A DevOps toolchain is a set or combination of tools that aid in the delivery, development, and management of software applications throughout the systems development life cycle, as coordinated by an organization that uses DevOps practices. Generally, DevOps tools fit into one or more activities, which supports specific DevOps initiatives: Plan, Create, Verify, Package, Release, Configure, Monitor, and Version Control. == Toolchains == In software, a toolchain is the set of programming tools that is used to perform a complex software development task or to create a software product, which is typically another computer program or a set of related programs. In general, the tools forming a toolchain are executed consecutively so the output or resulting environment state of each tool becomes the input or starting environment for the next one, but the term is also used when referring to a set of related tools that are not necessarily executed consecutively. As DevOps is a set of practices that emphasizes the collaboration and communication of both software developers and other information technology (IT) professionals, while automating the process of software delivery and infrastructure changes, its implementation can include the definition of the series of tools used at various stages of the lifecycle; because DevOps is a cultural shift and collaboration between development and operations, there is no one product that can be considered a single DevOps tool. Instead a collection of tools, potentially from a variety of vendors, are used in one or more stages of the lifecycle. == Stages of DevOps == === Plan === Plan consists of two elements: "define" and "plan". This activity refers to the business value and application requirements. Specifically "Plan" activities include: Production metrics, objects and feedback Requirements Business metrics Update release metrics Release plan, timing and business case Security policy and requirement A combination of the IT personnel will be involved in these activities: business application owners, software development, software architects, continual release management, security officers and the organization responsible for managing the production of IT infrastructure. === Create === Create consists of the building, coding, and configuring of the software development process. The specific activities are: Design of the software and configuration Coding including code quality and performance Software build and build performance Release candidate Tools and vendors in this category often overlap with other categories. Because DevOps is about breaking down silos, this is reflective in the activities and product solutions. === Verify === Verify is directly associated with ensuring the quality of the software release; activities designed to ensure code quality is maintained and the highest quality is deployed to production. The main activities in this are: Acceptance testing Regression testing Security and vulnerability analysis Performance Configuration testing Solutions for verify-related activities generally fall under four main categories: Test automation, Static analysis, Test Lab, and Security. === Package === Package refers to the activities involved once the release is ready for deployment, often also referred to as staging or Preproduction / "preprod". This often includes tasks and activities such as: Approval/preapprovals Package configuration Triggered releases Release staging and holding === Release === Release related activities include schedule, orchestration, provisioning and deploying software into production and targeted environment. The specific Release activities include: Release coordination Deploying and promoting applications Fallbacks and recovery Scheduled/timed releases Solutions that cover this aspect of the toolchain include application release automation, deployment automation and release management. === Configure === Configure activities fall under the operation side of DevOps. Once software is deployed, there may be additional IT infrastructure provisioning and configuration activities required. Specific activities including: Infrastructure storage, database and network provisioning and configuring Application provision and configuration. The main types of solutions that facilitate these activities are continuous configuration automation, configuration management, and infrastructure as code tools. === Monitor === Monitoring is an important link in a DevOps toolchain. It allows IT organization to identify specific issues of specific releases and to understand the impact on end-users. A summary of Monitor related activities are: Performance of IT infrastructure End-user response and experience Production metrics and statistics Information from monitoring activities often impacts Plan activities required for changes and for new release cycles. === Version Control === Version Control is an important link in a DevOps toolchain and a component of software configuration management. Version Control is the management of changes to documents, computer programs, large web sites, and other collections of information. A summary of Version Control related activities are: Non-linear development Distributed development Compatibility with existent systems and protocols Toolkit-based design Information from Version Control often supports Release activities required for changes and for new release cycles.
Distributed concurrency control
Distributed concurrency control is the concurrency control of a system distributed over a computer network (Bernstein et al. 1987, Weikum and Vossen 2001). In database systems and transaction processing (transaction management) distributed concurrency control refers primarily to the concurrency control of a distributed database. It also refers to the concurrency control in a multidatabase (and other multi-transactional object) environment (e.g., federated database, grid computing, and cloud computing environments. A major goal for distributed concurrency control is distributed serializability (or global serializability for multidatabase systems). Distributed concurrency control poses special challenges beyond centralized one, primarily due to communication and computer latency. It often requires special techniques, like distributed lock manager over fast computer networks with low latency, like switched fabric (e.g., InfiniBand). The most common distributed concurrency control technique is strong strict two-phase locking (SS2PL, also named rigorousness), which is also a common centralized concurrency control technique. SS2PL provides both the serializability and strictness. Strictness, a special case of recoverability, is utilized for effective recovery from failure. For large-scale distribution and complex transactions, distributed locking's typical heavy performance penalty (due to delays, latency) can be saved by using the atomic commitment protocol, which is needed in a distributed database for (distributed) transactions' atomicity.
The Cancer Imaging Archive
The Cancer Imaging Archive (TCIA) is an open-access database of medical images for cancer research. The site is funded by the National Cancer Institute's (NCI) Cancer Imaging Program, and the contract is operated by the University of Arkansas for Medical Sciences. Data within the archive is organized into collections which typically share a common cancer type and/or anatomical site. The majority of the data consists of CT, MRI, and nuclear medicine (e.g. PET) images stored in DICOM format, but many other types of supporting data are also provided or linked to, in order to enhance research utility. All data are de-identified in order to comply with the Health Insurance Portability and Accountability Act and National Institutes of Health data sharing policies. TCIA resources are intended to support: Development of computer aided diagnosis methods (quantitative imaging) Evaluation of unbiased science reproducibility by acceptable standard statistical methods Research on correlation of clinical diagnostic medical images with digital microscopic histological images Exploratory biomarker research for which imaging is a key element Collaboration between cross-disciplinary investigators where imaging is crucial to research on tumor heterogeneity, between patients and within the tumor; tissue temporal response tracking - objective measurements of tumor progression; imaging genomics and Big Data linkages and analysis (clinical, histo-pathology, genomics) TCIA is recognized as a recommended repository for the Scientific Data, PLOS One, and F1000Research journals. It is also listed in the Registry of Research Data Repositories. == History == Prior to the creation of TCIA, the NCI funded development of the National Biomedical Imaging Archive. NBIA is an open-source Web application which was designed to allow the storage and query of DICOM images. TCIA was subsequently initiated in December 2010 to expand data sharing activities by funding a service component which would help address the technical and policy challenges associated with medical imaging research. TCIA leverages open-source tools such as NBIA and Clinical Trials Processor in order to provide its services. == Organization of the archive == The site content is organized into five categories: About Us - Provides a general overview of the site the organizations responsible for operating it. Share Your Data - Provides an overview of how to apply to upload data to the archive. Access the Archive - Provides information about the available data, methods for accessing that data and system usage metrics. Research Activities - Provides information about major research initiatives being conducted using TCIA data as well as information about publication guidelines. Help - Provides information about how to get support using the archive as well as documentation and data usage policies. == Methods for accessing data == Most collections on the Cancer Imaging Archive can be accessed without an account, but a few are restricted to specific users and therefore require an account to access them. TCIA has several ways to browse, filter, and download data. They include: Downloading the entire contents of a collection in bulk Leveraging the NBIA application to filter or search within or across collections Utilizing the RESTful Application programming interface to filter or search within or across collections === Browsing, bulk downloading and access to supporting data === The home page includes a list of all available collections. Basic information about the data such as the cancer type, cancer location, modalities, and number of subjects are also provided. Clicking on a collection name presents a page which describes the data including its original research purpose, how the data were generated, and how it might be useful to other TCIA users. For example, doi:10.7937/K9/TCIA.2015.L4FRET6Z describes the NSCLC-Radiomics-Genomics Collection. In the lower section of the page there are links to search or download the images and any available supporting data in the Data Access tab. Additional tabs provide information about data versions and how to cite the data if used in publications. Many collections contain additional data types such as genomics, patient demographics, treatment details, and expert analyses of the images. This data is usually only found by browsing the collection pages as opposed to searching in NBIA or using the API. === Filtering or searching with NBIA === On each Collection page and also in the main menu of the site there are links to "Search TCIA". This will load the NBIA application which allows simple, advanced and free text searches. Search results follow the conventional DICOM hierarchy of patient -> study -> series. TCIA provides comprehensive documentation on the various features of the NBIA software. === RESTful API === A number of search and download commands are also available through the API. New iterations on the API are released as new versions, so that existing applications developed against older versions of the API continue to function. == Research activities == A list of known publications based on TCIA data is maintained as a convenience to researchers who might want to investigate how it has been used previously. In addition to peer-reviewed publications there are also several major research initiatives described in the Research Activities section of the site. === The CIP TCGA Radiology Initiative for Radiogenomics Research === A large number of collections contain subjects which were analyzed as part of the NIH/NHGRI database known as The Cancer Genome Atlas (TCGA). This offers researchers the ability to correlate clinical images using shared unique identifiers each study that has in TCGA extensive genomic analysis, digital pathology slides and bulk download of individual demographic data and clinical data. A multi-institutional network of investigators volunteering their time is using the data to develop methods to determine prognosis or predict the response to therapy. TCGA collections are designated by nomenclature shared by the TCGA Data Portal (e.g.: TCGA-BRCA, TCGA-GBM, etc). They are subject to a special publication policy which is unique from the other public data on TCIA. === Challenge competitions === TCIA also provides specific data sets used for "Challenge" competitions such as international digital image-focused professional societies like MICCAI, SPIE, or ISBI. A directory of previous and upcoming challenges is maintained on the site. === Digital object identifiers === To facilitate data sharing, many publications encourage authors to include data citations to the data that the authors used in creating the results described in their scholarly papers. In addition, new journals are now available for describing data collections outright (e.g., Nature Scientific Data). TCIA assigns digital object identifiers (DOIs) to all collections when they are submitted, and also has the ability to create persistent identifiers linked to subsets of data held within TCIA that authors may use for data citations in their scholarly papers.
Web-based simulation
Web-based simulation (WBS) is the invocation of computer simulation services over the World Wide Web, specifically through a web browser. Increasingly, the web is being looked upon as an environment for providing modeling and simulation applications, and as such, is an emerging area of investigation within the simulation community. == Application == Web-based simulation is used in several contexts: In e-learning, various principles can quickly be illustrated to students by means of interactive computer animations, for example during lecture demonstrations and computer exercises. In distance learning, web-based simulation may provide an alternative to installing expensive simulation software on the student computer, or an alternative to expensive laboratory equipment. In software engineering, web-based emulation allows application development and testing on one platform for other target platforms, for example for various mobile operating systems or mobile web browsers, without the need of target hardware or locally installed emulation software. In online computer games, 3D environments can be simulated, and old home computers and video game consoles can be emulated, allowing the user to play old computer games in the web browser. In medical education, nurse education and allied health education (like sonographer training), web-based simulations can be used for learning and practicing clinical healthcare procedures. Web-based procedural simulations emphasize the cognitive elements such as the steps of the procedure, the decisions, the tools/devices to be used, and the correct anatomical location. == Client-side vs server-side approaches == Web-based simulation can take place either on the server side or on the client side. In server-side simulation, the numerical calculations and visualization (generation of plots and other computer graphics) is carried out on the web server, while the interactive graphical user interface (GUI) often partly is provided by the client-side, for example using server-side scripting such as PHP or CGI scripts, interactive services based on Ajax or a conventional application software remotely accessed through a VNC Java applet. In client-side simulation, the simulation program is downloaded from the server side but completely executed on the client side, for example using Java applets, Flash animations, JavaScript, or some mathematical software viewer plug-in. Server-side simulation is not scalable for many simultaneous users, but places fewer demands on the user computer performance and web-browser plug-ins than client-side simulation. The term on-line simulation sometimes refers to server-side web-based simulation, sometimes to symbiotic simulation, i.e. a simulation that interacts in real-time with a physical system. The upcoming cloud-computing technologies can be used for new server-side simulation approaches. For instance, there are multi-agent-simulation applications which are deployed on cloud-computing instances and act independently. This allows simulations to be highly scalable. == Existing tools == AgentSheets – graphically programmed tool for creating web-based The Sims-like simulation games, and for teaching beginner students programming. AnyLogic – a graphically programmed tool that generates Java code for discrete-event simulation, system dynamics and agent-based models Easy Java Simulations – a tool for modelling and visualization of physical phenomenons, that automatically generates Java code from mathematical expressions. ExploreLearning Gizmos – a large library of interactive online simulations for math and science education in grades 3–12. FreeFem++ Javascript Version – FreeFem++ is a free and open source PDE solver using the finite element method. GNU Octave web interfaces – MATLAB compatible open-source software Lanner Group Ltd L-SIM Server – Java-based discrete-event simulation engine which supports model standards such as BPMN 2.0 Nanohub – web 2.0 in-browser interactive simulation of nanotechnology NetLogo – a multi-agent programming language and integrated modeling environment that runs on the Java Virtual Machine OpenPlaG – PHP-based function graph plotter for the use on websites OpenEpi – web-based packet of tools for biostatistics Recursive Porous Agent Simulation Toolkit (Repast) – agent-based modeling and simulation toolkit implemented in Java and many other languages SageMath – open-source numerical-analysis software with web interface, based on the Python programming language SimScale – web-based simulation platform supporting computational fluid dynamics, solid mechanics, and thermodynamics StarLogo – agent-based simulation language written in Java. VisSim viewer – graphically programmed data-flow diagrams for simulation of dynamical systems webMathematica and Mathematica Player – a computer algebra system and programming language. VisualSim Architect – VisualSim Explorer enables system-level models to be embedded in documents for viewing, simulation and analysis from within a web browser without any local software installation.
Apache Hama
Apache Hama is a distributed computing framework based on bulk synchronous parallel computing techniques for massive scientific computations e.g., matrix, graph and network algorithms. Originally a sub-project of Hadoop, it became an Apache Software Foundation top level project in 2012. It was created by Edward J. Yoon, who named it (short for "Hadoop Matrix Algebra"), and Hama also means hippopotamus in Yoon's native Korean language (하마), following the trend of naming Apache projects after animals and zoology (such as Apache Pig). Hama was inspired by Google's Pregel large-scale graph computing framework described in 2010. When executing graph algorithms, Hama showed a fifty-fold performance increase relative to Hadoop. Retired in April 2020, project resources are made available as part of the Apache Attic. Yoon cited issues of installation, scalability, and a difficult programming model for its lack of adoption. == Architecture == Hama consists of three major components: BSPMaster, GroomServers and Zookeeper. === BSPMaster === BSPMaster is responsible for: Maintaining groom server status Controlling super steps in a cluster Maintaining job progress information Scheduling jobs and assigning tasks to groom servers Disseminating execution class across groom servers Controlling fault Providing users with the cluster control interface. A BSP Master and multiple grooms are started by the script. Then, the bsp master starts up with a RPC server for groom servers. Groom servers starts up with a BSPPeer instance and a RPC proxy to contact the bsp master. After started, each groom periodically sends a heartbeat message that encloses its groom server status, including maximum task capacity, unused memory, and so on. Each time the BSP master receives a heartbeat message, it brings the groom server status up-to-date. The bsp master makes use of groom servers' status in order to assign tasks to idle groom servers - and returns a heartbeat response containing assigned tasks and others actions for a groom server to do. Currently BSP master has a FIFO job scheduler and simple task assignment algorithms. === GroomServer === A groom server (shortly referred to as groom) is a process that performs BSP tasks assigned by BSPMaster. Each groom contacts the BSPMaster, and it takes assigned tasks and reports its status by means of periodical piggybacks with BSPMaster. Each groom is designed to run with HDFS or other distributed storages. Basically, a groom server and a data node should be run on one physical node. === Zookeeper === A Zookeeper is used to manage the efficient barrier synchronisation of the BSPPeers.
The Outliner of Giants
The Outliner of Giants was commercial outlining software. Like other outliners, it allowed the user to create a document consisting of a series of nested lists. It was one of a number of browser-based outliners that are delivered as a web application, used through a web browser, rather than being installed as a stand-alone application. The Outliner of Giants was released in 2009. The service was shut down on December 31, 2017 and only exports are allowed at this time. == Feature set == Unlike most other browser-based outliners - which often focus on providing a minimum viable product - the Outliner of Giants had much of the functionality typically associated with a desktop outliner, such as the ability to use of columns to structure information. However, The Outliner of Giants did not support offline editing, requiring an active internet connection in order to make changes to an outline document. === Outlining === Like all outliners, The Outliner of Giants supported the creation of a hierarchy of items, with users modifying the parent-child relationship between items in order to structure a document. This included the ability to promote or demote items up or down the hierarchy, or move an item up or down a list of siblings on the same level. The Outliner of Giants did not support the true cloning of items (where an item can appear to be in multiple places within the hierarchy at the same time), although it did support the copying of single or multiple nodes. === Import === The Outliner of Giants could import both plain text and the OPML XML format, which is commonly used to transfer data between outlining applications. === Editing === Outline documents could be edited using a WYSIWYG editor, as well as the Markdown, and Textile markup languages. === Annotation === The Outliner of Giants supported functions to annotate an outline, such as the ability to add colored labels, highlights and text, as well as tags and hashtags. === Collaboration === The Outliner of Giants supported real-time collaboration, where multiple users could edit the same document, and can see the changes made by another user as they happened. === Publication === Outlines created through The Outliner of Giants could be published directly online through the service, either as outlines, pages or in a blog format. === Export === The Outliner of Giants can export outline data as plain text, HTML, as well as directly to the Google Docs word processor.
European Cloud Partnership
The European Cloud Partnership (ECP) is an advisory group set up by the European Commission as part of the European Cloud Computing Strategy to provide guidance on the development of cloud computing in the European Union. The ECP is led by a steering board composed of representatives of the IT and telecom industry as well as European government policymakers. == History == After publishing a document, "Unleashing the Potential of Cloud Computing in Europe", the European Commission set up the European Cloud Partnership in 2012, with a steering board including both government and industry representatives. The ECP's first meeting was held on 19 November 2012; it was chaired by the President of Estonia Toomas Hendrik Ilves. In 2013 the ECP began drafting its charter. That year, as information about the PRISM scandal came to light, the ECP emphasized the need for Europe to develop its own cloud infrastructure, rather than depend on that of the United States. It completed a report titled "Trusted Cloud Europe" in February 2014 defining its policy, and outlining a process for effective public and private sector participation in cloud computing development in Europe. The report recommended that the commission identify technical, legal and operational best practices, and promote these through certifications and guidelines, and facilitate recognition across national boundaries. The report also recommended that the commission identify cloud computing stakeholders and help them work together through consultations and workshops. In March 2014, the European Commission invited external parties to submit opinions, take part in a discussion forum and complete an online survey in response to the report.