the openCARP modeling workflow in a multi-scale example of atrial fibrillation simulations on single cell, tissue, organ and body level and finally outline future development potential.ConclusionAs an open simulator, openCARP can advance the computational cardiac electrophysiology field by making state-of-the-art simulations accessible. In combination with the carputils framework, it offers a tailored software solution for the scientific community and contributes towards increasing use, transparency, standardization and reproducibility of in silico experiments.

frvcpy: An Open-Source Solver for the Fixed Route Vehicle Charging Problem

Electric vehicles offer a pathway to more sustainable transportation, but their adoption entails new challenges not faced by their petroleum-based counterparts. A difficult task in vehicle routing problems addressing these challenges is determining how to make good charging decisions for an electric vehicle traveling a given route. This is known as the fixed route vehicle charging problem. An exact and efficient algorithm for this task exists, but its implementation is sufficiently complex to deter researchers from adopting it. In this work we introduce frvcpy, an open-source Python package implementing this algorithm. Our aim with the package is to make it easier for researchers to solve electric vehicle routing problems, facilitating the development of optimization tools that may ultimately enable the mass adoption of electric vehicles. Summary of Contribution: This work describes a novel software tool for the vehicle routing community. The tool, frvcpy, addresses one of the primary challenges faced by the vehicle routing community when considering problems involving the adoption of electric vehicles (EVs): how to make optimal charging decisions. The state-of-the-art algorithm for solving these problems is sufficiently complex to deter researchers from using it, leading them to adopt less robust methods. frvcpy offers an easy-to-use, lightweight implementation of this algorithm, providing optimal solutions in low (∼5 ms) runtime. It is designed to be easily embedded in larger solution schemes for general EV routing problems, requiring minimal input, offering compatibility with the community standard file types, and offering access both through the command line and a Python API. The tool has thus far proven adaptable, having been used by researchers studying EV routing problems with novel constraints. Our aim with frvcpy is to make it easier for researchers to solve EV routing problems, facilitating the development of optimization tools that may contribute toward the mass adoption of electric vehicles.

Evaluation and Optimization of Urban Basic Education Facilities Layout based on GIS——A Case Study in Xuzhou, China

The layout of educational facilities has become a hot topic in urban geography research. Guides by rational demand consensus, typical human settlements extraction and matching of physical property planning, this paper constructs an evaluation system for the spatial layout of urban basic education facilities from the perspective of “Homo-Urbanicus” theory. The content includes the evaluation of accessibility, evaluation of bearing pressure, classification of layout types, selection and analysis of excellent communities. This paper conducts an empirical research on the basic education facilities of kindergartens, elementary schools and middle schools in the main urban area of Xuzhou City. And then, we delineated excellent community, standard communities, under-covered communities, overstressed communities, undeveloped communities on the basis of evaluation results. Finally, we selected sample communities for analysis, and put forward relevant optimization strategies.