Multi-level Meta-workflows: New Concept for Regularly Occurring Tasks in Quantum Chemistry

Background: In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows. Significance: Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows. Conclusions: We investigated the operations that represent basic functionalities in Quantum Chemistry and developed that relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository

The effect of calorie restriction on insulin signaling in skeletal muscle and adipose tissue of Ames dwarf mice

Long-living Ames dwarf (df/df) mice are homozygous for a mutation of the Prop1(df) gene. As a result, mice are deficient in growth hormone (GH), prolactin (PRL) and thyrotropin (TSH). In spite of the hormonal deficiencies, df/df mice live significantly longer and healthier lives compared to their wild type siblings. We studied the effects of calorie restriction (CR) on the expression of insulin signaling genes in skeletal muscle and adipose tissue of normal and df/df mice. The analysis of genes expression showed that CR differentially affects the insulin signaling pathway in these insulin target organs. Moreover, results obtained in both normal and Ames dwarf mice indicate more direct effects of CR on insulin signaling genes in adipose tissue than in skeletal muscle. Interestingly, CR reduced the protein levels of adiponectin in the epididymal adipose tissue of normal and Ames dwarf mice, while elevating adiponectin levels in skeletal muscle and plasma of normal mice only. In conclusion, our findings suggest that both skeletal muscle and adipose tissue are important mediators of insulin effects on longevity. Additionally, the results revealed divergent effects of CR on expression of genes in the insulin signaling pathway of normal and Ames dwarf mice

Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)

This report records and discusses the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3). The report includes a description of the keynote presentation of the workshop, which served as an overview of sustainable scientific software. It also summarizes a set of lightning talks in which speakers highlighted to-the-point lessons and challenges pertaining to sustaining scientific software. The final and main contribution of the report is a summary of the discussions, future steps, and future organization for a set of self-organized working groups on topics including developing pathways to funding scientific software; constructing useful common metrics for crediting software stakeholders; identifying principles for sustainable software engineering design; reaching out to research software organizations around the world; and building communities for software sustainability. For each group, we include a point of contact and a landing page that can be used by those who want to join that group's future activities. The main challenge left by the workshop is to see if the groups will execute these activities that they have scheduled, and how the WSSSPE community can encourage this to happen

Pre-sorting and pen size effects on the stress responses at loading and unloading and transport losses in market weight pigs

Transport losses represent three challenges for the US swine industry and these are: 1) pig well-being, 2) increased rules and regulations, and 3) direct financial losses to producers and packers. Therefore; improving the well-being of pigs during transport and reducing the incidence of dead and non-ambulatory pigs is a priority for the US swine industry (NPB, 2007). Johnson et al. (2010) studied the effects of grow-finish pen size and manually pre-sorting pigs the day before loading on the stress responses at loading and unloading and transport losses in market weight pigs. The authors reported that pigs loaded from large pens (192 pigs/pen) that were pre-sorted from pen mates had 66% fewer dead and non-ambulatory pigs at the harvest facility compared to pigs loaded from small pens (32 pigs/pen) that were sorted from pen mates during loading. However, it is unclear if the reduction in transport losses was due to pen size and/or pre-sorting before marketing. Therefore, the objectives of the current two research trials were to 1) determine the effects of pre-sorting prior to loading on stress responses and transport losses at the harvest facility in the market weight pig; and 2) determine the effects of grow-finish pen size on stress responses and transport losses at the harvest facility in the market weight pig

Enhanced Usability of Managing Workflows in an Industrial Data Gateway

The Grid and Cloud User Support Environment (gUSE) enables users convenient and easy access to grid and cloud infrastructures by providing a general purpose, workflow-oriented graphical user interface to create and run workflows on various Distributed Computing Infrastructures (DCIs). Its arrangements for creating and modifying existing workflows are, however, non-intuitive and cumbersome due to the technologies and architecture employed by gUSE. In this paper, we outline the first integrated web-based workflow editor for gUSE with the aim of improving the user experience for those with industrial data workflows and the wider gUSE community. We report initial assessments of the editor's utility based on users' feedback. We argue that combining access to diverse scalable resources with improved workflow creation tools is important for all big data applications and research infrastructures