This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. Our developments are freely downloadable as open source components, and are already being integrated into many scientific applications.

Application of next-generation sequencing (NGS) methods for transcriptome analysis (RNA-seq) has become increasingly accessible in recent years and are of great interest to many biological disciplines including, eg, evolutionary biology, ecology, biomedicine, and computational biology. Although virtually any research group can now obtain RNA-seq data, only a few have the bioinformatics knowledge and computation facilities required for transcriptome analysis. Here, we present TRUFA (TRanscriptome User-Friendly Analysis), an open informatics platform offering a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. Due to the computationally intensive nature of such analyses, TRUFA is highly parallelized and benefits from accessing high-performance computing resources. The complete TRUFA pipeline was validated using four previously published transcriptomic data sets. TRUFA's results for the example datasets showed globally similar results when comparing with the original studies, and performed particularly better when analyzing the green tea dataset. The platform permits analyzing RNA-seq data in a fast, robust, and user-friendly manner. Accounts on TRUFA are provided freely upon request at https://trufa.ifca.es .

The FAIR Principles are a set of good practices to improve the reproducibility and quality of data in an Open Science context. Different sets of indicators have been proposed to evaluate the FAIRness of digital objects, including datasets that are usually stored in repositories or data portals. However, indicators like those proposed by the Research Data Alliance are provided from a high-level perspective that can be interpreted and they are not always realistic to particular environments like multidisciplinary repositories. This paper describes FAIR EVA, a new tool developed within the European Open Science Cloud context that is oriented to particular data management systems like open repositories, which can be customized to a specific case in a scalable and automatic environment. It aims to be adaptive enough to work for different environments, repository software and disciplines, taking into account the flexibility of the FAIR Principles. As an example, we present DIGITAL.CSIC repository as the first target of the tool, gathering the particular needs of a multidisciplinary institution as well as its institutional repository.

In this paper, we present a method to determine the volume of wine in different types of glass liquid containers from a single-view image. The proposed model predicts red wine volume from a photograph of the glass containing the wine. Experimental results demonstrated satisfactory performance of our image-based wine measurement system, with a Mean Absolute Error lower than $10\text{mL}$. To train and evaluate our system, we introduced the WineGut_BrainUp dataset, a new dataset of glasses of wine that contains 24305 laboratory images, including a wide range of containers, volumes of wine, backgrounds, object distances, angles and lightning, with or without calibration object. The proposed methodology is a suitable analytical tool for automate measurement of red wine volume. Indeed, it has potential real life applications in diet monitoring and wine consumption studies.

In the context of the EU H2020 INDIGO-DataCloud project several use case on large scale scientific data analysis regarding different research communities have been implemented. All of them require the availability of large amount of data related to either output of simulations or observed data from sensors and need scientific (big) data solutions to run data analysis experiments. More specifically, the paper presents the case studies related to the following research communities: (i) the European Multidisciplinary Seafloor and water column Observatory (INGV-EMSO), (ii) the Large Binocular Telescope, (iii) LifeWatch, and (iv) the European Network for Earth System Modelling (ENES).

The eXtreme-DataCloud (XDC) is an EU H2020 funded project aimed at developing scalable technologies for federating storage resources and managing data in highly distributed computing environments. XDC software stack is based on existing tools, whose technical maturity is proved, that the project enriches with new functionalities and plugins to address real life requirements from user communities belonging to a variety of scientific domains: Life Science, Astrophysics, High Energy Physics, Photon Science and Clinical Research. The XDC toolbox includes services like ONEDATA (AGH), dChace (DESY), EOS (CERN), the INDIGO-PaaS Orchestrator (INFN), DYNAFED (CERN). The targeted platforms are the current and next generation e-Infrastructures deployed in Europe, such as the European Open Science Cloud (EOSC), the European Grid Infrastructure (EGI), the Worldwide LHC Computing Grid (WLCG) and the computing infrastructures funded by other public and academic initiatives. The focus of the project is on policy driven data management, on orchestration based on Quality of Services and on pre-processing of ingested data with user-defined applications. Smart caching and storage federation technologies for the creation of the so-called “DataLakes” are also important topics for XDC. In this manuscript, we present the recent advancements in the project services architecture and the developments carried on in preparation of the first XDC release planned for the end of 2018.