A rapid retrieval tool for operating on large, flat archive files

Computer-aided sequencing and analysis facilities need to efficientlysearch flat archive files. Retrieval by e-mail or network serverconnections can become impractical in cases where large numbersof selected entries need to be accessed. Public versions ofthese archives can be retrieved via ftp and installed on a localhard disk as an alternative to network-based retrieval. Afterinstallation, a scheme is required for rapid access of the archivethat is consistent with the other production needs of the sequencingfacility. We have developed a retrieval system for entries insidea flat-file database. The system works for any flat-file databasesystem such as those used in the public DNA and protein archives.     

Collision avoidance and resolution multiple access (CARMA)

The collision avoidance and resolution multiple access (CARMA) protocol is presented and analyzed. CARMA uses a collision avoidance handshake in which the sender and receiver exchange a request to send (RTS) and a clear to send (CTS) before the sender transmits any data. CARMA is based on carrier sensing, together with collision resolution based on a deterministic tree-splitting algorithm. For analytical purposes, an upper bound is derived for the average number of steps required to resolve collisions of RTSs using the tree-splitting algorithm. This bound is then applied to the computation of the average channel utilization in a fully connected network with a large number of stations. Under light-load conditions, CARMA achieves the same average throughput as multiple access protocols based on RTS/CTS exchange and carrier sensing. It is also shown that, as the arrival rate of RTSs increases, the throughput achieved by CARMA is close to the maximum throughput that any protocol based on collision avoidance (i.e., RTS/CTS exchange) can achieve if the control packets used to acquire the floor are much smaller than the data packet trains sent by the stations. Simulation results validate the simplifying approximations made in the analytical model. Our analysis results indicate that collision resolution makes floor acquisition multiple access much more effective. This revised version was published online in August 2006 with corrections to the Cover Date.     

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.     

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     

Integrating data from biological experiments into metabolic networks with the DBE information system

Modern 'omics'-technologies result in huge amounts of data about life processes. For analysis and data mining purposes this data has to be considered in the context of the underlying biological networks. This work presents an approach for integrating data from biological experiments into metabolic networks by mapping the data onto network elements and visualising the data enriched networks automatically. This methodology is implemented in DBE, an information system that supports the analysis and visualisation of experimental data in the context of metabolic networks. It consists of five parts: (1) the DBE-Database for consistent data storage, (2) the Excel-Importer application for the data import, (3) the DBE-Website as the interface for the system, (4) the DBE-Pictures application for the up- and download of binary (e. g. image) files, and (5) DBE-Gravisto, a network analysis and graph visualisation system. The usability of this approach is demonstrated in two examples.     

Reference master: A microcomputer-based storage and retrieval system for bibliographic references

A complete system for housekeeping and retrieval of bibliographic references managing individual reprint collections is described. By the use of special hardware and individual data base software even large reprint collections in the range up to 65 000 papers are handled economically. A fast 8-bit microprocessor (HD 64180) in combination with a Winchester hard disk drive serves as the basis for rapid access to the desired information. An efficient string search algorithm written in assembly language guarantees a fast operation with a search speed of more than 6,000 entries/ minute. The system cannot only prepare reference lists and reference files, but also incorporates an editor and maintains the control whether reprints are already on file or requested. The implementation of back-up schemes assure against data losses. Using a state of the art design single board computer and the most recent mass storage device technology, the system is as well small and cost effective, and thus suitable for personal use. In addition, some general questions and pitfalls concerning the management of scientific literature collections are touched upon.     

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.     

''The surface management system'' (SuMS) database: a surface-based database to aid cortical surface reconstruction, visualization and analysis.

Surface reconstructions of the cerebral cortex are increasingly widely used in the analysis and visualization of cortical structure, function and connectivity. From a neuroinformatics perspective, dealing with surface-related data poses a number of challenges. These include the multiplicity of configurations in which surfaces are routinely viewed (e.g. inflated maps, spheres and flat maps), plus the diversity of experimental data that can be represented on any given surface. To address these challenges, we have developed a surface management system (SuMS) that allows automated storage and retrieval of complex surface-related datasets. SuMS provides a systematic framework for the classification, storage and retrieval of many types of surface-related data and associated volume data. Within this classification framework, it serves as a version-control system capable of handling large numbers of surface and volume datasets. With built-in database management system support, SuMS provides rapid search and retrieval capabilities across all the datasets, while also incorporating multiple security levels to regulate access. SuMS is implemented in Java and can be accessed via a Web interface (WebSuMS) or using downloaded client software. Thus, SuMS is well positioned to act as a multiplatform, multi-user 'surface request broker' for the neuroscience community.     

Towards organizing health knowledge on community-based health services

Online community-based health services accumulate a huge amount of unstructured health question answering (QA) records at a continuously increasing pace. The ability to organize these health QA records has been found to be effective for data access. The existing approaches for organizing information are often not applicable to health domain due to its domain nature as characterized by complex relation among entities, large vocabulary gap, and heterogeneity of users. To tackle these challenges, we propose a top-down organization scheme, which can automatically assign the unstructured health-related records into a hierarchy with prior domain knowledge. Besides automatic hierarchy prototype generation, it also enables each data instance to be associated with multiple leaf nodes and profiles each node with terminologies. Based on this scheme, we design a hierarchy-based health information retrieval system. Experiments on a real-world dataset demonstrate the effectiveness of our scheme in organizing health QA into a topic hierarchy and retrieving health QA records from the topic hierarchy.     

An off-line system for in-time analysis of cardiac catheterization data and for establishment of a cardiological database for retrospective studies.

The system described may be divided in two major parts: (i) automatic analysis of cardiac catheterization data running off-line on a Siemens 305 computer; (ii) storage and retrieval of the results from these analyses and additional data from related departments (thoracic surgery, internal medicine and clinical physiology) in a cardiological database on an IBM 370/155 computer. The first part is described with special regard to (i) operation and control during the phases of data collection, pre-processing, processing and storage of results; (ii) the presentation of the results in a complete and readable form and (iii) the modular design of the software. The results of an evaluation of the computer methods versus manual methods are also presented. The second part has been described with regard to the type of data entered in the cardiological database. The structure of the database and the programs used for storage and retrieval have not been described in detail in the present publication.     

Portable file management system in FORTRAN

It has been generally considered that FORTRAN is inferior to MUMPS and other computer languages in its facility to manipulate files and that it is not satisfactorily competent to handle databases. However, it is our finding that FORTRAN is the most widely used language in patient data management systems discussed in recently published papers. Therefore, it now seems appropriate to review and evaluate the validity of this general belief. The objective of this study is to establish a file management system in FORTRAN 77 for use in the construction of a clinical database. Comparative study is conducted on several problems associated with file manipulation, that is, time requirement for file access and access methods for data retrieval.     

GeVaDSs - decision support system for novel Genetic Vaccine development process

ABSTRACT: BACKGROUND: The lack of a uniform way for qualitative and quantitative evaluation of vaccine candidates under development led us to set up a standardized scheme for vaccine efficacy and safety evaluation. We developed and implemented molecular and immunology methods, and designed support tools for immunization data storage and analyses. Such collection can create a unique opportunity for immunologists to analyse data delivered from their laboratories. RESULTS: We designed and implemented GeVaDSs (Genetic Vaccine Decision Support system)- an interactive system for efficient storage, integration, retrieval and representation of data. Moreover, GeVaDSs allows for relevant association and interpretation of data, and thus for knowledge-based generation of testable hypotheses of vaccine responses. CONCLUSIONS: GeVaDSs has been tested by several laboratories in Europe, and proved its usefulness in vaccine analysis. Case study of its application is presented in the additional files. The system is available at: http://gevads.cs.put.poznan.pl/preview/ (login: viewer, password: password).     

GenBank.

The GenBank sequence database continues to expand its data coverage, quality control, annotation content and retrieval services for the scientific community. Besides handling direct submissions of sequence data from authors, GenBank also incorporates DNA sequences from all available public sources; an integrated retrieval system, known as Entrez, also makes available data from the major protein sequence and structural databases, and from U.S. and European patents. MIDLINE abstracts from published articles describing the sequences are also included as an additional source of biological annotation for sequence entries. GenBank supports distribution of the data via FTP, CD-ROM, and E-mail servers. Network server-client programs provide access to an integrated database for literature retrieval and sequence similarity searching.     

Remote data retrieval for bioinformatics applications: an agent migration approach

Some of the approaches have been developed to retrieve data automatically from one or multiple remote biological data sources. However, most of them require researchers to remain online and wait for returned results. The latter not only requires highly available network connection, but also may cause the network overload. Moreover, so far none of the existing approaches has been designed to address the following problems when retrieving the remote data in a mobile network environment: (1) the resources of mobile devices are limited; (2) network connection is relatively of low quality; and (3) mobile users are not always online. To address the aforementioned problems, we integrate an agent migration approach with a multi-agent system to overcome the high latency or limited bandwidth problem by moving their computations to the required resources or services. More importantly, the approach is fit for the mobile computing environments. Presented in this paper are also the system architecture, the migration strategy, as well as the security authentication of agent migration. As a demonstration, the remote data retrieval from GenBank was used to illustrate the feasibility of the proposed approach.     

Explicit coordination to prevent congestion in data center networks

Large cluster-based cloud computing platforms increasingly use commodity Ethernet technologies, such as Gigabit Ethernet, 10GigE, and Fibre Channel over Ethernet (FCoE), for intra-cluster communication. Traffic congestion can become a performance concern in the Ethernet due to consolidation of data, storage, and control traffic over a common layer-2 fabric, as well as consolidation of multiple virtual machines (VMs) over less physical hardware. Even as networking vendors race to develop switch-level hardware support for congestion management, we make the case that virtualization has opened up a complementary set of opportunities to reduce or even eliminate network congestion in cloud computing clusters. We present the design, implementation, and evaluation of a system called XCo, that performs explicit coordination of network transmissions over a shared Ethernet fabric to proactively prevent network congestion. XCo is a software-only distributed solution executing only in the end-nodes. A central controller uses explicit permissions to temporally separate (at millisecond granularity) the transmissions from competing senders through congested links. XCo is fully transparent to applications, presently deployable, and independent of any switch-level hardware support. We present a detailed evaluation of our XCo prototype across a number of network congestion scenarios, and demonstrate that XCo significantly improves network performance during periods of congestion. We also evaluate the behavior of XCo for large topologies using NS3 simulations.     

The jmzQuantML programming interface and validator for the mzQuantML data standard

The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools ( http://code.google.com/p/jmzquantml/ ). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool ( http://code.google.com/p/mzquantml‐validator/ ) for validating mzQuantML files, which is a formal part of the data standard.     

What are the benefits and risks of fitting patients with radiofrequency identification devices

Background to the debate: In 2004, the United States Food and Drug Administration approved a radiofrequency identification (RFID) device that is implanted under the skin of the upper arm of patients and that stores the patient's medical identifier. When a scanner is passed over the device, the identifier is displayed on the screen of an RFID reader. An authorized health professional can then use the identifier to access the patient's clinical information, which is stored in a separate, secure database. Such RFID devices may have many medical benefits--such as expediting identification of patients and retrieval of their medical records. But critics of the technology have raised several concerns, including the risk of the patient's identifying information being used for nonmedical purposes.     

Motion control of musculoskeletal systems with redundancy

Motion control of musculoskeletal systems for functional electrical stimulation (FES) is a challenging problem due to the inherent complexity of the systems. These include being highly nonlinear, strongly coupled, time-varying, time-delayed, and redundant. The redundancy in particular makes it difficult to find an inverse model of the system for control purposes. We have developed a control system for multiple input multiple output (MIMO) redundant musculoskeletal systems with little prior information. The proposed method separates the steady-state properties from the dynamic properties. The dynamic control uses a steady-state inverse model and is implemented with both a PID controller for disturbance rejection and an artificial neural network (ANN) feedforward controller for fast trajectory tracking. A mechanism to control the sum of the muscle excitation levels is also included. To test the performance of the proposed control system, a two degree of freedom ankle–subtalar joint model with eight muscles was used. The simulation results show that separation of steady-state and dynamic control allow small output tracking errors for different reference trajectories such as pseudo-step, sinusoidal and filtered random signals. The proposed control method also demonstrated robustness against system parameter and controller parameter variations. A possible application of this control algorithm is FES control using multiple contact cuff electrodes where mathematical modeling is not feasible and the redundancy makes the control of dynamic movement difficult.     

Recherche de cas médicaux multimodaux à l’aide d’arbres de décision

In this article, we present a Case-based Reasoning system for the retrieval of patient files similar to a case placed as query. We focus on patient files made up of several images with contextual information (such as the patient age, sex and medical history). Indeed, medical experts generally need varied sources of information (which might be incomplete) to diagnose a pathology. Consequently, we derive a retrieval framework from decision trees, which are well suited to process heterogeneous and incomplete information. To be integrated in the system, images are indexed by their digital content. The method is evaluated on a classified diabetic retinopathy database. On this database, results are promising: the retrieval sensitivity reaches 79.5% for a window of five cases, which is almost twice as good as the retrieval of single images alone.     

Integrating mass spectrometry data systems from different manufacturers in a local area network

Several scientific instruments suppliers are offering complete networking and automation packages for analytical laboratories. Nevertheless there is still considerable work to be done in the area of standardization of file formats generated by different data acquisition systems supplied by scientific instruments manufacturers. Recent work on the netCDF transfer protocol for mass spectrometry data suggests that good progress is being made in the area of data formats.Our laboratory operates a number of diverse instruments, including two high resolution systems (ZAB 2F, 70 SEQ) and one quadrupole (QMD 1000) from Fisons Instruments, one ion trap system from Finnigan (ITS 40) and one pyrolysis mass spectrometer from Horizon Instruments (RAPyD-400), all equipped with autosamplers. This instruments are physically located in two distinct laboratories. The data systems are based on very different computers, including a DEC PDP-11/24, a VAX 4000/90 and several PCs.The large amount of data produced by the MS laboratory and the implementation of GLPs, (Good Laboratory Practices) and GALPs (Good Automated Laboratory Practices) prompted us to examine the possibility of networking the instrumentation in a client/server computing environment. All instrument data systems have been connected to the institute network via ethernet, using either DECnet or TCP/IP. A VAXCluster consisting in a VAXStation 4000/90 host and a VAXStation 3100 satellite has been configured as a server using DEC PATHWORKS V.4.1 server software. This allows for file, disk, application and print services to all the PC clients connected network wide. Unattended distributed backup and restore services for PC hard disks are implemented. Mass spectrometry data files are permanently archived in their original format on 4 Gbyte tape cartridges and stored for later retrieval. Files can be transferred to any office PC running the appropriate mass spectrometry software. A centralized spectra and structure information management system based on the MassLib (Chemical Concepts) software allows for library searches using the SISCOM algorithm after specific file conversion programs or using JCAMP-DX files. Furthermore, the mass spectrometer data systems are readied for their eventual incorporation into a LIMS.