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

Quadriceps EMG in open and closed kinetic chain tasks in women with patellofemoral pain

The authors investigated whether the discrepancy noted in the literature regarding delayed and decreased activity in vastus medialis obliquus (VMO) in people with patellofemoral pain (PFP) depends on the nature of the open kinetic chain (OKC) and the closed kinetic chain (CKC) in the experimental task. They hypothesized that activity in VMO would be more delayed and decreased in CKC tasks than in OKC tasks. Women with PFP (n = 17) and healthy controls (n = 17) performed isometric quadriceps contractions in CKC and OKC tasks. The authors manipulated only the application of resistance. Electromyographs (EMGs) showed that participants with PFP reacted later and activated the quadriceps more in the CKC task but had intramuscular quadriceps coordination similar to that of controls. The nature of the OKC task or the CKC task does not seem to explain contradictory findings regarding VMO activation

A Data Driven Science Gateway for Computational Workflows

The MoSGrid Science Gateway provides convenient ways to analyse and model threedimensional molecular structures using computational chemistry workflows. Molecular dynamics, quantum chemistry, and docking are the considered application domains. The science gateway including the data repository and underlying infrastructures was developed on top of the Liferay-based version of WS-PGRADE (Web services Parallel Grid Runtime and Developer Environment) using gUSE (grid User Support Environment), UNICORE, and XtreemFS technologies. The gateway allows users to seamlessly interact with the chemistry applications using data from the MoSGrid repository and running on Distributed Computing Infrastructures (DCIs). Data in the repository is centred on the Molecular Simulation Markup Language (MSML), which was developed in MoSGrid. For applications on the one hand and for analysis and visualization on the other hand format conversions from and to MSML are performed. Metadata, extracted from the MSML, is used to search the repository. The MoSGrid Science Gateway offers the use of data-centric workflows by integrating and extending a multitude of technologies. Users are enabled to run molecular computational simulations easily and efficiently with consistent data representations