Making distributed computing infrastructures interoperable and accessible for e-scientists at the level of computational workflows

As distributed computing infrastructures evolve, and as their take up by user communities is growing, the importance of making different types of infrastructures based on a heterogeneous set of middleware interoperable is becoming crucial. This PhD submission, based on twenty scientific publications, presents a unique solution to the challenge of the seamless interoperation of distributed computing infrastructures at the level of workflows. The submission investigates workflow level interoperation inside a particular workflow system (intra-workflow interoperation), and also between different workflow solutions (inter-workflow interoperation). In both cases the interoperation of workflow component execution and the feeding of data into these components workflow components are considered. The invented and developed framework enables the execution of legacy applications and grid jobs and services on multiple grid systems, the feeding of data from heterogeneous file and data storage solutions to these workflow components, and the embedding of non-native workflows to a hosting meta-workflow. Moreover, the solution provides a high level user interface that enables e-scientist end-users to conveniently access the interoperable grid solutions without requiring them to study or understand the technical details of the underlying infrastructure. The candidate has also developed an application porting methodology that enables the systematic porting of applications to interoperable and interconnected grid infrastructures, and facilitates the exploitation of the above technical framework

Molecular docking with Raccoon2 on clouds: extending desktop applications with cloud computing

Molecular docking is a computer simulation that predicts the binding affinity between two molecules, a ligand and a receptor. Large-scale docking simulations, using one receptor and many ligands, are known as structure-based virtual screening. Often used in drug discovery, virtual screening can be very computationally demanding. This is why user-friendly domain-specific web or desktop applications that enable running simulations on powerful computing infrastructures have been created. Cloud computing provides on-demand availability, pay-per-use pricing, and great scalability which can improve the performance and efficiency of scientific applications. This paper investigates how domain-specific desktop applications can be extended to run scientific simulations on various clouds. A generic approach based on scientific workflows is proposed, and a proof of concept is implemented using the Raccoon2 desktop application for virtual screening, WS-PGRADE workflows, and gUSE services with the CloudBroker platform. The presented analysis illustrates that this approach of extending a domain-specific desktop application can run workflows on different types of clouds, and indeed makes use of the on-demand scalability provided by cloud computing. It also facilitates the execution of virtual screening simulations by life scientists without requiring them to abandon their favourite desktop environment and providing them resources without major capital investment

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

Extending Molecular Docking Desktop Applications with Cloud Computing Support and Analysis of Results

Structure-based virtual screening simulations, which are often used in drug discovery, can be very computationally demanding. This is why user-friendly domain-specific web or desktop applications that enable running simulations on powerful computing infrastructures have been created. This article investigates how domain-specific desktop applications can be extended to use cloud computing and how they can be part of scenarios that require sharing and analysing previous molecular docking results. A generic approach based on interviews with scientists and analysis of existing systems is proposed. A proof of concept is implemented using the Raccoon2 desktop application for virtual screening, WS-PGRADE workflows, gUSE services with the CloudBroker Platform, the structural alignment tool DeepAlign, and the ligand similarity tool LIGSIFT. The presented analysis illustrates that this approach of extending a domainspecific desktop application can use different types of clouds, thus facilitating the execution of virtual screening simulations by life scientists without requiring them to abandon their favourite desktop environment and providing them resources without major capital investment. It also shows that storing and sharing molecular docking results can produce additional conclusions such as viewing similar docking input files for verification or learning

Building Science Gateways for Analysing Molecular Docking Results Using a Generic Framework and Methodology

Molecular docking and virtual screening experiments require large computational and data resources and high-level user interfaces in the form of science gateways. While science gateways supporting such experiments are relatively common, there is a clearly identified need to design and implement more complex environments for further analysis of docking results. This paper describes a generic framework and a related methodology that supports the efficient development of such environments. The framework is modular enabling the reuse of already existing components. The methodology, which proposes three techniques that the development team can use, is agile and encourages active participation of end-users. Based on the framework and methodology, two prototype implementations of science-gateway-based docking environments are presented and evaluated. The first system recommends a receptor-ligand pair for the next docking experiment, and the second filters docking results based on ligand properties

Parametric Analysis of Particle Spreading with Discrete Element Method

The spreading of metallic powder on the printing platform is vital in most additive manufacturing methods, including direct laser sintering. Several processing parameters such as particle size, inter-particle friction, blade speed, and blade gap size affect the spreading process and, therefore, the final product quality. The objective of this study is to parametrically analyze the particle flow behavior and the effect of the aforementioned parameters on the spreading process using the discrete element method (DEM). To effectively address the vast parameter space within computational constraints, novel parameter sweep algorithms based on low discrepancy sequence (LDS) are utilized in conjunction with parallel computing. Based on the parametric analysis, optimal material properties and machine setup are proposed for a higher quality spreading. Modeling suggests that lower friction, smaller particle size, lower blade speed, and a gap of two times the particle diameter result in a higher quality spreading process. In addition, a twoparameter Weibull distribution is adopted to investigate the influence of particle size distribution. The result suggests that smaller particles with a narrower distribution produce a higher-quality flow, with a proper selection of gap. Finally, parallel computing, in conjunction with the LDS parameter sweep algorithm, effectively shrinks the parameter space and improves the overall computational efficiency

Analytical and computational methods towards a metabolic model of ageing in Caenorhabditis elegans

Human life expectancy is increasing globally. This has major socioeconomic implications, but also raises scientific questions about the biological bases of ageing and longevity. Research on appropriate model organisms, such as the nematode worm Caenorhabditis elegans, is a key component of answering these questions. Ageing is a complex phenomenon, with both environmental and genetic influences. Metabolomics, the analysis of all small molecules within a biological system, offers the ability to integrate these complex factors to help understand the role of metabolism in ageing. This thesis addresses the current lack of methods for C. elegans metabolite analysis, with a particular focus on combining analytical and computational approaches. As a first essential step, C. elegans metabolite extraction protocols for NMR, GC-MS and LC-MS based analysis were optimized. Several methods to improve the coverage, automatic annotation and data analysis steps of NMR and GC-MS are proposed. Next, stable isotope labelling was explored as a tool for C. elegans metabolomics. An automated stable isotope based workflow was developed, which identifies all biological, non-redundant features within a LC-MS acquisition and annotates them with molecular compositions. This demonstrated that the vast majority (> 99.5%) of detected features inside LC-MS metabolomics experiments are not of biological origin or redundant. This stable isotope workflow was then used to compare the metabolism of 24 different C. elegans mutant strains from different pathways (e.g. insulin signalling, TOR pathway, neuronal signalling), with differing levels of lifespan extension compared to wild-type worms. The biologically relevant features (metabolites) were detected and annotated, and compared across the mutants. Some metabolites were correlated with longevity across the mutant set, in particular, glycerophospholipids. This led to the formulation of a hypothesis, that lifespan extension in C. elegans requires increased activity of common downstream longevity effector mechanisms (autophagy, and mitochondrial biogenesis), that also involve subcellular compartmentation and hence membrane formation. This results in the alterations in lipid metabolism detected here.Open Acces

Scientific Workflows: Past, Present and Future

International audienceThis special issue and our editorial celebrate 10 years of progress with data-intensive or scientific workflows. There have been very substantial advances in the representation of workflows and in the engineering of workflow management systems (WMS). The creation and refinement stages are now well supported, with a significant improvement in usability. Improved abstraction supports cross-fertilisation between different workflow communities and consistent interpretation as WMS evolve. Through such re-engineering the WMS deliver much improved performance, significantly increased scale and sophisticated reliability mechanisms. Further improvement is anticipated from substantial advances in optimisation. We invited papers from those who have delivered these advances and selected 14 to represent today's achievements and representative plans for future progress. This editorial introduces those contributions with an overview and categorisation of the papers. Furthermore, it elucidates responses from a survey of major workflow systems, which provides evidence of substantial progress and a structured index of related papers. We conclude with suggestions on areas where further research and development is needed and offer a vision of future research directions