Open-source Infrastructure Research Articles

Start-up Story

How can open source infrastructure support a modernized, accelerated book production workflow? The California Digital Library, the University of California Press and the Collaborative Knowledge Foundation collaborated to design a new platform – Editoria – to do exactly this, following a new user-driven design method to result in a simple, people-centric interface. This case study details the main problem facing publishers who are restrained by outdated, print-oriented production platforms, the ‘reimagining’ exercise and the iterative design process that has resulted in new technology which can be adopted, adapted and integrated by publishers.

A Comparative Analysis on Open Source Infrastructure as a Service Cloud Framework

A Comparative Analysis on Open Source Infrastructure as a Service Cloud Framework

Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application

Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management.As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built.The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development.MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid achievement in cancer diagnosis and therapeutics.

Generic platform for registration and online offering of assistance-on-demand (AoD) services in an inclusive infrastructure

An increasing percentage of the population needs assistance services for a wide range of activities related to their independent living, which can be delivered either by humans or by machines. While cloud computing and emerging ICT solutions have introduced new types of services and service delivery paradigms, it remains costly and difficult to set up and market assistance services addressing the needs of very narrow end-user groups. The current work presents the design of a novel open-source infrastructure (web-based platform) which enables diverse stakeholders to easily set up web-based assistance-on-demand platform instances. Each of these AoD instances can be used by service providers to register and offer assistance-on-demand (AoD) services for catering individual needs of persons with disabilities. In this way, narrow end-user groups can be reached and enjoy a gamut of assistance services. The AoD platform is implemented in the context of a larger Global Public Inclusive Infrastructure (GPII), which is being developed in the context of the Prosperity4All project. The functional requirements for the design of the AoD infrastructure were iteratively fine-tuned through the definition and analysis of representative use models (sets of personas and use cases). The AoD platform architecture consists of two major components: front-end (GUI) and back-end (service infrastructure). Their implementation is mainly based on the Django framework which enables a Model–Template–View (MTV) software architectural pattern with highly configurable and flexible components. The evaluation of a demonstration instance of the AoD platform with end-users identified its advantages and pointed out additional functionality needed: multi-language, multi-modality, embedded social media feeding, dedicated menu for highly flexible service, etc. The overall perceived usefulness of the specific demonstration AoD platform instance that underwent evaluation was higher than 80%. The proposed AoD platform provides a flexible and sufficiently generic web-based infrastructure for the cost-effective setup, registration and web publication of services that can accommodate a highly diverse range of assistance needs. Furthermore, it is suitable for use by a wide range of different stakeholder/user groups interested in addressing the needs of persons with disabilities or otherwise at risk of exclusion.

An Efficient and Energy-Aware Cloud Consolidation Algorithm for Multimedia Big Data Applications

It is well known that cloud computing has many potential advantages over traditional distributed systems. Many enterprises can build their own private cloud with open source infrastructure as a service (IaaS) frameworks. Since enterprise applications and data are migrating to private cloud, the performance of cloud computing environments is of utmost importance for both cloud providers and users. To improve the performance, previous studies on cloud consolidation have been focused on live migration of virtual machines based on resource utilization. However, the approaches are not suitable for multimedia big data applications. In this paper, we reveal the performance bottleneck of multimedia big data applications in cloud computing environments and propose a cloud consolidation algorithm that considers application types. We show that our consolidation algorithm outperforms previous approaches.

Using hyperLOPIT to perform high-resolution mapping of the spatial proteome.

The organization of eukaryotic cells into distinct subcompartments is vital for all functional processes, and aberrant protein localization is a hallmark of many diseases. Microscopy methods, although powerful, are usually low-throughput and dependent on the availability of fluorescent fusion proteins or highly specific and sensitive antibodies. One method that provides a global picture of the cell is localization of organelle proteins by isotope tagging (LOPIT), which combines biochemical cell fractionation using density gradient ultracentrifugation with multiplexed quantitative proteomics mass spectrometry, allowing simultaneous determination of the steady-state distribution of hundreds of proteins within organelles. Proteins are assigned to organelles based on the similarity of their gradient distribution to those of well-annotated organelle marker proteins. We have substantially re-developed our original LOPIT protocol (published by Nature Protocols in 2006) to enable the subcellular localization of thousands of proteins per experiment (hyperLOPIT), including spatial resolution at the suborganelle and large protein complex level. This Protocol Extension article integrates all elements of the hyperLOPIT pipeline, including an additional enrichment strategy for chromatin, extended multiplexing capacity of isobaric mass tags, state-of-the-art mass spectrometry methods and multivariate machine-learning approaches for analysis of spatial proteomics data. We have also created an open-source infrastructure to support analysis of quantitative mass-spectrometry-based spatial proteomics data (http://bioconductor.org/packages/pRoloc) and an accompanying interactive visualization framework (http://www. bioconductor.org/packages/pRolocGUI). The procedure we outline here is applicable to any cell culture system and requires ∼1 week to complete sample preparation steps, ∼2 d for mass spectrometry data acquisition and 1-2 d for data analysis and downstream informatics.

Authentication and Authorization for the Internet of Things

Authentication and authorization are essential parts of basic security processes and are sorely needed in the Internet of Things (IoT). The emergence of edge and fog computing creates new opportunities for security and trust management in the IoT. In this article, the authors discuss existing solutions to establish and manage trust in networked systems and argue that these solutions face daunting challenges when scaled to the IoT. They give a vision of efficient and scalable trust management for the IoT based on locally centralized, globally distributed trust management using an open source infrastructure with local authentication and authorization entities to be deployed on edge devices.

LAND USER AND LAND COVER MAPS OF EUROPE: A WEBGIS PLATFORM

This paper presents the methods and implementation processes of a WebGIS platform designed to publish the available land use and land cover maps of Europe at continental scale. The system is built completely on open source infrastructure and open standards. The proposed architecture is based on a server-client model having GeoServer as the map server, Leaflet as the client-side mapping library and the Bootstrap framework at the core of the front-end user interface. The web user interface is designed to have typical features of a desktop GIS (e.g. activate/deactivate layers and order layers by drag and drop actions) and to show specific information on the activated layers (e.g. legend and simplified metadata). Users have the possibility to change the base map from a given list of map providers (e.g. OpenStreetMap and Microsoft Bing) and to control the opacity of each layer to facilitate the comparison with both other land cover layers and the underlying base map. In addition, users can add to the platform any custom layer available through a Web Map Service (WMS) and activate the visualization of photos from popular photo sharing services. This last functionality is provided in order to have a visual assessment of the available land coverages based on other user-generated contents available on the Internet. It is supposed to be a first step towards a calibration/validation service that will be made available in the future.

LAND USER AND LAND COVER MAPS OF EUROPE: A WEBGIS PLATFORM

Abstract. This paper presents the methods and implementation processes of a WebGIS platform designed to publish the available land use and land cover maps of Europe at continental scale. The system is built completely on open source infrastructure and open standards. The proposed architecture is based on a server-client model having GeoServer as the map server, Leaflet as the client-side mapping library and the Bootstrap framework at the core of the front-end user interface. The web user interface is designed to have typical features of a desktop GIS (e.g. activate/deactivate layers and order layers by drag and drop actions) and to show specific information on the activated layers (e.g. legend and simplified metadata). Users have the possibility to change the base map from a given list of map providers (e.g. OpenStreetMap and Microsoft Bing) and to control the opacity of each layer to facilitate the comparison with both other land cover layers and the underlying base map. In addition, users can add to the platform any custom layer available through a Web Map Service (WMS) and activate the visualization of photos from popular photo sharing services. This last functionality is provided in order to have a visual assessment of the available land coverages based on other user-generated contents available on the Internet. It is supposed to be a first step towards a calibration/validation service that will be made available in the future.

A Practical Application of TrimCloud

The current educational technologies in developing countries are not always successfully implemented and utilized due to infrastructure limitations, such as limited resources, limited training in educational technologies, and the unrealized potential usefulness of these technologies. Using an effective and relevant educational technology will efficiently maximize the use of the limited resources available to schools in developing countries in order to provide a larger outreach and increase access to up-to-date information and useful electronic resources. Thus, the authors propose TrimCloud as an alternative educational technology to help rebuild the education system and encourage innovation and development in developing countries. TrimCloud is an open-source virtual desktop infrastructure (VDI) that is offered as a software-as-a-service (SaaS) and a desktop-as-a-service (DaaS). In this paper, the authors examine possible solutions to issues plaguing the educational environment in developing countries by using TrimCloud at the primary, secondary, university/higher education, and administration levels. They propose the use of refurbished legacy systems as the alternative hardware source for using TrimCloud as an educational technology, which will also aid to alleviate the “e-waste dump” problem. Lastly, the authors explore further network enhancements to TrimCloud that will provide a reliable and robust option for developing countries.

Open Polar Server (OPS)—An Open Source Infrastructure for the Cryosphere Community

The Center for Remote Sensing of Ice Sheets (CReSIS) at the University of Kansas has collected approximately 1000 terabytes (TB) of radar depth sounding data over the Arctic and Antarctic ice sheets since 1993 in an effort to map the thickness of the ice sheets and ultimately understand the impacts of climate change and sea level rise. In addition to data collection, the storage, management, and public distribution of the dataset are also primary roles of the CReSIS. The Open Polar Server (OPS) project developed a free and open source infrastructure to store, manage, analyze, and distribute the data collected by CReSIS in an effort to replace its current data storage and distribution approach. The OPS infrastructure includes a spatial database management system (DBMS), map and web server, JavaScript geoportal, and MATLAB application programming interface (API) for the inclusion of data created by the cryosphere community. Open source software including GeoServer, PostgreSQL, PostGIS, OpenLayers, ExtJS, GeoEXT and others are used to build a system that modernizes the CReSIS data distribution for the entire cryosphere community and creates a flexible platform for future development. Usability analysis demonstrates the OPS infrastructure provides an improved end user experience. In addition, interpolating glacier topography is provided as an application example of the system.

Critical-blame analysis for OpenMP 4.0 offloading on Intel Xeon Phi

Critical-path detection in OpenMP 4.0 programs with offloaded code.Detection and quantification of load imbalances and their cause in OpenMP 4.0 codes.Implementation in the open-source tool infrastructure Score-P.Validation and evaluation with modified SPEC ACCEL benchmarks. Recent supercomputers rated in the TOP 500 list increasingly utilize accelerator or co-processor devices to improve performance and energy efficiency. Since version 4.0 of the specification OpenMP addresses this heterogeneity in computing with the target directives, which enable programmers to offload portions of the code to massively-parallel target devices. Due to this new complexity in hardware and software design, performance optimization of large-scale parallel programs becomes more and more challenging. As manual performance analysis is getting infeasible for complex high performance computing (HPC) codes, we propose an approach to automatically detect bottlenecks such as load imbalances in heterogeneous OpenMP applications. We developed a method to perform critical-path and root-cause analysis for the OpenMP4.0offloading model and integrated it into the tool CASITA. The post-mortem analysis is based on execution traces that are generated with an implementation of the evolving OpenMP Tools Interface into the measurement system Score-P. To validate the implementation of our method we ported several existing codes to OpenMP4.0, executed them with an Intel Xeon Phi as the target device and analyzed the resulting trace files.

Standard Interfaces for Open Source Infrastructure as a Service Platforms

IntroductionCloud Computing is an already established technology, already having lost its aura as one of the hottest and most rapid developing topics in the industry. At the base of its services stack, Infrastructure as a Service (IaaS) model utilizes well understood architectures, providing access, mostly, to the same type of computing and storage resources across all platform providers. New topics entered the spotlight, such as integrated management of IaaS platforms, selection of an IaaS platform, vendor lock-in, interoperability and identity in the Cloud and efforts were made to address them by defining and using standardized interfaces. Standard data models and technologies compatible with both the IaaS platforms and the existing Internet Infrastructure had to be used. This led to adoption of established standards and technologies such as XML web services or JSON over RESTful services.2 Open Cloud Computing InterfaceOpen Cloud Computing Interface (OCCI) is a collection of community generated open specifications built through Open Grid Forum [1]. Intended to be an open and interoperable RESTful protocol and an API for all cloudrelated management activities, it started with a focus on the Infrastructure-as-a-Service layer but later extended to include all the other layers in the Cloud stack.The specifications are broken into several modules in order to achieve a greater flexibility and extensibility. Separate modules describe· the core models, defines an abstract representation of real-world resources intended to be manipulated through OCCI renderings [1].· the rendering of the code model using HTTP/REST, describes the interactions available for an OCCI implementation with the resources built using the core models [2].· the extensions to the code models specific to implementation of an Infrastructure as a Service API [3], defining its parameters for compute, storage and network.The main reasons behind the development of OCCI were identified in [4] and [5] as:· Interoperability, demanding a standardized API and protocol.· Integration, allowing different service providers to bring together and interconnect platforms based on different technologies.· Portability, providing standardized data formats understood by different providers, allowing porting between them.· Innovation, considering that established standards can be a driver for innovation.· Reusability, Figure 1, working on two levels, first allowing reuse of code through basic standardized APIs and, second, promoting reuse of standards in different technology fields.3 Cloud Data Management InterfaceCloud Data Management Interface (CDMI) describes a functional interface allowing applications to create, retrieve, update and delete data elements from the Cloud [6]. The standard is developed by SNIA, a global organization of storage solution providers. Using a CDMI compatible interface, cloud data consumers are able to discover the storage features offered by IaaS platforms. Along with data elements, the standard also allows the management of containers, accounts and retrieval of monitoring and billing information, Figure 2.CDMI is not designed to replace other object access protocols but to complement them. The standard uses RESTful protocol for building its interfaces, to keep it as simple as possible and to encourage its adoption. Adding discovery functions, it allows future extensions to the standard without breaking client compatibility.CDMI serves as both a storage protocol while, at the same time, offering a layer of client to cloud management and cloud to cloud standardized interactions. Clients can manage credentials to domains defined in the cloud forming a hierarchical structure that have objects attached to them and building a path for accessing and controlling these objects. For cloud to cloud interaction it introduces globally unique identifiers linked to objects for the whole of their lifetime to persist their identity if moved or replicated between clouds. …

Adoption and Use of Open Source Infrastructure Software by Large Corporations

Adoption and continuance of use of open source infrastructure software by large business organizations is not well understood. This study fills this gap in research by conducting a longitudinal investigation of the adoption and use of MySQL by two large corporations. One organization, an early adopter, adopted and used MySQL for several years before reverting back to a proprietary product. The other, a late adopter, made an initial adoption decision but didn't deploy it in mission critical applications. Interestingly, free software and freedom to access and modify the source code, the hallmark of the open source model, were not found to be significant in promoting adoption. In contrast, high quality maintenance support and timely product enhancement to keep up with user needs were considered critical for initial adoption and continued use of software. The study also demonstrates the need to investigate continuance of use to get a complete picture of open source software adoption and use by organizations.

SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data.

One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. Currently available software solutions are largely limited to large scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies.

Multi-scale Coupling Simulation of Seismic Waves and Building Vibrations Using ppOpen-HPC

Abstract In order to simulate an earthquake shock originating from the earthquake source and the damage it causes to buildings, not only the seismic wave that propagates over a wide region of several 100 km2, but also the building vibrations that occur over a small region of several 10 m2 must be resolved concurrently. Such a multi-scale simulation is difficult because such kind of modeling and implementation by only a specific application are limited. To overcome these problems, a multi-scale weak-coupling simulation of seismic wave and building vibrations using “ppOpen-HPC” libraries is conducted. The ppOpen-HPC, wherein “pp” stands for “post-peta scale”, is an open source infrastructure for development and execution of optimized and reliable simulation codes on large-scale parallel computers. On the basis of our evaluation, we confirm that an acceptable result can be achieved that ensures that the overhead cost of the coupler is negligible and it can work on large-scale computational resources.

Hacking the academy: new approaches to scholarship and teaching from digital humanities

Can an algorithm edit a journal? Can a library exist without books? Can students build and manage their own learning management platforms? Can a conference be held without a program? Can Twitter replace a scholarly society? As recently as the mid-2000s, questions like these would have been unthinkable. But today serious scholars are asking whether the institutions of the academy as they have existed for decades, even centuries, aren't becoming obsolete. Every aspect of scholarly infrastructure is being questioned, and even more importantly, being hacked. Sympathetic scholars of traditionally disparate disciplines are cancelling their association memberships and building their own networks on Facebook and Twitter. Journals are being compiled automatically from self-published blog posts. Newly minted Ph.D.s are forgoing the tenure track for alternative academic careers that blur the lines between research, teaching, and service. Graduate students are looking beyond the categories of the traditional CV and building expansive professional identities and popular followings through social media. Educational technologists are punking established technology vendors by rolling out their own open source infrastructure. Hacking the Academy will both explore and contribute to ongoing efforts to rebuild scholarly infrastructure for a new millennium.

A new pedagogical design for geo-informatics courses using an e-training support system

The current study seeks to introduce a new pedagogical design for geo-informatics courses using an e-training support system. Laurillard's conversational approach based on conceptual representation for both instructor and learner was used to form the framework. As the current study specifically interested in training as a special form for learning, so, we sought methods and strategies to integrate requirements of both company and employee into the design of training programs. Therefore, a competency perspective was adopted into the conversational framework to use learning design that leads to learning activities tightly related to the needs of the company and employee. The above framework has been developed with special consideration to the underpinning pedagogical principles and the needs of lifelong learning that continues after the training has been completed. The implementation of the developed framework needs a special computerized system, so an e-training support system (ETSS) was developed to realize the framework. ETSS is an open source and standard-based infrastructure to enable and foster competence development and exchange of learning activities and learning units. Although the domain of the current study focuses on geo-informatics, ETSS is applicable to any other domain. The developed framework through its ETSS implementation were evaluated in a typical training environment. The results indicated that the best method in training was the training with the developed system with 91.5 % in comparison with the traditional training method with 81.4 %.

An open source infrastructure for quality assurance and preservation of a large digital book collection

This article presents an open source infrastructure for processing large collections of digital books available at the Austrian National Library with a special focus on quality assurance tasks in the context of the European project SCAPE (www.scapeproject-eu). It describes the cluster hardware and the software components used for building the experimental IT infrastructure.More concretely, a set of best practices for the data analysis of large document image collections on the basis of Apache Hadoop will be shown. Different types of Hadoop jobs (Hadoop-Streaming-API, Hadoop MapReduce, and Hive) are used as basic components, and the Taverna workflow description language and execution engine (www.taverna.org.uk) is used for orchestrating complex data processing tasks.

The National Alliance for Medical Image Computing, a roadmap initiative to build a free and open source software infrastructure for translational research in medical image analysis

The National Alliance for Medical Image Computing (NA-MIC), is a multi-institutional, interdisciplinary community of researchers, who share the recognition that modern health care demands improved technologies to ease suffering and prolong productive life. Organized under the National Centers for Biomedical Computing 7 years ago, the mission of NA-MIC is to implement a robust and flexible open-source infrastructure for developing and applying advanced imaging technologies across a range of important biomedical research disciplines. A measure of its success, NA-MIC is now applying this technology to diseases that have immense impact on the duration and quality of life: cancer, heart disease, trauma, and degenerative genetic diseases. The targets of this technology range from group comparisons to subject-specific analysis.