Alpha&ESMhFolds: A Web Server for Comparing AlphaFold2 and ESMFold Models of the Human Reference Proteome

We develop a novel database Alpha&ESMhFolds which allows the direct comparison of AlphaFold2 and ESMFold predicted models for 42,942 proteins of the Reference Human Proteome, and when available, their comparison with 2,900 directly associated PDB structures with at least a structure to sequence coverage of 70%. Statistics indicate that good quality models tend to overlap with a TM-score >0.6 as long as some PDB structural information is available. As expected, a direct model superimposition to the PDB structure highlights that AlphaFold2 models are slightly superior to ESMFold ones. However, some 55% of the database is endowed with models overlapping with TM-score <0.6. This highlights the different outputs of the two methods. The database is freely available for usage at https://alpha-esmhfolds.biocomp.unibo.it/.

In-plane reorientation induced single laser pulse magnetization reversal

Single Pulse All Optical Switching represents the ability to reverse the magnetization of a nanostructure using a femtosecond single laser pulse without any applied field. Since the first switching experiments carried out on GdFeCo ferrimagnets, this phenomena has been only recently extended to a few other materials, MnRuGa alloys and Tb/Co multilayers with a very specific range of thickness and composition. Here, we demonstrate that single pulse switching can be obtained for a large range of rare earth-transition metal multilayers, making this phenomenon much more general. Surprisingly, the threshold fluence for switching is observed to be independent of the laser pulse duration. Moreover, at high laser intensities, concentric ring domain structures are induced. These striking features contrast to those observed in Gd based materials pointing towards a different reversal mechanism. Concomitant with the demonstration of an in-plane magnetization reorientation, a precessional reversal mechanism explains all the observed features.

Enhancing the impact of Artificial Intelligence in Medicine: A joint AIFM-INFN Italian initiative for a dedicated cloud-based computing infrastructure

Artificial Intelligence (AI) techniques have been implemented in the field of Medical Imaging for more than forty years. Medical Physicists, Clinicians and Computer Scientists have been collaborating since the beginning to realize software solutions to enhance the informative content of medical images, including AI-based support systems for image interpretation. Despite the recent massive progress in this field due to the current emphasis on Radiomics, Machine Learning and Deep Learning, there are still some barriers to overcome before these tools are fully integrated into the clinical workflows to finally enable a precision medicine approach to patients' care. Nowadays, as Medical Imaging has entered the Big Data era, innovative solutions to efficiently deal with huge amounts of data and to exploit large and distributed computing resources are urgently needed. In the framework of a collaboration agreement between the Italian Association of Medical Physicists (AIFM) and the National Institute for Nuclear Physics (INFN), we propose a model of an intensive computing infrastructure, especially suited for training AI models, equipped with secure storage systems, compliant with data protection regulation, which will accelerate the development and extensive validation of AI-based solutions in the Medical Imaging field of research. This solution can be developed and made operational by Physicists and Computer Scientists working on complementary fields of research in Physics, such as High Energy Physics and Medical Physics, who have all the necessary skills to tailor the AI-technology to the needs of the Medical Imaging community and to shorten the pathway towards the clinical applicability of AI-based decision support systems.

The novel Mechanical Ventilator Milano for the COVID-19 pandemic

This paper presents the Mechanical Ventilator Milano (MVM), a novel intensive therapy mechanical ventilator designed for rapid, large-scale, low-cost production for the COVID-19 pandemic. Free of moving mechanical parts and requiring only a source of compressed oxygen and medical air to operate, the MVM is designed to support the long-term invasive ventilation often required for COVID-19 patients and operates in pressure-regulated ventilation modes, which minimize the risk of furthering lung trauma. The MVM was extensively tested against ISO standards in the laboratory using a breathing simulator, with good agreement between input and measured breathing parameters and performing correctly in response to fault conditions and stability tests. The MVM has obtained Emergency Use Authorization by U.S. Food and Drug Administration (FDA) for use in healthcare settings during the COVID-19 pandemic and Health Canada Medical Device Authorization for Importation or Sale, under Interim Order for Use in Relation to COVID-19. Following these certifications, mass production is ongoing and distribution is under way in several countries. The MVM was designed, tested, prepared for certification, and mass produced in the space of a few months by a unique collaboration of respiratory healthcare professionals and experimental physicists, working with industrial partners, and is an excellent ventilator candidate for this pandemic anywhere in the world.

First experiences with a portable analysis infrastructure for LHC at INFN

The challenges proposed by the HL-LHC era are not limited to the sheer amount of data to be processed: the capability of optimizing the analyser's experience will also bring important benefits for the LHC communities, in terms of total resource needs, user satisfaction and in the reduction of end time to publication. At the Italian National Institute for Nuclear Physics (INFN) a portable software stack for analysis has been proposed, based on cloud-native tools and capable of providing users with a fully integrated analysis environment for the CMS experiment. The main characterizing traits of the solution consist in the user-driven design and the portability to any cloud resource provider. All this is made possible via an evolution towards a “python-based” framework, that enables the usage of a set of open-source technologies largely adopted in both cloud-native and data-science environments. In addition, a “single sign on”-like experience is available thanks to the standards-based integration of INDIGO-IAM with all the tools. The integration of compute resources is done through the customization of a JupyterHUB solution, able to spawn identity-aware user instances ready to access data with no further setup actions. The integration with GPU resources is also available, designed to sustain more and more widespread ML based workflow. Seamless connections between the user UI and batch/big data processing framework (Spark, HTCondor) are possible. Eventually, the experiment data access latency is reduced thanks to the integrated deployment of a scalable set of caches, as developed in the context of ESCAPE project, and as such compatible with the future scenarios where a data-lake will be available for the research community.

The outcome of the evaluation of such a solution in action is presented, showing how a real CMS analysis workflow can make use of the infrastructure to achieve its results.

The DODAS Experience on the EGI Federated Cloud

The EGI Cloud Compute service offers a multi-cloud IaaS federation that brings together research clouds as a scalable computing platform for research accessible with OpenID Connect Federated Identity. The federation is not limited to single sign-on, it also introduces features to facilitate the portability of applications across providers: i) a common VM image catalogue VM image replication to ensure these images will be available at providers whenever needed; ii) a GraphQL information discovery API to understand the capacities and capabilities available at each provider; and iii) integration with orchestration tools (such as Infrastructure Manager) to abstract the federation and facilitate using heterogeneous providers. EGI also monitors the correct function of every provider and collects usage information across all the infrastructure. DODAS (Dynamic On Demand Analysis Service) is an open-source Platform-as-a-Service tool, which allows to deploy software applications over heterogeneous and hybrid clouds. DODAS is one of the so-called Thematic Services of the EOSC-hub project and it instantiates on-demand container-based clusters offering a high level of abstraction to users, allowing to exploit distributed cloud infrastructures with a very limited knowledge of the underlying technologies.This work presents a comprehensive overview of DODAS integration with EGI Cloud Federation, reporting the experience of the integration with CMS Experiment submission infrastructure system.

Lessons Learned from the Assessment of Software Defect Prediction on WLCG Software: A Study with Unlabelled Datasets and Machine Learning Techniques

Software defect prediction is an activity that aims at narrowing down the most likely defect-prone software modules and helping developers and testers to prioritize inspection and testing. This activity can be addressed by using Machine Learning techniques applied to software metrics datasets that are usually unlabelled, i.e. they lack modules classification in terms of defectiveness. To overcome this limitation, in addition to the usual data pre-processing operations to manage mission values and/or to remove inconsistencies, researches have to adopt an approach to label their unlabelled software datasets. The extraction of defectiveness data to label all the instances of the datasets is an extremely time and effort consuming operation. In literature, many studies have introduced approaches to build a defect prediction models on unlabelled datasets.

In this paper, we describe the analysis of new unlabelled datasets from WLCG software, coming from HEP-related experiments and middleware, by using Machine Learning techniques. We have experimented new approaches to label the various modules due to the heterogeneity of software metrics distribution. We discuss a number of lessons learned from conducting these activities, what has worked, what has not and how our research can be improved.

Dynamic integration of distributed, Cloud-based HPC and HTC resources using JSON Web Tokens and the INDIGO IAM Service

In the past couple of years, we have been actively developing the Dynamic On-Demand Analysis Service (DODAS) as an enabling technology to deploy container-based clusters over hybrid, private or public, Cloud infrastructures with almost zero effort. DODAS is particularly suitable for harvesting opportunistic computing resources; this is why several scientific communities already integrated their computing use cases into DODAS-instantiated clusters, automating the instantiation, management and federation of HTCondor batch systems. The increasing demand, availability and utilization of HPC resources by and for multidisciplinary user communities, often mandates the possibility to transparently integrate, manage and mix HTC and HPC resources. In this paper, we discuss our experience extending and using DODAS to connect HPC and HTC resources in the context of a distributed Italian regional infrastructure involving multiple sites and communities. In this use case, DODAS automatically generates HTCondor batch system on-demand. Moreover it dynamically and transparently federates sites that may also include HPC resources managed by SLURM; DODAS allows user workloads to make opportunistic and automated use of both HPC and HTC resources, thus effectively maximizing and optimizing resource utilization. We also report on our experience of using and federating HTCondor batch systems exploiting the JSON Web Token capabilities introduced in recent HTCondor versions, replacing the traditional X509 certificates in the whole chain of workload authorization. In this respect we also report on how we integrated HTCondor using OAuth with the INDIGO IAM service.

Exploiting private and commercial clouds to generate on-demand CMS computing facilities with DODAS

Minimising time and cost is key to exploit private or commercial clouds. This can be achieved by increasing setup and operational efficiencies. The success and sustainability are thus obtained reducing the learning curve, as well as the operational cost of managing community-specific services running on distributed environments. The greater beneficiaries of this approach are communities willing to exploit opportunistic cloud resources. DODAS builds on several EOSC-hub services developed by the INDIGO-DataCloud project and allows to instantiate on-demand container-based clusters. These execute software applications to benefit of potentially “any cloud provider”, generating sites on demand with almost zero effort. DODAS provides ready-to-use solutions to implement a “Batch System as a Service” as well as a BigData platform for a “Machine Learning as a Service”, offering a high level of customization to integrate specific scenarios. A description of the DODAS architecture will be given, including the CMS integration strategy adopted to connect it with the experiment’s HTCondor Global Pool. Performance and scalability results of DODAS-generated tiers processing real CMS analysis jobs will be presented. The Instituto de Física de Cantabria and Imperial College London use cases will be sketched. Finally a high level strategy overview for optimizing data ingestion in DODAS will be described.

Digital repository as a service: automatic deployment of an Invenio-based repository using TOSCA orchestration and Apache Mesos

In the framework of the H2020 INDIGO-DataCloud project, we have implemented an advanced solution for the automatic deployment of digital data repositories based on Invenio, the digital library framework developed by CERN. Exploiting cutting-edge technologies, such as Docker and Apache Mesos, and standard specifications to describe application architectures such as TOSCA, we are able to provide a service that simplifies the process of creating and managing repositories of various digital assets using cloud resources. An Invenio-based repository consists of a set of services (e.g. database, message queue, cache, workers and frontend) that need to be properly installed, configured and linked together. These operations, along with the provisioning of the resources and their monitoring and maintenance, can be challenging for individual researchers or small-to-moderate-sized research groups. To this purpose, the INDIGO-DataCloud platform provides advanced features for orchestrating the deployment of complex virtual infrastructures on distributed cloud environments: it is able to provision the required resources automatically over heterogeneous and/or hybrid cloud infrastructures and to configure them automatically ensuring dynamic elasticity and resilience. This approach has been successfully adapted to support the needs of the researchers and scholars in the domain of the Digital Arts and Humanities.