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.     

Failure-Atomic File Access in the Slice Interposed Network Storage System

This paper presents a recovery protocol for block I/O operations in Slice, a storage system architecture for high-speed LANs incorporating network-attached block storage. The goal of the Slice architecture is to provide a network file service with scalable bandwidth and capacity while preserving compatibility with off-the-shelf clients and file server appliances. The Slice prototype virtualizes the Network File System (NFS) protocol by interposing a request switching filter at the client's interface to the network storage system. The distributed Slice architecture separates functions typically combined in central file servers, introducing new challenges for failure atomicity. This paper presents a protocol for atomic file operations and recovery in the Slice architecture, and related support for reliable file storage using mirrored striping. Experimental results from the Slice prototype show that the protocol has low cost in the common case, allowing the system to deliver client file access bandwidths approaching gigabit-per-second network speeds.     

An adaptable multithreaded prefetching technique for client‐server object bases

Given the existence of powerful multiprocessor client workstations in many client-server object database applications, the performance bottleneck is the delay in transferring pages from the server to the client. We present a prefetching technique that can avoid this delay, especially where the client application requests pages from several database servers. This technique has been added to the EXODUS storage manager. Part of the novelty of this approach lies in the way that multithreading on the client workstation is exploited, in particular for activities such as prefetching and flushing dirty pages to the server. Using our own complex object benchmark, we analyze the performance of the prefetching technique with multiple clients and multiple servers. The technique is also tested under a variety of client host workload levels. This revised version was published online in July 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.     

MADGE: scalable distributed data management software for cDNA microarrays

MOTIVATION: The human genome project and the development of new high-throughput technologies have created unparalleled opportunities to study the mechanism of diseases, monitor the disease progression and evaluate effective therapies. Gene expression profiling is a critical tool to accomplish these goals. The use of nucleic acid microarrays to assess the gene expression of thousands of genes simultaneously has seen phenomenal growth over the past five years. Although commercial sources of microarrays exist, investigators wanting more flexibility in the genes represented on the array will turn to in-house production. The creation and use of cDNA microarrays is a complicated process that generates an enormous amount of information. Effective data management of this information is essential to efficiently access, analyze, troubleshoot and evaluate the microarray experiments. RESULTS: We have developed a distributable software package designed to track and store the various pieces of data generated by a cDNA microarray facility. This includes the clone collection storage data, annotation data, workflow queues, microarray data, data repositories, sample submission information, and project/investigator information. This application was designed using a 3-tier client server model. The data access layer (1st tier) contains the relational database system tuned to support a large number of transactions. The data services layer (2nd tier) is a distributed COM server with full database transaction support. The application layer (3rd tier) is an internet based user interface that contains both client and server side code for dynamic interactions with the user. AVAILABILITY: This software is freely available to academic institutions and non-profit organizations at http://www.genomics.mcg.edu/niddkbtc.     

MyDas,an Extensible Java DAS Server

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.     

TogoDoc server/client system: smart recommendation and efficient management of life science literature

In this paper, we describe a server/client literature management system specialized for the life science domain, the TogoDoc system (Togo, pronounced Toe-Go, is a romanization of a Japanese word for integration). The server and the client program cooperate closely over the Internet to provide life scientists with an effective literature recommendation service and efficient literature management. The content-based and personalized literature recommendation helps researchers to isolate interesting papers from the "tsunami" of literature, in which, on average, more than one biomedical paper is added to MEDLINE every minute. Because researchers these days need to cover updates of much wider topics to generate hypotheses using massive datasets obtained from public databases or omics experiments, the importance of having an effective literature recommendation service is rising. The automatic recommendation is based on the content of personal literature libraries of electronic PDF papers. The client program automatically analyzes these files, which are sometimes deeply buried in storage disks of researchers' personal computers. Just saving PDF papers to the designated folders makes the client program automatically analyze and retrieve metadata, rename file names, synchronize the data to the server, and receive the recommendation lists of newly published papers, thus accomplishing effortless literature management. In addition, the tag suggestion and associative search functions are provided for easy classification of and access to past papers (researchers who read many papers sometimes only vaguely remember or completely forget what they read in the past). The TogoDoc system is available for both Windows and Mac OS X and is free. The TogoDoc Client software is available at http://tdc.cb.k.u-tokyo.ac.jp/, and the TogoDoc server is available at https://docman.dbcls.jp/pubmed_recom.     

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.     

Content-Aware Dispatching Algorithms for Cluster-Based Web Servers

Cluster-based Web servers are leading architectures for highly accessed Web sites. The most common Web cluster architecture consists of replicated server nodes and a Web switch that routes client requests among the nodes. In this paper, we consider content-aware Web switches that can use application level information to assign client requests. We evaluate the performance of some representative state-of-the-art dispatching algorithms for Web switches operating at layer 7 of the OSI protocol stack. Specifically, we consider dispatching algorithms that use only client information as well as the combination of client and server information for load sharing, reference locality or service partitioning. We demonstrate through a wide set of simulation experiments that dispatching policies aiming to improve locality in server caches give best results for traditional Web publishing sites providing static information and some simple database searches. On the other hand, when we consider more recent Web sites providing dynamic and secure services, dispatching policies that aim to share the load are the most effective.     

ORBIT: an integrated environment for user-customized bioinformatics tools

MOTIVATION: There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. RESULTS: We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.     

On energy impact of web user interface approaches

Developers base selection of a User Interface (UI) development approach on functionality, development and maintenance costs, usability, responsiveness, etc. User expectations continue to grow for greater functionality and continuous interactivity, extending demands on computational resources. To facility scale, recent approaches push more UI computation to clients. Such client-side delegation of functionality increase, continuous usage, and localized computation create ever-growing energy demands, which may negatively impact battery life on mobile platforms. Nonetheless, developers given little attention to the power demands aspects of UI framework selection. We evaluate the impact of contemporary UI framework selection on resource utilization and energy consumption. We suggest an alternative delivery approach designed to preserve low energy demands on clients while still allowing offloading of computation from server to client. Our work focuses on web-based mobile applications; however, we believe our approach to energy demand reduction and framework evaluation to be generally applicable.     

电子通讯与生物大分子序列分析

交互网络(Internet)的发展为联网的计算机用户之间进行信息交流提供了有效途径.就分子生物学家而言,他们不仅可以利用电子邮件系统发送和接收信息,而且更重要的是能够存取大量的分子生物学数据库和软件.利用Internet可以开展多种序列分析作业,包括序列数据库的类似性检索、基因编码区鉴定和蛋白质二级结构分析等.一个数据库,例如GenBank,可以通过多种方式来存取:a.电子邮件文件服务器,b.文件传送协议(FTP),c.Gopher,WAIS或WWW等服务器-客户机(Server-Client)系统.专为分子生物学家设计的BIOSCI电子公告牌为研究人员开展学术讨论、寻求别人帮助和与数据库人员交流提供了极大的方便.     

Protein Information and Knowledge Extractor: Discovering biological information from proteomics data

One of the main goals in proteomics is to solve biological and molecular questions regarding a set of identified proteins. In order to achieve this goal, one has to extract and collect the existing biological data from public repositories for every protein and afterward, analyze and organize the collected data. Due to the complexity of this task and the huge amount of data available, it is not possible to gather this information by hand, making it necessary to find automatic methods of data collection. Within a proteomic context, we have developed Protein Information and Knowledge Extractor (PIKE) which solves this problem by automatically accessing several public information systems and databases across the Internet. PIKE bioinformatics tool starts with a set of identified proteins, listed as the most common protein databases accession codes, and retrieves all relevant and updated information from the most relevant databases. Once the search is complete, PIKE summarizes the information for every single protein using several file formats that share and exchange the information with other software tools. It is our opinion that PIKE represents a great step forward for information procurement and drastically reduces manual database validation for large proteomic studies. It is available at http://proteo.cnb.csic.es/pike .     

Tracker: continuous HMMER and BLAST searching

SUMMARY: Tracker is a web-based email alert system for monitoring protein database searches using HMMER and Blast-P, nucleotide searches using Blast-N and literature searches of the PubMed database. Users submit searches via a web-based interface. Searches are saved and run against updated databases to alert users about new information. If there are new results from the saved searches, users will be notified by email and will then be able to access results and link to additional information on the NCBI website. Tracker supports Boolean AND/OR operations on HMMER and BLASTP result sets to allow users to broaden or narrow protein searches. AVAILABILITY: The server is located at http://jay.bioinformatics.ku.edu/tracker/index.html. A distribution package including detailed installation procedure is freely available from http://jay.bioinformatics.ku.edu/download/tracker/.     

HIVToolbox, an integrated web application for investigating HIV

Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories. Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site. Weblink: [http://hivtoolbox.bio-toolkit.com].     

The design of Jemboss: a graphical user interface to EMBOSS

DESIGN: Jemboss is a graphical user interface (GUI) for the European Molecular Biology Open Software Suite (EMBOSS). It is being developed at the MRC UK HGMP-RC as part of the EMBOSS project. This paper explains the technical aspects of the Jemboss client-server design. The client-server model optionally allows that a Jemboss user have an account on the remote server. The Jemboss client is written in Java and is downloaded automatically to a user's workstation via Java Web Start using the HTML protocol. The client then communicates with the remote server using SOAP (Simple Object Access Protocol). A Tomcat server listens on the remote machine and communicates the SOAP requests to a Jemboss server, again written in Java. This Java server interprets the client requests and executes them through Java Native Interface (JNI) code written in the C language. Another C program having setuid privilege, jembossctl, is called by the JNI code to perform the client requests under the user's account on the server. The commands include execution of EMBOSS applications, file management and project management tasks. Jemboss allows the use of JSSE for encryption of communication between the client and server. The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings. RESULTS: This interface is part of the EMBOSS distribution and has attracted much interest. It has been set up at many other sites globally as well as being used at the HGMP-RC for registered users. AVAILABILITY: The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server: http://www.uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/     

Cache algorithms based on adaptive invalidation reports for mobile environments

Caching of frequently accessed data items can reduce the bandwidth requirement in a mobile wireless computing environment. Periodical broadcast of invalidation reports is an efficient cache invalidation strategy. However, this strategy is severely affected by the disconnection and mobility of the clients. In this paper, we present three adaptive cache invalidation report methods, in which the server broadcasts different invalidation reports according to the update and query rates/patterns and client disconnection time while spending little uplink cost. Simulation results show that the adaptive invalidation methods are efficient in improving mobile caching and reducing the uplink and downlink costs without degrading the system throughput. This revised version was published online in July 2006 with corrections to the Cover Date.     

GenBank.

The GenBank sequence database incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from authors and from large-scale sequencing projects. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive coverage. GenBank continues to focus on quality control and annotation while expanding data coverage and retrieval services. An integrated retrieval system, known asEntrez, incorporates data from the major DNA and protein sequence databases, along with genome maps and protein structure information. MEDLINE abstracts from published articles describing the sequences are also included as an additional source of biological annotation. Sequence similarity searching is offered through the BLAST family of programs. All of NCBI's services are offered through the World Wide Web. In addition, there are specialized server/client versions as well as FTP and e-mail server access.