Thu, 21 Aug 2008 00:50:57 BST CiteULike: moborg's library [188 articles] http://www.citeulike.org/user/moborg CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/moborg/article/1234345 <i>(1999)</i><br /><br />This document contains technical definitions for terms used in the workflow Workflow Management Coalition Terminology Glossary Document (1999) 2007-04-18T15:50:32-00:00 1999 diplomarbeit standard wfmc http://www.citeulike.org/user/moborg/article/2784670 <i>Vol. 0.4 (August 2006)</i> InGrid - Innovative Grid Entwicklungen für ingenieurwissenschaftliche Anwendungen Thomas Friese Christian Schridde Matthew Smith Thomas Barth Tim Dörneman Vol. 0.4 (August 2006) 2008-05-11T16:52:26-00:00 2006 0.4 diplomarbeit grid workflow http://www.citeulike.org/user/moborg/article/2784664 <i>OBJEKTspektrum, Vol. 3 (2007), pp. 34-39.</i><br /><br />Ingenieure erstellen Prototypen, um ausgewählte Merkmale einer neuen Lösung unter Beweis zu stellen. User Interface Prototyping (UI-Prototyping) wird im Usability-Engineering eingesetzt, um Aspekte der Benutzungsschnittstelle zu entwerfen, zu beurteilen und zu verbessern, noch bevor ein lauffähiges System vorhanden ist. Die Prototypen dienen als einfach verständliche und gemeinsame Sprache zwischen Benutzern, Auftraggebern und Entwicklern. Dieser Artikel gibt Ihnen einen Einstieg in die Methodik des UI-Prototyping und zeigt, wie dieses in einem Software-Entwicklungsprojekt nutzbringend eingesetzt werden kann. User Interface Prototyping Markus Flück OBJEKTspektrum, Vol. 3 (2007), pp. 34-39. 2008-05-11T16:47:17-00:00 2007 OBJEKTspektrum 3 34 39 diplomarbeit gui http://www.citeulike.org/user/moborg/article/2770258 <i>Nature reviews. Genetics, Vol. 3, No. 11. (November 2002), pp. 883-889.</i><br /><br />During the past 20 years, the flowering plant Arabidopsis thaliana has been adopted as a model organism by thousands of biologists. This community has developed important tools, resources and experimental approaches that have greatly stimulated plant biological research. Here, we review some of the key events that led to the uptake of Arabidopsis as a model plant and to the growth of the Arabidopsis community. A fortunate choice: the history of Arabidopsis as a model plant. C Somerville M Koornneef doi:10.1038/nrg927 Nature reviews. Genetics, Vol. 3, No. 11. (November 2002), pp. 883-889. 2008-05-08T08:53:23-00:00 2002 Nature reviews. Genetics 1471-0056 3 11 883 889 arabidopsis diplomarbeit http://www.citeulike.org/user/moborg/article/2758357 <i>Nature, Vol. 353, No. 6339. (5 September 1991), pp. 31-37.</i><br /><br />The analysis of mutations affecting flower structure has led to the identification of some of the genes that direct flower development. Cloning of these genes has allowed the formulation of molecular models of how floral meristem and organ identity may be specified, and has shown that the distantly related flowering plants Arabidopsis thaliana and Antirrhinum majus use homologous mechanisms in floral pattern formation. The war of the whorls: genetic interactions controlling flower development. ES Coen EM Meyerowitz doi:10.1038/353031a0 Nature, Vol. 353, No. 6339. (5 September 1991), pp. 31-37. 2008-05-05T16:18:16-00:00 1991 Nature 0028-0836 353 6339 31 37 abc bioinformatic diplomarbeit http://www.citeulike.org/user/moborg/article/2733205 <i>BMC Genomics, Vol. 9 (28 April 2008), 194.</i> Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots Elke Mangelsen Joachim Kilian Kenneth Berendzen Uener Kolukisaoglu Klaus Harter Christer Jansson Dierk Wanke doi:10.1186/1471-2164-9-194 BMC Genomics, Vol. 9 (28 April 2008), 194. 2008-04-29T09:23:53-00:00 2008 BMC Genomics 1471-2164 9 194 diplomarbeit http://www.citeulike.org/user/moborg/article/99946 <i>(15 March 2001)</i><br /><br />WSDL is an XML format for describing network services as a set of endpoints operating on messages containing either document-oriented or procedure-oriented information. The operations and messages are described abstractly, and then bound to a concrete network protocol and message format to define an endpoint. Related concrete endpoints are combined into abstract endpoints (services). WSDL is extensible to allow description of endpoints and their messages regardless of what message formats or network protocols are used to communicate, however, the only bindings described in this document describe how to use WSDL in conjunction with SOAP 1.1, HTTP GET/POST, and MIME Web Service Definition Language (WSDL) Erik Christensen Francisco Curbera Greg Meredith Sanjiva Weerawarana (15 March 2001) 2005-02-21T14:00:59-00:00 2001 diplomarbeit webservices wsdl http://www.citeulike.org/user/moborg/article/115151 <i>(05 November 2002)</i> Patterns of Enterprise Application Architecture Martin Fowler (05 November 2002) 2005-03-06T00:35:57-00:00 2002 Addison-Wesley Professional diplomarbeit patterns http://www.citeulike.org/user/moborg/article/2702484 <i>Forschung und Wissenschaftliches Rechnen, Vol. 68 (2004), pp. 0176-2516.</i> A work flow engine for microbial genome research M Rampp T Soddemann Forschung und Wissenschaftliches Rechnen, Vol. 68 (2004), pp. 0176-2516. 2008-04-22T15:50:46-00:00 2004 Forschung und Wissenschaftliches Rechnen 68 0176 2516 bioinformatic diplomarbeit http://www.citeulike.org/user/moborg/article/2702365 <i>Mobile Networks and Applications, Vol. 9, No. 5. (1 October 2004), pp. 473-480.</i><br /><br />Current workflow management systems have several limitations that need to be addressed by the research community. This paper deals with two of them: the lack of flexibility necessary in a changing business environment, and the lack of transactional guarantees for workflow applications. Providing Transactional Properties for Migrating Workflows Andrzej Cichocki Marek Rusinkiewicz doi:10.1023/B:MONE.0000034701.73879.cf Mobile Networks and Applications, Vol. 9, No. 5. (1 October 2004), pp. 473-480. 2008-04-22T14:35:49-00:00 2004 Mobile Networks and Applications 9 5 473 480 diplomarbeit sec workflow http://www.citeulike.org/user/moborg/article/2701040 <i>(2005)</i><br /><br />Scientific workflows are becoming increasingly important as a unifying mechanism for interlinking scientific data management, analysis, simulation, and visualization tasks. Scientific workflow systems are problem-solving environments, supporting scientists in the creation and execution of scientific workflows. Actor-oriented design of scientific workflows S Bowers B Ascher (2005) 2008-04-22T11:55:51-00:00 2005 diplomarbeit kepler wfms workflow http://www.citeulike.org/user/moborg/article/2701025 <i>Data Integration in the Life Sciences (2006), pp. 248-263.</i><br /><br />Steps in scientific workflows often generate collections of results, causing the data flowing through workflows to become increasingly nested. Because conventional workflow components (or actors) typically operate on simple or application-specific data types, additional actors often are required to manage these nested data collections. As a result, conventional workflows become increasingly complex as data becomes more nested. This paper describes a new paradigm for developing scientific workflows that transparently manages nested data collections. Collection-oriented workflows have a number of advantages over conventional approaches including simpler workflow designs (e.g., requiring fewer actors and control-flow constructs) that are invariant under changes in data nesting. Our implementation within the Kepler scientific workflow system enables the explicit representation of collections and collection schemas, concurrent operation over collection contents via multi-level pipeline parallelism, and allows collection-aware actors to be composed readily from conventional actors. Collection-Oriented Scientific Workflows for Integrating and Analyzing Biological Data Timothy Mcphillips Shawn Bowers Bertram Ludäscher doi:10.1007/11799511_23 Data Integration in the Life Sciences (2006), pp. 248-263. 2008-04-22T11:45:03-00:00 2006 Data Integration in the Life Sciences 248 263 bioinformatic diplomarbeit kepler wfms http://www.citeulike.org/user/moborg/article/2624422 <i>Scientific and Statistical Database Management, 2004. Proceedings. 16th International Conference on (2004), pp. 423-424.</i><br /><br />Most scientists conduct analyses and run models in several different software and hardware environments, mentally coordinating the export and import of data from one environment to another. The Kepler scientific workflow system provides domain scientists with an easy-to-use yet powerful system for capturing scientific workflows (SWFs). SWFs are a formalization of the ad-hoc process that a scientist may go through to get from raw data to publishable results. Kepler attempts to streamline the workflow creation and execution process so that scientists can design, execute, monitor, re-run, and communicate analytical procedures repeatedly with minimal effort. Kepler is unique in that it seamlessly combines high-level workflow design with execution and runtime interaction, access to local and remote data, and local and remote service invocation. SWFs are superficially similar to business process workflows but have several challenges not present in the business workflow scenario. For example, they often operate on large, complex and heterogeneous data, can be computationally intensive and produce complex derived data products that may be archived for use in reparameterized runs or other workflows. Moreover, unlike business workflows, SWFs are often dataflow-oriented as witnessed by a number of recent academic systems (e.g., DiscoveryNet, Taverna and Triana) and commercial systems (Scitegic/Pipeline-Pilot, Inforsense). In a sense, SWFs are often closer to signal-processing and data streaming applications than they are to control-oriented business workflow applications. Kepler: an extensible system for design and execution of scientific workflows I Altintas C Berkley E Jaeger M Jones B Ludascher S Mock doi:10.1109/SSDM.2004.1311241 Scientific and Statistical Database Management, 2004. Proceedings. 16th International Conference on (2004), pp. 423-424. 2008-04-02T20:46:26-00:00 2004 Scientific and Statistical Database Management, 2004. Proceedings. 16th International Conference on 423 424 diplomarbeit wfms workflow http://www.citeulike.org/user/moborg/article/1778884 <i>Genome Res, Vol. 13, No. 4. (April 2003), pp. 662-672.</i><br /><br />Gene Ontology Annotation (GOA) is a project run by the European Bioinformatics Institute (EBI) that aims to provide assignments of terms from the Gene Ontology (GO) resource to gene products in a number of its databases (http://www.ebi.ac.uk/GOA). In the first stage of this project, GO assignments have been applied to a data set representing the complete human proteome by a combination of electronic mappings and manual curation. This vocabulary has also been applied to the nonredundant proteome sets for all other completely sequenced organisms as well as to proteins from a wide range of organisms where the proteome is not yet complete. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. E Camon M Magrane D Barrell D Binns W Fleischmann P Kersey N Mulder T Oinn J Maslen A Cox R Apweiler doi:10.1101/gr.461403 Genome Res, Vol. 13, No. 4. (April 2003), pp. 662-672. 2007-10-17T08:35:09-00:00 2003 Genome Res 1088-9051 13 4 662 672 bioinformatic diplomarbeit standard http://www.citeulike.org/user/moborg/article/2695990 <i>Nucleic Acids Research, Vol. 24, No. 1. (1 January 1996)</i> The Molecular Biology Database Collection DA Benson Nucleic Acids Research, Vol. 24, No. 1. (1 January 1996) 2008-04-21T13:22:54-00:00 1996 Nucleic Acids Research 24 1 Oxford University Press dbcollection diplomarbeit standard http://www.citeulike.org/user/moborg/article/1946925 <i>Nucl. Acids Res. (19 November 2007), gkm1037.</i><br /><br />The Nucleic Acids Research online Molecular Biology Database Collection is a public repository that lists more than 1000 databases described in this and previous Nucleic Acids Research annual database issues, as well as a selection of molecular biology databases described in other journals. All databases included in this Collection are freely available to the public. The 2008 update includes 1078 databases, 110 more than the previous one. The links to more than 80 databases have been updated and 25 obsolete databases have been removed from the list. The complete database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oxfordjournals.org/. 10.1093/nar/gkm1037 The Molecular Biology Database Collection: 2008 update Michael Galperin doi:10.1093/nar/gkm1037 Nucl. Acids Res. (19 November 2007), gkm1037. 2007-11-20T19:51:33-00:00 2007 Nucl. Acids Res. gkm1037 bioinformatic diplomarbeit http://www.citeulike.org/user/moborg/article/2689030 <i>BMC Bioinformatics, Vol. 6, No. 1. (2005)</i><br /><br />BACKGROUND:We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level.RESULTS:In the present paper, we discuss strengths and weaknesses of DIALIGN in view of the underlying objective function. Based on these results, we propose several heuristics to improve the segment-based alignment approach. For pairwise alignment, we implemented a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, we use an improved greedy procedure that is less sensitive to spurious local sequence similarities. To evaluate our method on globally related protein families, we used the well-known database BAliBASE. For benchmarking tests on locally related sequences, we created a new reference database called IRMBASE which consists of simulated conserved motifs implanted into non-related random sequences.CONCLUSION:On BAliBASE, our new program performs significantly better than the previous version of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment. On the locally related test sets in IRMBASE, our method outperforms all other programs that we evaluated. DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment Amarendran Subramanian Jan Menkhoff Michael Kaufmann Burkhard Morgenstern doi:10.1186/1471-2105-6-66 BMC Bioinformatics, Vol. 6, No. 1. (2005) 2008-04-18T18:23:25-00:00 2005 BMC Bioinformatics 6 1 bioinformatic diplomarbeit http://www.citeulike.org/user/moborg/article/2677597 <i>(2007), pp. 603-610.</i> Designing the myExperiment Virtual Research Environment for the Social Sharing of Workflows David De Roure Carole Goble Robert Stevens doi:10.1109/E-SCIENCE.2007.29 (2007), pp. 603-610. 2008-04-16T11:09:01-00:00 2007 603 610 IEEE Computer Society diplomarbeit myexperiment taverna http://www.citeulike.org/user/moborg/article/2677582 <i>Nature, Vol. 451, No. 7181. (21 February 2008), pp. 1024-1025.</i> The new networking nexus. V Gewin Nature, Vol. 451, No. 7181. (21 February 2008), pp. 1024-1025. 2008-04-16T11:02:32-00:00 2008 Nature 1476-4687 451 7181 1024 1025 diplomarbeit myexperiment taverna http://www.citeulike.org/user/moborg/article/1823735 <i>(15 December 2007)</i> Web 2.0 Design Patterns: What entrepreneurs and information architects need to know Duane Nickull Dion Hinchcliffe James Governor (15 December 2007) 2007-10-26T05:40:31-00:00 2007 Adobe Dev Library diplomarbeit patterns http://www.citeulike.org/user/moborg/article/463562 <i>(31 July 2004)</i> Entwurfsmuster John Vlissides (31 July 2004) 2006-01-12T19:52:16-00:00 2004 Addison Wesley Verlag diplomarbeit patterns http://www.citeulike.org/user/moborg/article/1028656 <i>(1997)</i><br /><br />Asynchronous Completion Token pattern allows applications to efficiently associate state with the completion of asynchronous operations. Contemporary applications must respond to many types of events, ranging from user interface notifications to network messages. Delay-sensitive applications, such as network management systems, often perform long-running operations asynchronously to avoid blocking the processing of other pending events. When these asynchronous operations complete, applications... Asynchronous Completion Token: an Object Behavioral Pattern for Efficient Asynchronous Event Handling I Pyarali T Harrison D Schmidt (1997) 2007-01-07T01:14:41-00:00 1997 diplomarbeit patterns http://www.citeulike.org/user/moborg/article/853308 <i>Computerwoche, No. 6/2006. (10 February 2006)</i><br /><br />Die Business Process Execution Language (BPEL) erlaubt es, Geschäftsprozess-Management auf IT-Ebene durchzusetzen. Voraussetzung ist ein mutiger Umbau der Organisation zugunsten besserer Workflows. Mit BPEL in eine neue Entwicklungs-Ära Torsten Winterberg Rolf Scheuch Computerwoche, No. 6/2006. (10 February 2006) 2006-09-21T17:23:16-00:00 2006 Computerwoche 6/2006 bpel diplomarbeit http://www.citeulike.org/user/moborg/article/576119 <i>Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2814-2820.</i><br /><br />MOTIVATION: The NCBI dbSNP database lists over 9 million single nucleotide polymorphisms (SNPs) in the human genome, but currently contains limited annotation information. SNPs that result in amino acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity. RESULTS: We have developed LS-SNP, a genomic scale software pipeline to annotate nsSNPs. LS-SNP comprehensively maps nsSNPs onto protein sequences, functional pathways and comparative protein structure models, and predicts positions where nsSNPs destabilize proteins, interfere with the formation of domain-domain interfaces, have an effect on protein-ligand binding or severely impact human health. It currently annotates 28,043 validated SNPs that produce amino acid residue substitutions in human proteins from the SwissProt/TrEMBL database. Annotations can be viewed via a web interface either in the context of a genomic region or by selecting sets of SNPs, genes, proteins or pathways. These results are useful for identifying candidate functional SNPs within a gene, haplotype or pathway and in probing molecular mechanisms responsible for functional impacts of nsSNPs. AVAILABILITY: http://www.salilab.org/LS-SNP CONTACT: rachelk@salilab.org SUPPLEMENTARY INFORMATION: http://salilab.org/LS-SNP/supp-info.pdf. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. R Karchin M Diekhans L Kelly DJ Thomas U Pieper N Eswar D Haussler A Sali Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2814-2820. 2006-04-04T18:29:25-00:00 2005 Bioinformatics 1367-4803 21 12 2814 2820 bioinformatic diplomarbeit standard http://www.citeulike.org/user/moborg/article/2634537 <i>Pädiatrische Hämatologie und Onkologie (2006), pp. 560-577.</i><br /><br />»How is it that we know so little, given that we have so much information?« (Noam Chomsky). Gerade auf dem Gebiet der molekularen Medizin und Pharmakologie ist ein enormer Wissenszuwachs zu verzeichnen, der neue therapeutische Perspektiven eröffnet. Trotzdem erfolgt der Einsatz der Chemotherapie derzeit noch weitgehend empirisch. Dieses Kapitel soll zur rationalen Anwendung der Chemotherapie beitragen. Chemotherapie Leo Kager Claudia Langebrake Ulrike Kastner doi:10.1007/3-540-29036-2_50 Pädiatrische Hämatologie und Onkologie (2006), pp. 560-577. 2008-04-06T11:30:25-00:00 2006 Pädiatrische Hämatologie und Onkologie 560 577 ausblick chemo diplomarbeit http://www.citeulike.org/user/moborg/article/294515 <i>(08 September 1999)</i> Production Workflow: Concepts and Techniques Frank Leymann Dieter Roller (08 September 1999) 2005-08-16T18:10:42-00:00 1999 Prentice Hall PTR diplomarbeit standard workflow http://www.citeulike.org/user/moborg/article/2580389 <i>Informatik-Spektrum, Vol. 22, No. 2. (10 April 1999), pp. 99-109.</i><br /><br />Zusammenfassung   Mit der Geschäftsprozeßorientierung der Unternehmen stellt auch die Informationstechnologie (IT) mit Workflow-Management-Systemen (WfMS) entsprechende Werkzeuge bereit. WfMS vollziehen dabei die Integration der einzelnen Aufgaben und der verschiedenen Applikationen eines Geschäftsprozesses zu einem vollständigen Ablauf. Dazu haben sie sämtliche notwendigen organisatorischen Informationen eines Geschäftsprozesse hinterlegt wie z.B. wer wann was macht bzw. machen darf. – Zweier wichtiger Punkte von WfMS widmen sich verschiedene Standards: Integration und Interoperabilität. Zu nennen sind hier die Workflow Management Coalition (WfMC) und die Simple Workflow Access Protocol Initiative (SWAP). Ein anderer Punkt ist die Frage des geeigneten WfMS für die identifizierten Prozesse. Dazu kann die Klassifikation an Hand von Prozeßfrequenz und Prozeßstrukturierung in Ad-hoc-WfMS, Collborate-WfMS und Produktions-WfMS helfen. Insgesamt erhalten Anwender mit WfMS ein Werkzeug, das das Auschöpfen der hohen Einsparungspotentiale ermöglicht. Diese können laut einer Studie bis zu 90% der Durchlaufzeit eines Geschäftsprozesses betragen. Workflow-Management-Systeme Ein Beitrag der IT zur Geschäftsprozeß-Orientierung & -Optimierung – Grundlagen, Standards und Trends – Christian Hastedt-Marckwardt doi:10.1007/s002870050129 Informatik-Spektrum, Vol. 22, No. 2. (10 April 1999), pp. 99-109. 2008-03-24T12:32:08-00:00 1999 Informatik-Spektrum 22 2 99 109 diplomarbeit wfms http://www.citeulike.org/user/moborg/article/2560639 <i>Formal Methods for Mobile Computing (2005), pp. 234-270.</i><br /><br />Hermes is a middleware system for design and execution of activity-based applications in distributed environments. It supports mobile computation as an application implementation strategy. While middleware for mobile computing has typically been developed to support physical and logical mobility, Hermes provides an integrated environment where application domain experts can focus on designing activity workflow and ignore the topological structure of the distributed environment. Generating mobile agents from a workflow specification is the responsibility of a context-aware compiler.Hermes is structured as a component-based, agent-oriented system with a 3-layer software architecture. It can be configured for specific application domains by adding domain-specific component libraries. The Hermes middleware layer, compilers, libraries, services and other developed tools together result in a very general programming environment, which has been validated in two quite disparate application domains, one in industrial control and the other in bioinformatics. In the industrial control domain, embedded systems with scarce computational resources control product lines. Mobile agents are used to trace products and support self-healing. In the bionformatics domain, mobile agents are used to support data collection and service discovery, and to simulate biological system through autonomous components interactions. Hermes: Agent-Based Middleware for Mobile Computing Flavio Corradini Emanuela Merelli doi:10.1007/11419822_8 Formal Methods for Mobile Computing (2005), pp. 234-270. 2008-03-19T13:21:57-00:00 2005 Formal Methods for Mobile Computing 234 270 biowms diplomarbeit middleware http://www.citeulike.org/user/moborg/article/2552020 <i>(May 2008, accepted)</i><br /><br />Workflow design is often an effort of distributed and inhomogeneous teams. We present a collaborative workflow design tool, which is implemented as a Rich Internet Application. The tool provides a desktop like user experience, but can easily be embedded into web sites. It enables synchronous as well as asynchronous cooperation of design team members and encourages a well coordinated design process. Collaborative BPEL Design with a Rich Internet Application Markus Held Wolfgang Blochinger (May 2008, accepted) 2008-03-18T16:32:01-00:00 bpel diplomarbeit hobbes http://www.citeulike.org/user/moborg/article/1724080 <i>BMC Bioinformatics, Vol. 8, No. 1. (2007)</i><br /><br />BACKGROUND:Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources.RESULTS:We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a webinterface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB.CONCLUSIONS:BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org. BNDB - The Biochemical Network Database Jan Kuentzer Christina Backes Torsten Blum Andreas Gerasch Michael Kaufmann Oliver Kohlbacher Hans Lenhof doi:10.1186/1471-2105-8-367 BMC Bioinformatics, Vol. 8, No. 1. (2007) 2007-10-03T13:48:03-00:00 2007 BMC Bioinformatics 8 1 bioinformatic db dbcollection http://www.citeulike.org/user/moborg/article/2549578 <i>(30 April 2007)</i> Orchestrierung datenintensiver Prozesse Maik Thiele Dirk Habich (30 April 2007) 2008-03-18T09:19:34-00:00 2007 VDM Verlag bioinformatic bpel diplomarbeit webservices http://www.citeulike.org/user/moborg/article/94348 <i>Nucleic Acids Res, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680.</i><br /><br />The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson doi:10.1093/nar/22.22.4673 Nucleic Acids Res, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680. 2005-02-14T12:22:21-00:00 1994 Nucleic Acids Res 0305-1048 22 22 4673 4680 algorithms bioinformatic diplomarbeit http://www.citeulike.org/user/moborg/article/2072522 <i>Gene, Vol. 73, No. 1. (15 December 1988), pp. 237-244.</i><br /><br />An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following the order of branching in the tree. The method is sufficiently fast and economical with memory to be easily implemented on a microcomputer, and yet the results obtained are comparable to those from packages requiring mainframe computer facilities. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer Desmond Higgins Paul Sharp doi:10.1016/0378-1119(88)90330-7 Gene, Vol. 73, No. 1. (15 December 1988), pp. 237-244. 2007-12-07T10:57:13-00:00 1988 Gene 73 1 237 244 algorithms bioinformatic diplomarbeit http://www.citeulike.org/user/moborg/article/1040391 <i>Drug Discovery Today, Vol. 10, No. 22. (15 November 2005), pp. 1566-1572.</i><br /><br />Since the Life Science Identifier (LSID) data identification and access standard made its official debut in late 2004, several organizations have begun to use LSIDs to simplify the methods used to uniquely name, reference and retrieve distributed data objects and concepts. In this review, the authors build on introductory work that describes the LSID standard by documenting how five early adopters have incorporated the standard into their technology infrastructure and by outlining several common misconceptions and difficulties related to LSID use, including the impact of the byte identity requirement for LSID-identified objects and the opacity recommendation for use of the LSID syntax. The review describes several shortcomings of the LSID standard, such as the lack of a specific metadata standard, along with solutions that could be addressed in future revisions of the specification. The impact of Life Science Identifier on informatics data Sean Martin Moses Hohman Ted Liefeld doi:10.1016/S1359-6446(05)03651-2 Drug Discovery Today, Vol. 10, No. 22. (15 November 2005), pp. 1566-1572. 2007-01-13T23:46:09-00:00 2005 Drug Discovery Today 10 22 1566 1572 bioinformatic diplomarbeit lsid notprinted http://www.citeulike.org/user/moborg/article/749414 <i>Biodiversity Informatics, Vol. 3 (2006), pp. 1-15.</i><br /><br />Life Science Identifiers (LSIDs) offer an attractive solution to the problem of globally unique identifiers for digital objects in biology. However, I suggest that in the context of taxonomic names, the most compelling benefit of adopting these identifiers comes from the metadata associated with each LSID. By using existing vocabularies wherever possible, and using a simple vocabulary for taxonomy-specific concepts we can quickly capture the essential information about a taxonomic name in the Resource Description Framework (RDF) format. This opens up the prospect of using technologies developed for the Semantic Web to add “taxonomic intelligence" to biodiversity databases. This essay explores some of these ideas in the context of providing a taxonomic framework for the phylogenetic database TreeBASE. Taxonomic names, metadata, and the Semantic Web Roderic Page Biodiversity Informatics, Vol. 3 (2006), pp. 1-15. 2006-07-10T14:05:03-00:00 2006 Biodiversity Informatics 3 1 15 bioinformatic diplomarbeit lsid http://www.citeulike.org/user/moborg/article/2365227 <i>Nucl. Acids Res. (5 November 2007), gkm965.</i><br /><br />The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research community. New developments at TAIR include the addition of the GBrowse genome viewer to the TAIR site, a redesigned home page, navigation structure and portal pages to make the site more intuitive and easier to use, the launch of several TAIR web services and a new genome annotation release (TAIR7) in April 2007. A combination of manual and computational methods were used to generate this release, which contains 27 029 protein-coding genes, 3889 pseudogenes or transposable elements and 1123 ncRNAs (32 041 genes in all, 37 019 gene models). A total of 681 new genes and 1002 new splice variants were added. Overall, 10 098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release. 10.1093/nar/gkm965 The Arabidopsis Information Resource (TAIR): gene structure and function annotation David Swarbreck Christopher Wilks Philippe Lamesch Tanya Berardini Margarita Garcia-Hernandez Hartmut Foerster Donghui Li Tom Meyer Robert Muller Larry Ploetz Amie Radenbaugh Shanker Singh Vanessa Swing Christophe Tissier Peifen Zhang Eva Huala doi:10.1093/nar/gkm965 Nucl. Acids Res. (5 November 2007), gkm965. 2008-02-12T08:40:24-00:00 2007 Nucl. Acids Res. gkm965 arabidopsis diplomarbeit notprinted http://www.citeulike.org/user/moborg/article/190338 <i>Nature, Vol. 408, No. 6814. (14 December 2000), pp. 796-815.</i><br /><br />The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. doi:10.1038/35048692 Nature, Vol. 408, No. 6814. (14 December 2000), pp. 796-815. 2005-05-09T20:19:21-00:00 2000 Nature 0028-0836 408 6814 796 815 arabidopsis diplomarbeit notprinted http://www.citeulike.org/user/moborg/article/907402 <i>Brief Bioinform, Vol. 7, No. 3. (September 2006), pp. 287-296.</i><br /><br />This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources. Open source tools and toolkits for bioinformatics: significance, and where are we? JE Stajich H Lapp doi:10.1093/bib/bbl026 Brief Bioinform, Vol. 7, No. 3. (September 2006), pp. 287-296. 2006-10-20T03:47:36-00:00 2006 Brief Bioinform 1467-5463 7 3 287 296 bioinformatic diplomarbeit notprinted opensource http://www.citeulike.org/user/moborg/article/2319728 <i>Brief Bioinform, Vol. 9, No. 1. (January 2008), pp. 57-68.</i><br /><br />Data integration is needed in order to cope with the huge amounts of biological information now available and to perform data mining effectively. Current data integration systems have strict limitations, mainly due to the number of resources, their size and frequency of updates, their heterogeneity and distribution on the Internet. Integration must therefore be achieved by accessing network services through flexible and extensible data integration and analysis network tools. EXtensible Markup Language (XML), Web Services and Workflow Management Systems (WMS) can support the creation and deployment of such systems. Many XML languages and Web Services for bioinformatics have already been designed and implemented and some WMS have been proposed. In this article, we review a methodology for data integration in biomedical research that is based on these technologies. We also briefly describe some of the available WMS and discuss the current limitations of this methodology and the ways in which they can be overcome. Automation of in-silico data analysis processes through workflow management systems. P Romano doi:10.1093/bib/bbm056 Brief Bioinform, Vol. 9, No. 1. (January 2008), pp. 57-68. 2008-02-01T15:12:26-00:00 2008 Brief Bioinform 1477-4054 9 1 57 68 bioinformatic diplomarbeit notprinted wfms xml http://www.citeulike.org/user/moborg/article/2515041 <i>Ann Bot, Vol. 91, No. 5. (1 April 2003), pp. 547-557.</i><br /><br />Recent genome sequencing papers have given genome sizes of 180 Mb for Drosophila melanogaster Iso-1 and 125 Mb for Arabidopsis thaliana Columbia. The former agrees with early cytochemical estimates, but numerous cytometric estimates of around 170 Mb imply that a genome size of 125 Mb for arabidopsis is an underestimate. In this study, nuclei of species pairs were compared directly using flow cytometry. Co-run Columbia and Iso-1 female gave a 2C peak for arabidopsis only approx. 15 % below that for drosophila, and 16C endopolyploid Columbia nuclei had approx. 15 % more DNA than 2C chicken nuclei (with >2280 Mb). Caenorhabditis elegans Bristol N2 (genome size approx. 100 Mb) co-run with Columbia or Iso-1 gave a 2C peak for drosophila approx. 75 % above that for 2C C. elegans, and a 2C peak for arabidopsis approx. 57 % above that for C. elegans. This confirms that 1C in drosophila is approx. 175 Mb and, combined with other evidence, leads us to conclude that the genome size of arabidopsis is not approx. 125 Mb, but probably approx. 157 Mb. It is likely that the discrepancy represents extra repeated sequences in unsequenced gaps in heterochromatic regions. Complete sequencing of the arabidopsis genome until no gaps remain at telomeres, nucleolar organizing regions or centromeres is still needed to provide the first precise angiosperm C-value as a benchmark calibration standard for plant genomes, and to ensure that no genes have been missed in arabidopsis, especially in centromeric regions, which are clearly larger than once imagined. 10.1093/aob/mcg057 Comparisons with Caenorhabditis (~100 Mb) and Drosophila (~175 Mb) Using Flow Cytometry Show Genome Size in Arabidopsis to be ~157 Mb and thus ~25 % Larger than the Arabidopsis Genome Initiative Estimate of ~125 Mb Michael Bennett Ilia Leitch James Price Spencer Johnston doi:10.1093/aob/mcg057 Ann Bot, Vol. 91, No. 5. (1 April 2003), pp. 547-557. 2008-03-11T13:56:40-00:00 2003 Ann Bot 91 5 547 557 arabidopsis diplomarbeit http://www.citeulike.org/user/moborg/article/1203876 <i>Bioinformatics, Vol. 23, No. 6. (15 March 2007), pp. 780-782.</i><br /><br />Summary: DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow services. The use of an automated BioMoby workflow, rather than manual surfing', to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMoby Services enables fine-grained reusing of each service in other workflows, thus reducing the effort required to achieve similar investigations in the future. Availability: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml. Contact: stebbutt@mrl.ubc.ca Supplementary information: Additional information, including test result data, is available from the iCAPTURE Centre web site (see above). 10.1093/bioinformatics/btl648 DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs Young Song Edward Kawas Ben Good Mark Wilkinson Scott Tebbutt doi:10.1093/bioinformatics/btl648 Bioinformatics, Vol. 23, No. 6. (15 March 2007), pp. 780-782. 2007-04-03T09:18:16-00:00 2007 Bioinformatics 23 6 780 782 bioinformatic biomoby diplomarbeit http://www.citeulike.org/user/moborg/article/2318440 <i>Brief Bioinform (31 January 2008), bbn003.</i><br /><br />The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby.org/. 10.1093/bib/bbn003 Interoperability with Moby 1.0--It's better than sharing your toothbrush! The Consortium doi:10.1093/bib/bbn003 Brief Bioinform (31 January 2008), bbn003. 2008-02-01T08:26:50-00:00 2008 Brief Bioinform bbn003 bioinformatic biomoby diplomarbeit http://www.citeulike.org/user/moborg/article/1877930 <i>Distributed and Parallel Databases, Vol. 13, No. 1. (1 January 2003), pp. 7-42.</i><br /><br />Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [26]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration of Molecular Biology data from different sources. This paper is primarily intended for an audience of computer scientists with a limited background in Biology. A Computational Biology Database Digest: Data, Data Analysis, and Data Management François Bry Peer Kröger doi:10.1023/A:1021540705916 Distributed and Parallel Databases, Vol. 13, No. 1. (1 January 2003), pp. 7-42. 2007-11-07T16:11:49-00:00 2003 Distributed and Parallel Databases 13 1 7 42 bioinformatic db diplomarbeit standard http://www.citeulike.org/user/moborg/article/1874718 <i>Genome Biology, Vol. 3, No. 7. (2002), pp. comment1010.1-comment1010.2.</i> No place like Ome Gregory Petsko doi:10.1186/gb-2002-3-7-comment1010 Genome Biology, Vol. 3, No. 7. (2002), pp. comment1010.1-comment1010.2. 2007-11-06T17:40:16-00:00 2002 Genome Biology 3 7 comment1010.1 comment1010.2 bioinformatic diplomarbeit omics http://www.citeulike.org/user/moborg/article/1874228 <i>The Scientist, Vol. 17, No. 7. (2 April 2001)</i> The Scientist : 'Ome Sweet 'Omics-- A Genealogical Treasury of Words Joshua Lederberg Alexa Mccray The Scientist, Vol. 17, No. 7. (2 April 2001) 2007-11-06T14:48:29-00:00 2001 The Scientist 17 7 bioinformatic diplomarbeit standard http://www.citeulike.org/user/moborg/article/802634 <i>Bioinformatics, Vol. 22, No. 15. (1 August 2006), pp. 1910-1916.</i><br /><br />Motivation: The complexity of cancer is prompting researchers to find new ways to synthesize information from diverse data sources and to carry out coordinated research efforts that span multiple institutions. There is a need for standard applications, common data models, and software infrastructure to enable more efficient access to and sharing of distributed computational resources in cancer research. To address this need the National Cancer Institute (NCI) has initiated a national-scale effort, called the cancer Biomedical Informatics Grid (caBIGTM), to develop a federation of interoperable research information systems. Results: At the heart of the caBIG approach to federated interoperability effort is a Grid middleware infrastructure, called caGrid. In this paper we describe the caGrid framework and its current implementation, caGrid version 0.5. caGrid is a model-driven and service-oriented architecture that synthesizes and extends a number of technologies to provide a standardized framework for the advertising, discovery, and invocation of data and analytical resources. We expect caGrid to greatly facilitate the launch and ongoing management of coordinated cancer research studies involving multiple institutions, to provide the ability to manage and securely share information and analytic resources, and to spur a new generation of research applications that empower researchers to take a more integrative, trans-domain approach to data mining and analysis. Availability: The caGrid version 0.5 release can be downloaded from https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/. The operational test bed Grid can be accessed through the client included in the release, or through the caGrid-browser web application http://cagrid-browser.nci.nih.gov. Contact: joel.saltz@osumc.edu 10.1093/bioinformatics/btl272 caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid Joel Saltz Scott Oster Shannon Hastings Stephen Langella Tahsin Kurc William Sanchez Manav Kher Arumani Manisundaram Krishnakant Shanbhag Peter Covitz doi:10.1093/bioinformatics/btl272 Bioinformatics, Vol. 22, No. 15. (1 August 2006), pp. 1910-1916. 2006-08-16T10:27:14-00:00 2006 Bioinformatics 22 15 1910 1916 bpel diplomarbeit evaluation grid wfms workflow http://www.citeulike.org/user/moborg/article/1869029 <i>(December 2006)</i> Reliable Scientific Service Compositions B Wassermann W Emmerich (December 2006) 2007-11-05T15:20:46-00:00 2006 Springer Verlag bibtex-import diplomarbeit printed webservices http://www.citeulike.org/user/moborg/article/100088 <i>J Mol Biol, Vol. 215, No. 3. (5 October 1990), pp. 403-410.</i><br /><br />A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman doi:10.1006/jmbi.1990.9999 J Mol Biol, Vol. 215, No. 3. (5 October 1990), pp. 403-410. 2005-02-21T16:47:03-00:00 1990 J Mol Biol 0022-2836 215 3 403 410 bioinformatic blast diplomarbeit standard http://www.citeulike.org/user/moborg/article/1810832 <i>Informatik-Spektrum, Vol. 28, No. 5. (12 October 2005), pp. 413-416.</i><br /><br />Das Schlagwort der serviceorientierten Architektur (SOA) beherrscht gegenwärtig die Diskussion um die Gestaltung unternehmensweiter Anwendungslandschaften. Dabei wird SOA häufig gleichgesetzt mit der Verwendung von Web Services und deren assoziierten Technologien. SOA sollte aber als fachliches Architekturmuster interpretiert werden, das technologieunabhängig angewendet werden kann. Serviceorientierte Architektur Jan-Peter Richter Harald Haller Peter Schrey doi:10.1007/s00287-005-0021-4 Informatik-Spektrum, Vol. 28, No. 5. (12 October 2005), pp. 413-416. 2007-10-23T14:07:46-00:00 2005 Informatik-Spektrum 28 5 413 416 diplomarbeit informatic soa standard toget vpn http://www.citeulike.org/user/moborg/article/1806909 <i>BMC Bioinformatics, Vol. 2, No. 1. (2001)</i><br /><br />BACKGROUND:Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory.RESULTS:Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example.CONCLUSIONS:The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/. The Distributed Annotation System Robin Dowell Rodney Jokerst Allen Day Sean Eddy Lincoln Stein doi:10.1186/1471-2105-2-7 BMC Bioinformatics, Vol. 2, No. 1. (2001) 2007-10-22T15:05:22-00:00 2001 BMC Bioinformatics 2 1 bioinformatic das diplomarbeit sequences standard