Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques.
Checkpointing is a technique that provides fault tolerance for computing systems. It basically consists of saving a snapshot of the application's state, so that applications can restart from that point in case of failure. This is particularly important for the long running applications that are executed in the failure-prone computing systems.
Utility computing or The Computer Utility is a service provisioning model in which a service provider makes computing resources and infrastructure management available to the customer as needed, and charges them for specific usage rather than a flat rate. Like other types of on-demand computing, the utility model seeks to maximize the efficient use of resources and/or minimize associated costs. Utility is the packaging of system resources, such as computation, storage and services, as a metered service. This model has the advantage of a low or no initial cost to acquire computer resources; instead, resources are essentially rented.
Apache Hadoop is a collection of open-source software utilities that facilitates using a network of many computers to solve problems involving massive amounts of data and computation. It provides a software framework for distributed storage and processing of big data using the MapReduce programming model. Hadoop was originally designed for computer clusters built from commodity hardware, which is still the common use. It has since also found use on clusters of higher-end hardware. All the modules in Hadoop are designed with a fundamental assumption that hardware failures are common occurrences and should be automatically handled by the framework.
Desktop virtualization is a software technology that separates the desktop environment and associated application software from the physical client device that is used to access it.
Ceph is an open-source software storage platform, implements object storage on a single distributed computer cluster, and provides 3-in-1 interfaces for object-, block- and file-level storage. Ceph aims primarily for completely distributed operation without a single point of failure, scalable to the exabyte level, and freely available.
In computing, virtualization or virtualisation is the act of creating a virtual version of something, including virtual computer hardware platforms, storage devices, and computer network resources.
Cloud computing is the on-demand availability of computer system resources, especially data storage and computing power, without direct active management by the user. The term is generally used to describe data centers available to many users over the Internet. Large clouds, predominant today, often have functions distributed over multiple locations from central servers. If the connection to the user is relatively close, it may be designated an edge server.
Eucalyptus is a paid and open-source computer software for building Amazon Web Services (AWS)-compatible private and hybrid cloud computing environments, originally developed by the company Eucalyptus Systems. Eucalyptus is an acronym for Elastic Utility Computing Architecture for Linking Your Programs To Useful Systems. Eucalyptus enables pooling compute, storage, and network resources that can be dynamically scaled up or down as application workloads change. Mårten Mickos was the CEO of Eucalyptus. In September 2014, Eucalyptus was acquired by Hewlett-Packard and then maintained by DXC Technology. After DXC stopped developing the product in late 2017, AppScale Systems forked the code and started supporting Eucalyptus customers.
Luminex Software, Inc. is a developer and provider of mainframe connectivity, storage and data protection solutions, including virtual tape and data integration products.
Data-intensive computing is a class of parallel computing applications which use a data parallel approach to process large volumes of data typically terabytes or petabytes in size and typically referred to as big data. Computing applications which devote most of their execution time to computational requirements are deemed compute-intensive, whereas computing applications which require large volumes of data and devote most of their processing time to I/O and manipulation of data are deemed data-intensive.
IBM cloud computing is a set of cloud computing services for business offered by the information technology company IBM. IBM Cloud includes infrastructure as a service (IaaS), software as a service (SaaS) and platform as a service (PaaS) offered through public, private and hybrid cloud delivery models, in addition to the components that make up those clouds.
Software-defined storage (SDS) is a marketing term for computer data storage software for policy-based provisioning and management of data storage independent of the underlying hardware. Software-defined storage typically includes a form of storage virtualization to separate the storage hardware from the software that manages it. The software enabling a software-defined storage environment may also provide policy management for features such as data deduplication, replication, thin provisioning, snapshots and backup.
The Neuroimaging Tools and Resources Collaboratory is a neuroimaging informatics knowledge environment for MR, PET/SPECT, CT, EEG/MEG, optical imaging, clinical neuroinformatics, imaging genomics, and computational neuroscience tools and resources.
Cloud management is the management of cloud computing products and services.
Computation offloading is the transfer of resource intensive computational tasks to a separate processor, such as a hardware accelerator, or an external platform, such as a cluster, grid, or a cloud. Offloading to a coprocessor can be used to accelerate applications including; image rendering and mathematical calculations. Offloading computing to an external platform over a network can provide computing power and overcome hardware limitations of a device, such as limited computational power, storage, and energy.
PrecisionFDA is a secure, collaborative, high-performance computing platform that has established a growing community of experts around the analysis of biological datasets in order to advance precision medicine, inform regulatory science, and enable improvements in health outcomes. This cloud-based platform is developed and served by the United States Food and Drug Administration (FDA). PrecisionFDA connects experts, citizen scientists, and scholars from around the world and provides them with a library of computational tools, workflow features, and reference data. The platform allows researchers to upload and compare data against reference genomes, and execute bioinformatic pipelines. The variant call file (VCF) comparator tool also enables users to compare their genetic test results to reference genomes. The platform's code is open source and available on GitHub. The platform also features a crowdsourcing model to sponsor community challenges in order to stimulate the development of innovative analytics that inform precision medicine and regulatory science. Community members from around the world come together to participate in scientific challenges, solving problems that demonstrate the effectiveness of their tools, testing the capabilities of the platform, sharing their results, and engaging the community in discussions. Globally, precisionFDA has more than 5,000 users.
The BioCompute Object (BCO) Project is a community-driven initiative to build a framework for standardizing and sharing computations and analyses generated from High-throughput sequencing. The project has since been standardized as IEEE 2791-2020, and the project files are maintained in an open source repository. The July 22nd, 2020 edition of the Federal Register announced that the FDA now supports the use of BioCompute in regulatory submissions, and the inclusion of the standard in the Data Standards Catalog for the submission of HTS data in NDAs, ANDAs, BLAs, and INDs to CBER, CDER, and CFSAN.
Originally started as a collaborative contract between the George Washington University and the Food and Drug Administration, the project has grown to include over 20 universities, biotechnology companies, public-private partnerships and pharmaceutical companies including Seven Bridges and Harvard Medical School. The BCO aims to ease the exchange of HTS workflows between various organizations, such as the FDA, pharmaceutical companies, contract research organizations, bioinformatic platform providers, and academic researchers. Due to the sensitive nature of regulatory filings, few direct references to material can be published. However, the project is currently funded to train FDA Reviewers and administrators to read and interpret BCOs, and currently has 4 publications either submitted or nearly submitted.
Alluxio is an open-source virtual distributed file system (VDFS). Initially as research project "Tachyon", Alluxio was created at the University of California, Berkeley's AMPLab as Haoyuan Li's Ph.D. Thesis, advised by Professor Scott Shenker & Professor Ion Stoica. Alluxio sits between computation and storage in the big data analytics stack. It provides a data abstraction layer for computation frameworks, enabling applications to connect to numerous storage systems through a common interface. The software is published under the Apache License.
