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标准类型：国际电工委员会标准

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JCoast -: A biologist-centric software tool for data mining and comparison of prokaryotic (meta) genomes

BMC BIOINFORMATICS 2008年第1期9卷 177-177页

作者： Richter, Michael Lombardot, Thierry Kostadinov, Ivaylo Kottmann, Renzo Duhaime, Melissa Beth Peplies, Joerg Gloeckner, Frank Oliver Max Planck Inst Marine Microbiol Microbial Genom Grp D-28359 Bremen Germany Jacobs Univ Bremen gGmbH D-28759 Bremen Germany Ribocon GmbH D-28359 Bremen Germany

Background: Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions. Results: The JCoast software tool was primarily designed to analyse and compare ( meta) genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets. Conclusion: JCoast combines all functions required for the mining, annotation, and interpretation of ( meta) genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage.

关键词： Graphical User interface application program interface Magnetotactic Bacterium Relational Database System Pfam Model

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The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

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BMC BIOINFORMATICS 2010年第1期11卷 5-5页

作者： van Iersel, Martijn P. Pico, Alexander R. Kelder, Thomas Gao, Jianjiong Ho, Isaac Hanspers, Kristina Conklin, Bruce R. Evelo, Chris T. Maastricht Univ Dept Bioinformat BiGCaT Maastricht Netherlands Gladstone Inst Cardiovasc Dis San Francisco CA 94158 USA Univ Missouri Dept Comp Sci Columbia MO 65201 USA Univ Calif San Francisco Dept Med San Francisco CA 94143 USA Univ Calif San Francisco Dept Cellular & Mol Pharmacol San Francisco CA 94143 USA

Background: Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. Results: Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications. Conclusion: By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://***.

关键词： application program interface Biological Entity Mapping Service Gene Identifier Database File

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A Comprehensive Review of Practical Issues for Interoperability Using the Common Information Model in Smart Grids

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ENERGIES 2020年第6期13卷 1435页

作者： Kim, Hyun Joong Jeong, Chang Min Sohn, Jin-Man Joo, Jhi-Young Donde, Vaibhav Ko, Youngmi Yoon, Yong Tae Seoul Natl Univ Dept Elect & Comp Engn Seoul 08826 South Korea Hoseo Univ Dept Elect Engn 20Hoseo Ro 79beon Gil Asan 31499 Chungcheongnam South Korea Lawrence Livermore Natl Lab Computat Engn Dept Livermore CA 94450 USA Soongsil Univ Dept Global Law 369 Sangdo Ro Seoul 06978 South Korea

Smart grids with interoperability improve grid reliability by collecting system information and transferring it to an energy management system and associated applications through a seamless end-to-end connection. To achieve interoperability, it is required to exchange the semantic information within the different domains. The international electrotechnical commission has established the Common Information Model (CIM) tool, which is a standard application programming interface for the exchange of semantic information in power systems. CIM provides a robust framework for accurate data sharing, merging, and transformation into reusable information. However, as CIM provides a basic framework for information exchange, various practical issues arise in establishing an energy management system capable of exchanging information using CIM. This paper aims to offer a comprehensive understanding by summarizing and categorizing the research on the practical use of CIM for interoperability in smart grids. Many papers are analyzed and the issues are classified into CIM extension, harmonization, and validation to address the issues that arise when establishing an integrated information exchange system.

关键词： interoperability common information model IEC 61970 IEC 61968 IEC 61850 model extension harmonization validation application program interface

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A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

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BMC BIOINFORMATICS 2011年第1期12卷 1-13页

作者： Luna, Augustin Karac, Evrim I. Sunshine, Margot Chang, Lucas Nussinov, Ruth Aladjem, Mirit I. Kohn, Kurt W. NCI Mol Pharmacol Lab Ctr Canc Res NIH Bethesda MD 20892 USA Boston Univ Bioinformat Program Boston MA 02215 USA Bogazici Univ Dept Comp Engn TR-80815 Bebek Turkey NCI Ctr Canc Res Nanobiol Program SAIC Frederick Inc Frederick MD 21702 USA Tel Aviv Univ Dept Human Genet & Mol Med Sackler Sch Med IL-69978 Tel Aviv Israel

Background: The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. Results: A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. Conclusions: The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://***/mim.

关键词： application program interface Glyph Document Object Model Syntax Rule System Biology Graphical Notation

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An IoT-Based Solution for Monitoring and Controlling Battery Energy Storage Systems at Residential and Commercial Levels

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ENERGIES 2023年第7期16卷 3140页

作者： Burgio, Alessandro Cimmino, Domenico Nappo, Andrea Smarrazzo, Luigi Donatiello, Giuseppe Evolvere SpA Benefit Co Dept Innovat & Operat I-20124 Milan Italy

Today, increasing numbers of batteries are installed in residential and commercial buildings;by coordinating their operation, it is possible to favor both the exploitation of renewable sources and the safe operation of electricity grids. However, how can this multitude of battery storage systems be coordinated? Using the application programming interfaces of the storage systems' manufacturers is a feasible solution, but it has a huge limitation: communication to and from storage systems must necessarily pass through the manufacturers' cloud infrastructure. Therefore, this article presents an IoT-based solution which allows monitoring/controlling battery storage systems, independently from the manufacturers' cloud infrastructure. More specifically, a home gateway locally controls the battery storage using local APIs via Wi-Fi on the condition that the manufacturer enables them. If not, an auxiliary device allows the home gateway to establish a wired communication with the battery storage via the SunSpec protocol. Validations tests demonstrate the effectiveness of the proposed IoT solution in monitoring and controlling ABB, Sonnen and SolarEdge storage systems.

关键词： IoT battery storage battery monitoring battery control energy community energy storage system cloud computing cloud platforms application program interface SunSpec

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The Gene Set Builder: collation, curation, and distribution of sets of genes

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BMC BIOINFORMATICS 2005年第1期6卷 305-305页

作者： Yusuf, D Lim, JS Wasserman, WW CMMT Child & Family Res Inst Vancouver BC Canada Univ British Columbia Dept Med Genet Vancouver BC Canada

Background: In bioinformatics and genomics, there are many applications designed to investigate the common properties for a set of genes. Often, these multi-gene analysis tools attempt to reveal sequential, functional, and expressional ties. However, while tremendous effort has been invested in developing tools that can analyze a set of genes, minimal effort has been invested in developing tools that can help researchers compile, store, and annotate gene sets in the first place. As a result, the process of making or accessing a set often involves tedious and time consuming steps such as finding identifiers for each individual gene. These steps are often repeated extensively to shift from one identifier type to another;or to recreate a published set. In this paper, we present a simple online tool which - with the help of the gene catalogs Ensembl and GeneLynx - can help researchers build and annotate sets of genes quickly and easily. Description: The Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored to facilitate easy access. Gene sets stored in the system can be "exported" in a variety of output formats - as lists of identifiers, in tables, or as sequences. In addition, gene sets can be "shared" with specific users to facilitate collaborations or fully released to provide access to published results. The application also features a Perl API (application programming interface) for direct connectivity to custom analysis tools. A downloadable Quick Reference guide and an online tutorial are available to help new users learn its functionalities. Conclusion: The Gene Set Builder is an Ensembl-facilitated online tool designed to help researchers compile and manage sets of genes

关键词： application program interface Confidence Rating Gene Identifier Staging Area Sequence Retrieval System

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libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny

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BMC BIOINFORMATICS 2005年第1期6卷 138-138页

作者： Butt, D Roger, AJ Blouin, C Dalhousie Univ Fac Comp Sci Halifax NS B3H 1W5 Canada Dalhousie Univ Dept Biochem & Mol Biol Halifax NS B3H 1X5 Canada Canadian Inst Adv Res Toronto ON Canada

Background: An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. Results: The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used to compute likelihoods, search tree topologies, estimate site rates, cluster sequences, manipulate tree structures and compare phylogenies for a broad selection of applications. Conclusion: Using this library, it is possible to rapidly prototype applications that use the sophistication of phylogenetic likelihoods without getting involved in a major software engineering project. libcov is thus a potentially valuable building block to develop in-house methodologies in the field of protein phylogenetics.

关键词： application program interface Standard Template Library Major Software Protein Phylogeny Valuable Building Block

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A taxonomic search engine: Federating taxonomic databases using web services

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BMC BIOINFORMATICS 2005年第1期6卷 48-48页

作者： Page, RDM Univ Glasgow Inst Biomed & Life Sci Div Environm & Evolutionary Biol Glasgow G12 8QQ Lanark Scotland

Background: The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results: The Taxonomic Search Engine ( TSE) is a web application written in PHP that queries multiple taxonomic databases ( ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier ( LSID) authority for the source taxonomic databases, providing globally unique identifiers ( and associated metadata) for each name. Conclusion: The Taxonomic Search Engine is available at http://***/similar to rpage/ portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.

关键词： application program interface Source Database NCBI Taxonomy Query String Median Response Time

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Synergizing human expertise and AI efficiency with language model for microscopy operation and automated experiment design

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MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2024年第2期5卷 02LT01页

作者： Liu, Yongtao Checa, Marti Vasudevan, Rama K. Oak Ridge Natl Lab Ctr Nanophase Mat Sci Oak Ridge TN 37830 USA

With the advent of large language models (LLMs), in both the open source and proprietary domains, attention is turning to how to exploit such artificial intelligence (AI) systems in assisting complex scientific tasks, such as material synthesis, characterization, analysis and discovery. Here, we explore the utility of LLMs, particularly ChatGPT4, in combination with application program interfaces (APIs) in tasks of experimental design, programming workflows, and data analysis in scanning probe microscopy, using both in-house developed APIs and APIs given by a commercial vendor for instrument control. We find that the LLM can be especially useful in converting ideations of experimental workflows to executable code on microscope APIs. Beyond code generation, we find that the GPT4 is capable of analyzing microscopy images in a generic sense. At the same time, we find that GPT4 suffers from an inability to extend beyond basic analyses for more in-depth technical experimental design. We argue that an LLM specifically fine-tuned for individual scientific domains can potentially be a better language interface for converting scientific ideations from human experts to executable workflows. Such a synergy between human expertise and LLM efficiency in experimentation can open new doors for accelerating scientific research, enabling effective experimental protocols sharing in the scientific community.

关键词： automated experiment microscopy language model application program interface

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