rCASC implementation in Laniakea: porting containerization-based-reproducibility to a cloud Galaxy on-demand platform

Integrating rCASC in Laniakea: rCASC, Cluster Analysis of Single Cells [Alessandri et al. BioRxiv], is part of the reproducible-bioinformatics.org project and provides single cell analysis functionalities within the reproducible rules described by Sandve et al. [PLoS Comp Biol. 2013]. Laniakea [Tangaro et al. BioRxiv Bioinformatics] provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians. The final goal is to offer rCASC as a Galaxy flavor in the Laniakea Galaxy on-demand environment

Laniakea : an open solution to provide Galaxy "on-demand" instances over heterogeneous cloud infrastructures

Background: While the popular workflow manager Galaxy is currently made available through several publicly accessible servers, there are scenarios where users can be better served by full administrative control over a private Galaxy instance, including, but not limited to, concerns about data privacy, customisation needs, prioritisation of particular job types, tools development, and training activities. In such cases, a cloud-based Galaxy virtual instance represents an alternative that equips the user with complete control over the Galaxy instance itself without the burden of the hardware and software infrastructure involved in running and maintaining a Galaxy server. Results: We present Laniakea, a complete software solution to set up a \u201cGalaxy on-demand\u201d platform as a service. Building on the INDIGO-DataCloud software stack, Laniakea can be deployed over common cloud architectures usually supported both by public and private e-infrastructures. The user interacts with a Laniakea-based service through a simple front-end that allows a general setup of a Galaxy instance, and then Laniakea takes care of the automatic deployment of the virtual hardware and the software components. At the end of the process, the user gains access with full administrative privileges to a private, production-grade, fully customisable, Galaxy virtual instance and to the underlying virtual machine (VM). Laniakea features deployment of single-server or cluster-backed Galaxy instances, sharing of reference data across multiple instances, data volume encryption, and support for VM image-based, Docker-based, and Ansible recipe-based Galaxy deployments. A Laniakea-based Galaxy on-demand service, named Laniakea@ReCaS, is currently hosted at the ELIXIR-IT ReCaS cloud facility. Conclusions: Laniakea offers to scientific e-infrastructures a complete and easy-to-use software solution to provide a Galaxy on-demand service to their users. Laniakea-based cloud services will help in making Galaxy more accessible to a broader user base by removing most of the burdens involved in deploying and running a Galaxy service. In turn, this will facilitate the adoption of Galaxy in scenarios where classic public instances do not represent an optimal solution. Finally, the implementation of Laniakea can be easily adapted and expanded to support different services and platforms beyond Galaxy

Laniakea: a Galaxy-on-demand Provider Platform Through Cloud Technologies

Galaxy is rapidly becoming the de facto standard workflow manager for bioinformatics. Although several Galaxy public services are currently available, the usage of a private Galaxy instance is still mandatory or preferable for several use cases, including heavy workloads, data privacy concerns or particular customization needs. In this context, cloud computing technologies and infrastructures can provide a powerful and scalable solution to avoid the onerous deployment and maintenance of a local hardware and software infrastructure. Laniakea is a software framework that facilitates the provisioning of on-demand Galaxy instances as a cloud service over e-infrastructures, by leveraging on the open source software catalogue developed by the INDIGO-DataCloud H2020 project, which aimed to make cloud e-infrastructures more accessible by scientific communities. End-users interact with Laniakea through a web front-end that allows a general setup of a Galaxy instance. The deployment of the virtual hardware and of the Galaxy software ecosystem is subsequently performed by the INDIGO Platform as a Service layer. At the end of the process, the user gains access to a private, production-grade, fully customizable, Galaxy virtual instance. Laniakea features the deployment of a stand-alone or cluster backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours for specific tasks. We present here the latest development iteration of Laniakea, introducing a novel and strongly configurable web interface that facilitates a more straightforward customisation of the user experience through human readable YAML syntax and a reworked encryption procedure that exploits Hashicorp Vault as encryption keys management system

Laniakea@ReCaS: an ELIXIR-ITALY Galaxyon-demand cloud service

Although several Galaxy public services are available, a private Galaxy instance is still mandatory or preferable for several use cases including heavy workloads, data privacy concerns or particular customization needs. Cloud computing technologies provide a viable way to deploy Galaxy private instances, freeing users from the onerous deployment and maintenance of local IT infrastructures. In the last few years, ELIXIR-IT led the development of Laniakea, a software framework that facilitates the provisioning of on-demand Galaxy instances as a cloud service over e-infrastructures. The user interacts with a Laniakea service through a web front-end that allows to configure and launch a production-grade Galaxy instance in a straightforward way. Through the interface, the user can deploy Galaxy instances over single VMs or virtual clusters, link them to shared reference data volumes and plain or encrypted volumes for storing data. A selection of \u201cflavours\u201d, that is Galaxy instances pre-configured with sets of tools for specific tasks, is also available. When the users is satisfied, Laniakea takes oved and deploys the desired Galaxy instance over the cloud, providing a public IP and full administrative privileges over the new instance. In Dec-2018, we launched the beta-test phase of the first Laniakea-based Galaxy on-demand ELIXIR-IT service: Laniakea@ReCaS. After six months of helpful testing, we are now ready to announce the production phase of this service. Access to the service will be provided on a per-project basis through an open-ended call defining terms and conditions, project proposals will be evaluated by a scientific and technical board. Accepted proposals will be granted a package of computational resources for running on-demand Galaxy instances for a duration compatible with the project requirements

VINYL: Variant prIoritizatioN bY survivaL analysis

Motivation: Clinical applications of genome re\uadsequencing technologies typically generate large amounts of data that need to be carefully annotated and interpreted to identify genetic variants associated with pathological conditions. In this context, accurate and reproducible methods for the functional annotation and prioritization of genetic variants are of fundamental importance, especially when large volumes of data \uad like those produced by modern sequencing technologies \uad are involved. Results: In this paper, we present VINYL, a highly accurate and fully automated system for the functional annotation and prioritization of genetic variants in large scale clinical studies. Extensive analyses of both real and simulated datasets suggest that VINYL show higher accuracy and sensitivity when compared to equivalent state of the art methods, allowing the rapid and systematic identification of potentially pathogenic variants in different experimental settings

Laniakea: an open solution to provide Galaxy "on-demand" instances over heterogeneous cloud infrastructures

Background: Galaxy is rapidly becoming the de facto standard among workflow managers for bioinformatics. A rich feature set, its overall flexibility, and a thriving community of enthusiastic users are among the main factors contributing to the popularity of Galaxy and Galaxy based applications. One of the main advantages of Galaxy consists in providing access to sophisticated analysis pipelines, e.g., involving numerous steps and large data sets, even to users lacking computer proficiency, while at the same time improving reproducibility and facilitating teamwork and data sharing among researchers. Although several Galaxy public services are currently available, these resources are often overloaded with a large number of jobs and offer little or no customization options to end users. Moreover, there are scenarios where a private Galaxy instance still constitutes a more viable alternative, including, but not limited to, heavy workloads, data privacy concerns or particular needs of customization. In such cases, a cloud-based virtual Galaxy instance can represent a solution that overcomes the typical burdens of managing the local hardware and software infrastructure needed to run and maintain a production-grade Galaxy service. Results: Here we present Laniakea, a robust and feature-rich software suite which can be deployed on any scientific or commercial Cloud infrastructure in order to provide a "Galaxy on demand" Platform as a Service (PaaS). Laying its foundations on the INDIGO-DataCloud middleware, which has been developed to accommodate the needs of a large number of scientific communities, Laniakea can be deployed and provisioned over multiple architectures by private or public e-infrastructures. The end user interacts with Laniakea through a front-end that allows a general setup of the Galaxy instance, then Laniakea takes charge of the deployment both of the virtual hardware and all the software components. At the end of the process the user has access to a private, production-grade, yet fully customizable, Galaxy virtual instance. Laniakea's supports the deployment of plain or cluster backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours, that is Galaxy configurations tailored for specific tasks. As a proof of concept, we provide a demo Laniakea instance hosted at an ELIXIR-IT Cloud facility. Conclusions: The migration of scientific computational services towards virtualization and e-infrastructures is one of the most visible trends of our times. Laniakea provides Cloud administrators with a ready-to-use software suite that enables them to offer Galaxy, a popular workflow manager for bioinformatics, as an on-demand PaaS to their users. We believe that Laniakea can concur in making the many advantages of using Galaxy more accessible to a broader user base by removing most of the burdens involved in running a private instance. Finally, Laniakea's design is sufficiently general and modular that could be easily adapted to support different services and platforms beyond Galaxy

Chronic kidney disease progression and outcome according to serum phosphorus in mild-to-moderate kidney dysfunction

BACKGROUND AND OBJECTIVES: Several factors might alter serum phosphate homeostasis and induce hyperhosphatemia in patients with chronic kidney disease (CKD) not requiring dialysis. However, whether and to what extent hyperphosphatemia is associated with a poor prognosis in different CKD patient groups remain to be elucidated. DESIGN, SETTING, PARTICIPANTS & MEASUREMENTS: We utilized the "Prevenzione Insufficienza Renale Progressiva" (PIRP) database, a large project sponsored by the Emilia-Romagna Health Institute. PIRP is a collaborative network of nephrologists and general practitioners located in the Emilia-Romagna region, Italy, aimed at increasing awareness of CKD complications and optimizing CKD patient care. We identified 1716 patients who underwent a GFR and serum phosphorous assessment between 2004 and 2007. We tested whether phosphate levels 654.3 mg/dl are associated with the risk of CKD progression or all causes of death. RESULTS: Older age and male sex were associated with lower phosphate levels. Instead, higher phosphate levels were noted in patients with diabetes. Patients with phosphate levels 654.3 mg/dl were at an increased risk of starting dialysis or dying (hazard ratio 2.04; 95% confidence interval [1.44, 2.90]). Notably, subgroup analyses revealed that the magnitude of the risk associated with hyperphosphatemia varied depending on age, sex, diabetes, and different stages of CKD. CONCLUSIONS: These analyses lend support to the hypothesis that phosphorous abnormalities might have a negative effect on the residual renal function and prognosis in different groups of CKD patients. However, the risk associated with hyperphosphatemia might vary in specific CKD patient subgroups

EU H2020 FIRST- vF Interoperation suppoRting buSiness innovation

The manufacturing industry is entering a new era in which new ICT technologies and collaboration applications are integrated with traditional manufacturing practices and processes to increase flexibility in manufacturing, mass customization, increase speed, better quality and to improve productivity. Virtual factories are key building blocks for Manufacturing 2.0, enabling the creation of new business ecosystems. In itself, the concept of virtual factories is a major expansion upon virtual enterprises in the context of manufacturing, which only integrates collaborative business processes from different enterprises to simulate, model and test different design options, to evaluate performance, thus to save time-to-production. Creating virtual factories requires the integration of product design processes, manufacturing processes, and general collaborative business processes across factories and enterprises. An important aspect of this integration is ensure straightforward compatibility between the machines, products, processes, related products and services, as well as any descriptions of those

EU H2020 MSCA RISE Project FIRST - “virtual Factories: Interoperation suppoRting buSiness innovation”

FIRST – “virtual Factories: Interoperation suppoRting buSiness innovation”, is a European H2020 project, founded by the RESEARCH AND INNOVATION STAFF EXCHANGE (RISE) Work Programme as part of the Marie Skłodowska-Curie actions. The project concerns with Manufacturing 2.0 and aims at providing the new technology and methodology to describe manufacturing assets; to compose and integrate the existing services into collaborative virtual manufacturing processes; and to deal with evolution of changes. This Chapter provides an overview of the state of the art for the research topics related to the project research objectives, and then it presents the progresses the project achieved up to now towards the implementation of the proposed innovations