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NeuroTerrain - a client-server system for browsing 3D biomedical image data sets

BMC BIOINFORMATICS 2007年第1期8卷 40-40页

作者： Gustafson, Carl Bug, William J. Nissanov, Jonathan Drexel Univ Coll Med Lab Bioimaging & Anat Informat Dept Neurobiol & Anat Philadelphia PA 19129 USA

Background: Three dimensional biomedical image sets are becoming ubiquitous, along with the canonical atlases providing the necessary spatial context for analysis. To make full use of these 3D image sets, one must be able to present views for 2D display, either surface renderings or 2D cross-sections through the data. Typical display software is limited to presentations along one of the three orthogonal anatomical axes (coronal, horizontal, or sagittal). However, data sets precisely oriented along the major axes are rare. To make fullest use of these datasets, one must reasonably match the atlas' orientation;this involves resampling the atlas in planes matched to the data set. Traditionally, this requires the atlas and browser reside on the user's desktop;unfortunately, in addition to being monolithic programs, these tools often require substantial local resources. In this article, we describe a network-capable, client-server framework to slice and visualize 3D atlases at off-axis angles, along with an open client architecture and development kit to support integration into complex data analysis environments. Results: Here we describe the basic architecture of a client-server 3D visualization system, consisting of a thin Java client built on a development kit, and a computationally robust, high-performance server written in ANSI C++. The Java client components (NetOStat) support arbitrary-angle viewing and run on readily available desktop computers running Mac OS X, Windows XP, or Linux as a downloadable Java application. Using the NeuroTerrain Software Development Kit (NT-SDK), sophisticated atlas browsing can be added to any Java-compatible application requiring as little as 50 lines of Java glue code, thus making it eminently re-useable and much more accessible to programmers building more complex, biomedical data analysis tools. The NT-SDK separates the interactive GUI components from the server control and monitoring, so as to support development of non-interac

关键词： application program interface Atlas Data Login Message Magnetic Resonance Microscopy Digital Atlas

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QTREDS: a Ruby on Rails-based platform for omics laboratories

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BMC BIOINFORMATICS 2014年第1-Sup期15卷 S13-S13页

作者： Palla, Piergiorgio Frau, Gianfranco Vargiu, Laura Rodriguez-Tome, Patricia Ctr Adv Studies Res & Dev Sardinia CRS4 I-09010 Loc Piscina Manna Pula Italy Univ Cagliari Dept Elect & Elect Engn DIEE I-09123 Cagliari Italy Univ Cagliari Dept Life & Environm Sci I-09042 Cagliari Italy

Background: In recent years, the experimental aspects of the laboratory activities have been growing in complexity in terms of amount and diversity of data produced, equipment used, of computer-based workflows needed to process and analyze the raw data generated. To enhance the level of quality control over the laboratory activities and efficiently handle the large amounts of data produced, a Laboratory Management Information System (LIMS) is highly-recommended. A LIMS is a complex software platform that helps researchers to have a complete knowledge of the laboratory activities at each step encouraging them to adopt good laboratory practices. Results: We have designed and implemented Quality and TRacEability Data System - QTREDS, a software platform born to address the specific needs of the CRS4 Sequencing and Genotyping Platform (CSGP). The system written in the Ruby programming language and developed using the Rails framework is based on four main functional blocks: a sample handler, a workflow generator, an inventory management system and a user management system. The wizard-based sample handler allows to manage one or multiple samples at a time, tracking the path of each sample and providing a full chain of custody. The workflow generator encapsulates a user-friendly JavaScript-based visual tool that allows users to design customized workflows even for those without a technical background. With the inventory management system, reagents, laboratory glassware and consumables can be easily added through their barcodes and minimum stock levels can be controlled to avoid shortages of essential laboratory supplies. QTREDS provides a system for privileges management and authorizations to create different user roles, each with a well-defined access profile. Conclusions: Tracking and monitoring all the phases of the laboratory activities can help to identify and troubleshoot problems more quickly, reducing the risk of process failures and their related costs. QTREDS was

关键词： application program interface Generation LIMS Laboratory Information Management System User Story Visual Tool

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An overview of the CellML API and its implementation

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BMC BIOINFORMATICS 2010年第1期11卷 1-12页

作者： Miller, Andrew K. Marsh, Justin Reeve, Adam Garny, Alan Britten, Randall Halstead, Matt Cooper, Jonathan Nickerson, David P. Nielsen, Poul F. Univ Auckland Auckland Bioengn Inst Auckland 1 New Zealand Dept Physiol Anat & Genet Oxford OX1 3PT England Univ Oxford Comp Lab Oxford OX1 3QD England Univ Auckland Dept Engn Sci Auckland 1 New Zealand

Background: CellML is an XML based language for representing mathematical models, in a machine-independent form which is suitable for their exchange between different authors, and for archival in a model repository. Allowing for the exchange and archival of models in a computer readable form is a key strategic goal in bioinformatics, because of the associated improvements in scientific record accuracy, the faster iterative process of scientific development, and the ability to combine models into large integrative models. However, for CellML models to be useful, tools which can process them correctly are needed. Due to some of the more complex features present in CellML models, such as imports, developing code ab initio to correctly process models can be an onerous task. For this reason, there is a clear and pressing need for an application programming interface (API), and a good implementation of that API, upon which tools can base their support for CellML. Results: We developed an API which allows the information in CellML models to be retrieved and/or modified. We also developed a series of optional extension APIs, for tasks such as simplifying the handling of connections between variables, dealing with physical units, validating models, and translating models into different procedural languages. We have also provided a Free/Open Source implementation of this application programming interface, optimised to achieve good performance. Conclusions: Tools have been developed using the API which are mature enough for widespread use. The API has the potential to accelerate the development of additional tools capable of processing CellML, and ultimately lead to an increased level of sharing of mathematical model descriptions.

关键词： application program interface Code Fragment System Biology Markup Language Computation Target interface Pointer

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Setup and application of a structural seismic hybrid simulation system on local area network

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Journal of Chongqing University 2012年第3期11卷 103-111页

作者：王大鹏 School of Civil Engineering Suzhou University of Science and Technology

To implement structural hybrid simulation independent of the control system of any testing equipment in civil engineering, an external command control approach is put forward. Several setup technologies and the corresponding API approaches are investigated to simultaneously combine numerical simulation with physical testing. Hybrid program technology is put forward and described in detail, using Visual C++ program to effectively and accurately control testing equipment and MATLAB program to implement numerical simulation with easy extension. The control program of testing equipment and numerical simulation program are integrated by calling MATLAB engine in Visual C++. A hybrid simulation about a full-scale six-story masonry structure is carried out. The testing results manifest that the external command control approach has the versatility because of simple hardware connection and control program independent on control software of testing equipment; powerful program function of Visual C++ and flexible program of MATLAB are integrated by hybrid program technology; hybrid simulation system provides a realistic and cost-effective testing platform that enables earthquake engineer researchers to accurately and efficiently capture the seismic performance of large or complex structures without having to carry out physical testing of the entire structure.

关键词： hybrid simulation external command control application program interface hybrid program control structural seismic testing

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A FAST FILE SYSTEM FOR UNIX

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ACM TRANSACTIONS ON COMPUTER SYSTEMS 1984年第3期2卷 181-197页

作者： MCKUSICK, MK JOY, WN LEFFLER, SJ FABRY, RS Computer Systems Research Group Computer Systems Research Group Computer Systems Research Group Computer Systems Research Group

A reimplementation of the UNIX TM file system is described. The reimplementation provides sub- stantially higher throughput rates by using more flexible allocation policies that allow better locality of reference and can be adapted to a wide range of peripheral and processor characteristics. The new file system clusters data that is sequentially accessed and provides two block sizes to allow fast access to large files while not wasting large amounts of space for small files. File access rates of up to ten times faster than the traditional UNIX file system are experienced. Long-needed enhancements to the programmers" interface are discussed. These include a mechanism to place advisory locks on files, extensions of the name space across file systems, the ability to use long file names, and provisions for administrative control of resource usage.

关键词： UNIX application program interface file system design file system organization file system performance

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The development and deployment of Common Data Elements for tissue banks for translational research in cancer - An emerging standard based approach for the Mesothelioma Virtual Tissue Bank

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BMC CANCER 2008年第0期8卷 91-91页

作者： Mohanty, Sambit K. Mistry, Amita T. Amin, Waqas Parwani, Anil V. Pople, Andrew K. Schmandt, Linda Winters, Sharon B. Milliken, Erin Kim, Paula Whelan, Nancy B. Farhat, Ghada Melamed, Jonathan Taioli, Emanuela Dhir, Rajiv Pass, Harvey I. Becich, Michael J. Univ Pittsburgh Sch Med Dept Biomed Informat Pittsburgh PA 15260 USA Univ Pittsburgh Sch Med Dept Pathol Pittsburgh PA USA Univ Pittsburgh Sch Med Dept Epidemiol Pittsburgh PA USA NYU Sch Med Dept Pathol New York NY USA NYU Sch Med Dept Cardiothorac Surg Div Thorac Surg & Thorac Oncol New York NY USA

Background: Recent advances in genomics, proteomics, and the increasing demands for biomarker validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists ( CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) - compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health ( NIOSH) of the Center for Disease Control and Prevention ( CDC). Methods: The purpose of the project is to develop a core set of data elements for annotating mesothelioma specimens, following standards established by the CAP checklist, ADASP cancer protocols, and the NAACCR elements. We have associated these elements with modeling architecture to enhance both syntactic and semantic interoperability. The system has a Java-based multi-tiered architecture based on Unified Modeling Language (UML). Results: Common Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology. The CDEs for each case are of different types: demographic, epidemiologic data, cl

关键词： Unify Modeling Language application program interface Protect Health Information Unify Modeling Language Model Semantic Interoperability Unify Modeling Language application program interface Protect Health Information Unify Modeling Language Model Semantic Interoperability

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Genome Projector: zoomable genome map with multiple views

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BMC BIOINFORMATICS 2009年第1期10卷 31-31页

作者： Arakawa, Kazuharu Tamaki, Satoshi Kono, Nobuaki Kido, Nobuhiro Ikegami, Keita Ogawa, Ryu Tomita, Masaru Keio Univ Inst Adv Biosci Fujisawa Kanagawa 2528520 Japan

Background: Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional nature of biological information, software interfaces for database browsing should provide an intuitive interface that allows for rapid migration across different views and scales. The Zoomable User interface (ZUI) and tabbed browsing have proven successful for this purpose in other areas, especially to navigate the vast information in the World Wide Web. Results: This paper presents Genome Projector, a Web-based gateway for genomics information with a zoomable user interface using Google Maps API, equipped with four seamlessly accessible and searchable views: a circular genome map, a traditional genome map, a biochemical pathways map, and a DNA walk map. The Web application for 320 bacterial genomes is available at http://***/GenomeProjector/. All data and software including the source code, documentations, and development API are freely available under the GNU General Public License. Zoomable maps can be easily created from any image file using the development API, and an online data mapping service for Genome Projector is also available at our Web site. Conclusion: Genome Projector is an intuitive Web application for browsing genomics information, implemented with a zoomable user interface and tabbed browsing utilising Google Maps API and Asynchronous JavaScript and XML (AJAX) technology.

关键词： Genome Projector Genome Browser application program interface Bacterial Genome Replication Origin

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Ensembl variation resources

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BMC GENOMICS 2010年第1期11卷 293-293页

作者： Chen, Yuan Cunningham, Fiona Rios, Daniel McLaren, William M. Smith, James Pritchard, Bethan Spudich, Giulietta M. Brent, Simon Kulesha, Eugene Marin-Garcia, Pablo Smedley, Damian Birney, Ewan Flicek, Paul European Bioinformat Inst Cambridge CB10 1SD England Wellcome Trust Sanger Inst Cambridge CB10 1SA England

Background: The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description: The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions: Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://*** and from the public MySQL database server at ***.

关键词： Variation Data application program interface High Linkage Disequilibrium National Human Genome Research Institute Ensembl Variation

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Feature Analysis of STEP application Protocol and its application

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Tsinghua Science and Technology 1999年第2期4卷 31-34页

作者：李兵孟明辰李振宏童秉枢 Department of Precision Irstrurrents and Tsinghua University Beijing 100084

This paper uses semantic data modelling and CAD/CAPP/CAM integration to analyze the features defined in the STEP AP214, its characteristics of definition and distribution, and its influence on the complexity of CAD/CAPP/CAM application integration. A framework is developed for applications of CAD/CAPP/CAM integration based on the STEP to reduce the complexity of integration implementation. Two application program interfaces (API), namely, application protocol API and application API, are developed. The frameworks hierarchy structure and the application program interfaces between the layers make the integration of applications easier.

关键词： standard for the exchange of product model data integration framework feature application program interface CAD/CAPP/CAM integration

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NBLAST: a cluster variant of BLAST for NxN comparisons

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BMC BIOINFORMATICS 2002年第13期3卷 1-1页

作者： Dumontier, M Hogue, CWV Univ Toronto Dept Biochem Toronto ON M5S 1A8 Canada Mt Sinai Hosp Samuel Lunenfeld Res Inst Toronto ON M5G 1X5 Canada

Background: The BLAST algorithm compares biological sequences to one another in order to determine shared motifs and common ancestry. However, the comparison of all non-redundant (NR) sequences against all other NR sequences is a computationally intensive task. We developed NBLAST as a cluster computer implementation of the BLAST family of sequence comparison programs for the purpose of generating pre-computed BLAST alignments and neighbour lists of NR sequences. Results: NBLAST performs the heuristic BLAST algorithm and generates an exhaustive database of alignments, but it only computes N(N - 1)/2 alignments (i.e. the upper triangle) of a possible N-2 alignments, where N is the set of all sequences to be compared. A task-partitioning algorithm allows for cluster computing across all cluster nodes and the NBLAST master process produces a BLAST sequence alignment database and a list of sequence neighbours for each sequence record. The resulting sequence alignment and neighbour databases are used to serve the SeqHound query system through a C/C++ and PERIL application programming interface (API). Conclusions: NBLAST offers a local alternative to the NCBI's remote Entrez system for precomputed BLAST alignments and neighbour queries. On our 216-processor 450 MHz Pill cluster, NBLAST requires similar to24 hrs to compute neighbours for 850000 proteins currently in the non-redundant protein database.

关键词： application program interface Neighbour List Sequence Record Sequence Neighbour Blast Sequence

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