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BioCompute Object
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 (HTS -- also referred to as next-generation sequencing or massively parallel sequencing). The project has since beestandardizedas IEEE 2791-2020, and the project files are maintained in aopen source repository ThJuly 22nd, 2020 editionof the Federal Register announced that the FDA now supports the use of BioCompute (officially known as IEEE 2791-2020) in regulatory submissions, and the inclusion of the standard in the Data Standards Catalog for the submission of HTS data iNDAs, ANDAs, BLAs, and INDsto 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Common Workflow Language
The Common Workflow Language (CWL) is a standard for describing computational data-analysis workflows. Development of CWL is focused particularly on serving the data-intensive sciences, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. A key goal of the CWL is to allow the creation of a workflow that is portable and thus may be run reproducibly in different computational environments. The CWL originated from discussions in 2014 betweePeter Amstutz an Michael R. Crusoe (at that time their respective affiliations were: [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Interoperability
Interoperability is a characteristic of a product or system to work with other products or systems. While the term was initially defined for information technology or systems engineering services to allow for information exchange, a broader definition takes into account social, political, and organizational factors that impact system-to-system performance. Types of interoperability include syntactic interoperability, where two systems can communicate with each other, and cross-domain interoperability, where multiple organizations work together and exchange information. Types If two or more systems use common data formats and communication protocols and are capable of communicating with each other, they exhibit ''syntactic interoperability''. XML and SQL are examples of common data formats and protocols. Lower-level data formats also contribute to syntactic interoperability, ensuring that alphabetical characters are stored in the same ASCII or a Unicode format in all the commun ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Software
The list of bioinformatics software tools can be split up according to the license used: *List of proprietary bioinformatics software *List of open-source bioinformatics software Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: *Sequence analysis software **List of sequence alignment software ** List of alignment visualization software **Alignment-free sequence analysis **De novo sequence assemblers **List of gene prediction software ** List of disorder prediction software ** List of Protein subcellular localization prediction tools **List of phylogenetics software **List of phylogenetic tree visualization software ** :Metagenomics_software *Structural biology software **List of molecular graphics systems **List of protein-ligand docking software **List of RNA structure prediction software **List of software for protein model error verification **List of protein secondary structure prediction programs **List of protein struct ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Galaxy (computational Biology)
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system. Functionality Galaxy is a scientific workflow system. These systems provide a means to build multi-step computational analyses akin to a recipe. They typically provide a graphical user interface for specifying what data to operate on, what steps to take, and what order to do them in. Galaxy is also a data integration platform for biological data. It supports data uploads from the user's computer, by URL, and directly from many online resources (such as the UCSC Genome Browser, BioMart and InterMine). Galaxy supports a range of widely used biological data ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Standard
An open standard is a standard that is openly accessible and usable by anyone. It is also a prerequisite to use open license, non-discrimination and extensibility. Typically, anybody can participate in the development. There is no single definition, and interpretations vary with usage. The terms ''open'' and ''standard'' have a wide range of meanings associated with their usage. There are a number of definitions of open standards which emphasize different aspects of openness, including the openness of the resulting specification, the openness of the drafting process, and the ownership of rights in the standard. The term "standard" is sometimes restricted to technologies approved by formalized committees that are open to participation by all interested parties and operate on a consensus basis. The definitions of the term ''open standard'' used by academics, the European Union, and some of its member governments or parliaments such as Denmark, France, and Spain preclude open standard ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
High-performance Integrated Virtual Environment
ThHigh-performance Integrated Virtual Environment(HIVE) is a distributed computing environment used for healthcare-IT and biological research, including analysis of Next Generation Sequencing (NGS) data, preclinical, clinical and post market data, adverse events, metagenomic data, etc. Currently it is supported and continuously developed by US Food and Drug Administration (government domain), George Washington University (academic domain), and by DNA-HIVE, WHISE-Global and Embleema (commercial domain). HIVE currently operates fully functionally within the US FDA supporting wide variety (+60) of regulatory research and regulatory review projects as well as for supporting MDEpiNet medical device postmarket registries. Academic deployments of HIVE are used for research activities and publications in NGS analytics, cancer research, microbiome research and in educational programs for students at GWU. Commercial enterprises use HIVE for oncology, microbiology, vaccine manufacturing, gene ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cloud Computing
Cloud computing is the on-demand availability of computer system resources, especially data storage ( cloud storage) and computing power, without direct active management by the user. Large clouds often have functions distributed over multiple locations, each of which is a data center. Cloud computing relies on sharing of resources to achieve coherence and typically uses a "pay as you go" model, which can help in reducing capital expenses but may also lead to unexpected operating expenses for users. Value proposition Advocates of public and hybrid clouds claim that cloud computing allows companies to avoid or minimize up-front IT infrastructure costs. Proponents also claim that cloud computing allows enterprises to get their applications up and running faster, with improved manageability and less maintenance, and that it enables IT teams to more rapidly adjust resources to meet fluctuating and unpredictable demand, providing burst computing capability: high computing p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amazon Elastic Compute Cloud
Amazon Elastic Compute Cloud (EC2) is a part of Amazon.com's cloud-computing platform, Amazon Web Services (AWS), that allows users to rent virtual computers on which to run their own computer applications. EC2 encourages scalable deployment of applications by providing a web service through which a user can boot an Amazon Machine Image (AMI) to configure a virtual machine, which Amazon calls an "instance", containing any software desired. A user can create, launch, and terminate server-instances as needed, paying by the second for active servershence the term "elastic". EC2 provides users with control over the geographical location of instances that allows for latency optimization and high levels of redundancy. In November 2010, Amazon switched its own retail website platform to EC2 and AWS. History Amazon announced a limited public beta test of EC2 on August 25, 2006, offering access on a first-come, first-served basis. Amazon added two new instance types (Large and Extra- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amazon Web Services
Amazon Web Services, Inc. (AWS) is a subsidiary of Amazon.com, Amazon that provides Software as a service, on-demand cloud computing computing platform, platforms and Application programming interface, APIs to individuals, companies, and governments, on a metered pay-as-you-go basis. These cloud computing web services provide distributed computing processing capacity and software tools via AWS server farms. One of these services is Amazon Elastic Compute Cloud (EC2), which allows users to have at their disposal a Virtualization, virtual Computer cluster, cluster of computers, available all the time, through the Internet. AWS's virtual computers emulate most of the attributes of a real computer, including hardware central processing units (CPUs) and graphics processing units (GPUs) for processing; local/Random-access memory, RAM memory; hard-disk/Solid-state drive, SSD storage; a choice of operating systems; networking; and pre-loaded application software such as web servers, dat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source Software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open-source software may be developed in a collaborative public manner. Open-source software is a prominent example of open collaboration, meaning any capable user is able to participate online in development, making the number of possible contributors indefinite. The ability to examine the code facilitates public trust in the software. Open-source software development can bring in diverse perspectives beyond those of a single company. A 2008 report by the Standish Group stated that adoption of open-source software models has resulted in savings of about $60 billion per year for consumers. Open source code can be used for studying and allows capable end users to adapt software to their personal needs in a similar way user scripts an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Public–private Partnership
A public–private partnership (PPP, 3P, or P3) is a long-term arrangement between a government and private sector institutions.Hodge, G. A and Greve, C. (2007), Public–Private Partnerships: An International Performance Review, Public Administration Review, 2007, Vol. 67(3), pp. 545–558 Typically, it involves private capital financing government projects and services up-front, and then drawing revenues from taxpayers and/or users over the course of the PPP contract. Public–private partnerships have been implemented in multiple countries and are primarily used for infrastructure projects. They have been employed for building, equipping, operating and maintaining schools, hospitals, transport systems, and water and sewerage systems. Cooperation between private actors, corporations and governments has existed since the inception of sovereign states, notably for the purpose of tax collection and colonization. However, contemporary "public-private partnerships" came into being ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FHIR
The Fast Healthcare Interoperability Resources' (FHIR, pronounced "fire") standard is a set of rules and specifications for exchanging electronic health care data. It is designed to be flexible and adaptable, so that it can be used in a wide range of settings and with different health care information systems. The goal of FHIR is to enable the seamless and secure exchange of health care information, so that patients can receive the best possible care. The standard describes data formats and elements (known as "resources") and an application programming interface (API) for exchanging electronic health records (EHR). The standard was created by the Health Level Seven International (HL7) health-care standards organization. FHIR builds on previous data format standards from HL7, like HL7 version 2.x and HL7 version 3.x. But it is easier to implement because it uses a modern web-based suite of API technology, including a HTTP-based RESTful protocol, and a choice of JSON, XML or RDF ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
