A computer program for on-line measurement, storage, analysis and retrieval of urodynamic data

A computer program is presented which allows for direct connection of a minicomputer to a urodynamic set-up. The program stores measured pressure and flow data in a random access disc file with minimal intervention of the urodynamicist, and enables the direct application of a number of methods of analysis to the data. The program is modular, and other analysis methods are easily added. Results of analyses are stored in the same disc file, and both results and measured data can be quickly and easily retrieved. The program is written in FORTRAN; hardware-dependent functions (analog input, graphics display, and random access disc storage) are implemented in subroutines (partly assembler) which can easily be replaced.     

Scalable Session Locking for a Distributed File System

File systems provide an interface for applications to obtain exclusive access to files, in which a process holds privileges to a file that cannot be preempted and restrict the capabilities of other processes. Local file systems do this by maintaining information about the privileges of current file sessions, and checking subsequent sessions for compatibility. Implementing exclusive access in this manner for distributed file systems degrades performance by requiring every new file session to be registered with a lock server that maintains global session state. We present two techniques for improving the performance of session management in the distributed environment. We introduce a distributed lock for managing file access, called a semi-preemptible lock, that allows clients to cache privileges. Under a semi-preemptible lock, a file system creates new sessions without messages to the lock manager. This improves performance by exploiting locality – the affinity of files to clients. We also present data structures and algorithms for the dynamic evaluation of locks that allow a distributed file system to efficiently manage arbitrarily complex locking. In this case, complex means that an object can be locked in a large number of unique modes. The combination of these techniques results in a distributed locking scheme that supports fine-grained concurrency control with low memory and message overhead and with the assurance that their locking system is correct and avoids unnecessary deadlocks.     

The MOSIX Direct File System Access Method for Supporting Scalable Cluster File Systems

MOSIX is a cluster management system that supports preemptive process migration. This paper presents the MOSIX Direct File System Access (DFSA), a provision that can improve the performance of cluster file systems by allowing a migrated process to directly access files in its current location. This capability, when combined with an appropriate file system, could substantially increase the I/O performance and reduce the network congestion by migrating an I/O intensive process to a file server rather than the traditional way of bringing the file's data to the process. DFSA is suitable for clusters that manage a pool of shared disks among multiple machines. With DFSA, it is possible to migrate parallel processes from a client node to file servers for parallel access to different files. Any consistent file system can be adjusted to work with DFSA. To test its performance, we developed the MOSIX File-System (MFS) which allows consistent parallel operations on different files. The paper describes DFSA and presents the performance of MFS with and without DFSA.     

Cost-intelligent application-specific data layout optimization for parallel file systems

Parallel file systems have been developed in recent years to ease the I/O bottleneck of high-end computing system. These advanced file systems offer several data layout strategies in order to meet the performance goals of specific I/O workloads. However, while a layout policy may perform well on some I/O workload, it may not perform as well for another. Peak I/O performance is rarely achieved due to the complex data access patterns. Data access is application dependent. In this study, a cost-intelligent data access strategy based on the application-specific optimization principle is proposed. This strategy improves the I/O performance of parallel file systems. We first present examples to illustrate the difference of performance under different data layouts. By developing a cost model which estimates the completion time of data accesses in various data layouts, the layout can better match the application. Static layout optimization can be used for applications with dominant data access patterns, and dynamic layout selection with hybrid replications can be used for applications with complex I/O patterns. Theoretical analysis and experimental testing have been conducted to verify the proposed cost-intelligent layout approach. Analytical and experimental results show that the proposed cost model is effective and the application-specific data layout approach can provide up to a 74% performance improvement for data-intensive applications.     

Adaptive hybrid storage systems leveraging SSDs and HDDs in HPC cloud environments

Cloud computing should inherently support various types of data-intensive workloads with different storage access patterns. This makes a high-performance storage system in the Cloud an important component. Emerging flash device technologies such as solid state drives (SSDs) are a viable choice for building high performance computing (HPC) cloud storage systems to address more fine-grained data access patterns. However, the bit-per-dollar SSD price is still higher than the prices of HDDs. This study proposes an optimized progressive file layout (PFL) method to leverage the advantages of SSDs in a parallel file system such as Lustre so that small file I/O performance can be significantly improved. A PFL can dynamically adjust chunk sizes and stripe patterns according to various I/O traffics. Extensive experimental results show that this approach (i.e. building a hybrid storage system based on a combination of SSDs and HDDs) can actually achieve balanced throughput over mixed I/O workloads consisting of large and small file access patterns.     

Adopting a database as a solution to managing electron image data

A database was used for data management and interprogram communication in an image processing and three-dimensional reconstruction program suite for biological bundles. The programs were modified from the MRC crystallographic package. The database server works with local and remote programs and data sets, allows simultaneous requests from multiple clients, and maintains multiple databases and data tables within them. It has built-in security for the data access. Several graphical user interfaces are available to view and/or edit data tables. In addition, FORTRAN interface and function libraries are written to communicate with image processing software. The data management overhead is inexpensive, requiring only narrow bandwidth from the network. It easily handles several data tables with over 1000 entries.     

BioTorrents: A File Sharing Service for Scientific Data

The transfer of scientific data has emerged as a significant challenge, as datasets continue to grow in size and demand for open access sharing increases. Current methods for file transfer do not scale well for large files and can cause long transfer times. In this study we present BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology. BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. BioTorrents is available at http://www.biotorrents.net.     

A flexible online metadata editing and management system

Our team developed a metadata editing and management system employing state of the art XML technologies initially aimed at the environmental sciences but with the potential to be useful across multiple domains. We chose a modular and distributed design for scalability, flexibility, options for customizations, and the possibility to add more functionality at a later stage. The system consists of a desktop design tool that generates code for the actual online editor, a native XML database, and an online user access management application. A Java Swing application that reads an XML schema, the design tool provides the designer with options to combine input fields into online forms with user-friendly tags and determine the flow of input forms. Based on design decisions, the tool generates XForm code for the online metadata editor which is based on the Orbeon XForms engine. The design tool fulfills two requirements: First data entry forms based on a schema are customized at design time and second the tool can generate data entry applications for any valid XML schema without relying on custom information in the schema. A configuration file in the design tool saves custom information generated at design time. Future developments will add functionality to the design tool to integrate help text, tool tips, project specific keyword lists, and thesaurus services.Cascading style sheets customize the look-and-feel of the finished editor. The editor produces XML files in compliance with the original schema, however, a user may save the input into a native XML database at any time independent of validity. The system uses the open source XML database eXist for storage and uses a MySQL relational database and a simple Java Server Faces user interface for file and access management. We chose three levels to distribute administrative responsibilities and handle the common situation of an information manager entering the bulk of the metadata but leave specifics to the actual data provider.     

Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network

New ‘omics’ technologies are changing nutritional sciences research. They enable to tackle increasingly complex questions but also increase the need for collaboration between research groups. An important challenge for successful collaboration is the management and structured exchange of information that accompanies data-intense technologies. NuGO, the European Nutrigenomics Organization, the major collaborating network in molecular nutritional sciences, is supporting the application of modern information technologies in this area. We have developed and implemented a concept for data management and computing infrastructure that supports collaboration between nutrigenomics researchers. The system fills the gap between “private” storing with occasional file sharing by email and the use of centralized databases. It provides flexible tools to share data, also during experiments, while preserving ownership. The NuGO Information Network is a decentral, distributed system for data exchange based on standard web technology. Secure access to data, maintained by the individual researcher, is enabled by web services based on the the BioMoby framework. A central directory provides information about available web services. The flexibility of the infrastructure allows a wide variety of services for data processing and integration by combining several web services, including public services. Therefore, this integrated information system is suited for other research collaborations.     

ACNUC - a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage

ACNUC is a database structure and retrieval software for usewith either the GenBank or EMBL nucleic acid sequence data collections.The nucleotide and textual data furnished by both collectionsare each restructured into a database that allows sequence retrievalon a multi-criterion basis. The main selection criteria are:species (or higher order taxon), keyword, reference, journal,author, and organelle; all logical combinations of these criteriacan be used. Direct access to sequence regions that code fora specific product (protein, tRNA or rRNA) is provided. A versatileextraction procedure copies selected sequences, or fragmentsof them, from the database to user files suitable to be analysedby user-supplied application programs. A detailed help mechanismis provided to aid the user at any time during the retrievalsession. All software has been written in FORTRAN 77 which guaranteesa high degree of transportability to minicomputers or mainframes.reference, journal, author, and organelle; all logical combinationsof these criteria can be used. Direct access to sequence regionsthat code for a specific product (protein, tRNA or rRNA) isprovided. A versatile extraction procedure copies selected sequences,or fragments of them, from the database to user files suitableto be analysed by user-supplied application programs. A detailedhelp mechanism is provided to aid the user at any time duringthe retrieval session. All software has been written in FORTRAN77 which guarantees a high degree of transportability to minicomputersor mainframes. Received on May 1, 1985; accepted on June 13, 1985     

"SCINT," a Fortran IV program for the analysis of data for doubly labeled and variably quenched liquid scintillation samples

For some time now, we have been using double label techniques in our laboratory. In our work we generate large numbers of samples containing ¹⁴C and ³H and varying amounts of quenching agents. The analysis of this data led us to develop SCINT, a simple and versatile program written in FORTRAN IV for use on our Control Data 1700 computer facility. We feel that such a program may be of use to the many workers now involved with dual isotope procedures who also have access to similar computer facilities.     

Enabling secure auditing and deduplicating data without owner-relationship exposure in cloud storage

The public cloud storage auditing with deduplication has been studied to assure the data integrity and improve the storage efficiency for cloud storage in recent years. The cloud, however, has to store the link between the file and its data owners to support the valid data downloading in previous schemes. From this file-owner link, the cloud server can identify which users own the same file. It might expose the sensitive relationship among data owners of this multi-owners file, which seriously harms the data owners’ privacy. To address this problem, we propose an identity-protected secure auditing and deduplicating data scheme in this paper. In the proposed scheme, the cloud cannot learn any useful information on the relationship of data owners. Different from existing schemes, the cloud does not need to store the file-owner link for supporting valid data downloading. Instead, when the user downloads the file, he only needs to anonymously submit a credential to the cloud, and can download the file only if this credential is valid. Except this main contribution, our scheme has the following advantages over existing schemes. First, the proposed scheme achieves the constant storage, that is, the storage space is fully independent of the number of the data owners possessing the same file. Second, the proposed scheme achieves the constant computation. Only the first uploader needs to generate the authenticator for each file block, while subsequent owners do not need to generate it any longer. As a result, our scheme greatly reduces the storage overhead of the cloud and the computation overhead of data owners. The security analysis and experimental results show that our scheme is secure and efficient.     

Workload characterization in a high-energy data grid and impact on resource management

The analysis of data usage in a large set of real traces from a high-energy physics collaboration revealed the existence of an emergent grouping of files that we coined “filecules”. This paper presents the benefits of using this file grouping for prestaging data and compares it with previously proposed file grouping techniques along a range of performance metrics. Our experiments with real workloads demonstrate that filecule grouping is a reliable and useful abstraction for data management in science Grids; that preserving time locality for data prestaging is highly recommended; that job reordering with respect to data availability has significant impact on throughput; and finally, that a relatively short history of traces is a good predictor for filecule grouping. Our experimental results provide lessons for workload modeling and suggest design guidelines for data management in data-intensive resource-sharing environments.

On clustering in database servers for supporting mobile clients

The use of mobile computers is gaining popularity. There is an increasing trend in the number of users with laptops, PDAs, and smart phones. Access to information repositories in the future will be dominated by mobile clients rather than traditional “fixed” clients. These mobile clients download information by periodically connecting to repositories of data stored in either databases or file systems. Such mobile clients constitute a new and different kind of workload and exhibit a different access pattern than seen in traditional client server systems. Though file systems have been modified to handle clients that can download information, disconnect, and later reintegrate, databases have not been redesigned to accommodate mobile clients. There is a need to support mobile clients in the context of client server databases. This paper is about organizing the database server to take into consideration the access patterns of mobile clients. We propose the concept of hoard attributes which capture these access patterns. Three different techniques for organizing data on the server based on the hoard attribute are presented. We argue that each technique is suited for a particular workload. The workload is a combination of requests from mobile clients and traditional clients. This reorganization also allows us to address issues of concurrency control, disconnection and replica control in mobile databases. We present simulation results that show the performance of server reorganization using hoard attributes. We also provide an elaborate discussion of issues resulting from this reorganization in this new paradigm taking into account both mobile and traditional clients. This revised version was published online in August 2006 with corrections to the Cover Date.     

Querying and computing with BioCyc databases

We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database.     

Web servlet-assisted, dial-in flow cytometry data analysis

BACKGROUND: The obvious benefits of centralized data storage notwithstanding, the size of modern flow cytometry data files discourages their transmission over commonly used telephone modem connections. The proposed solution is to install at the central location a web servlet that can extract compact data arrays, of a form dependent on the requested display type, from the stored files and transmit them to a remote client computer program for display. METHODS: A client program and a web servlet, both written in the Java programming language, were designed to communicate over standard network connections. The client program creates familiar numerical and graphical display types and allows the creation of gates from combinations of user-defined regions. Data compression techniques further reduce transmission times for data arrays that are already much smaller than the data file itself. RESULTS: For typical data files, network transmission times were reduced more than 700-fold for extraction of one-dimensional (1-D) histograms, between 18 and 120-fold for 2-D histograms, and 6-fold for color-coded dot plots. Numerous display formats are possible without further access to the data file. CONCLUSIONS: This scheme enables telephone modem access to centrally stored data without restricting flexibility of display format or preventing comparisons with locally stored files.     

Proteomics FASTA archive and reference resource

A FASTA file archive and reference resource has been added to ProteomeCommons.org. Motivation for this new functionality derives from two primary sources. The first is the recent FASTA standardization work done by the Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI). Second is the general lack of a uniform mechanism to properly cite FASTA files used in a study, and to publicly access such FASTA files post-publication. An extension to the Tranche data sharing network has been developed that includes web-pages, documentation, and tools for facilitating the use of FASTA files. These include conversion to the new HUPO-PSI format, and provisions for both citing and publicly archiving FASTA files. This new resource is available immediately, free of charge, and can be accessed at http://www.proteomecommons.org/data/fasta/. Source-code for related tools is also freely available under the BSD license.     

A proposal for a flow cytometric data file standard

The increasing complexity of multiparameter data collection and analysis in flow cytometry and the development of relatively inexpensive arc-lamp-based flow cytometers, which increases the probability that laboratories or institutions may have more than one type of instrument, creates a need for shareable analysis programs and for the transport of flow cytometric data files within an installation or from one institution to another. To address this need, we propose a standard file format to be used for all flow cytometric data. The general principles of this proposal are: (1) The data file will contain a minimum of three segments, TEXT, DATA, and ANALYSIS; (2) The TEXT and ANALYSIS segments consist of KEYWORDS, which are the names of data fields, and their values; (3) All TEXT is encoded in ASCII; (4) KEYWORDS and their values may be of any length; (5) Certain KEYWORDS will be standard, i.e., having specified formats to be recognized by all programs. The structure of the DATA segment will be uniquely defined by the values of KEYWORDS in the TEXT area. It may be in any bit resolution, facilitating compatibility between machines with different word length and/or allowing bit compression of the data. The structured nature of the TEXT area should facilitate management of flow cytometric data using existing data base management systems. The proposed file format has been implemented on VAX, PDP-11, and HP9920 based flow cytometry data acquisition systems.     

Principle of codification for quick comparisons with the entire biomolecule databanks and associated programs in FORTRAN 77.

We propose a new method for homology search of nucleic acids or proteins in databanks. All the possible subsequences of a specific length in a sequence are converted into a code and stored in an indexed file (hash-coding). This preliminary work of codifying an entire bank is rather long but it enables an immediate access to all the sequence fragments of a given type. With our method a strict homology pattern of twenty nucleotides can be found for example in the Los Alamos bank (GENBANK) in less than 2 seconds. We can also use this data storage to considerably speed up the non-strict homology search programs and to write a program to help in the selection of nucleic acid hybridization probes.     

GLP机构档案室的建立和管理与科研档案管理之比较

档案的建立和管理在药物非临床安全性评价和科学研究中都起到非常重要的作用。我们通过查阅文献发现,关于GLP机构档案管理的文献综述极少,涉及到将它与科研档案管理作系统全面的比较的文章是没有的。现从资料档案保存机构的硬件设施、档案管理规范和应注意的问题3个方面详细介绍了资料档案管理的相关规定和经验,并将GLP档案管理规范与科研档案管理规范作比较,我们根据国家档案局发布的《科学技术研究档案管理暂行规定》和7年GLP档案管理经验以及多次国家食品药品监督管理局（SFDA）认证现场检查的经历,总结出两者在功能实现、硬件设施、温湿度要求、档案防护、制定SOP、档案管理人员资质、各方人员职责、归档范围、归档形式、资料档案的接收与审查、归档时间、保管期限、借阅返还规定、资料的书写规范性、进出记录和电子文件的保存这16个方面的异同之处,突出GLP档案管理规范的特点和重点。通过这一深入全面的比较分析,得出GLP档案管理更加明确、具体、细致和可操作。