Integration Of External Tools Research Articles

ALSoD: A user-friendly online bioinformatics tool for amyotrophic lateral sclerosis genetics

Amyotrophic lateral sclerosis (ALS) is the commonest adult onset motor neuron disease, with a peak age of onset in the seventh decade. With advances in genetic technology, there is an enormous increase in the volume of genetic data produced, and a corresponding need for storage, analysis, and interpretation, particularly as our understanding of the relationships between genotype and phenotype mature. Here, we present a system to enable this in the form of the ALS Online Database (ALSoD at http://alsod.iop.kcl.ac.uk), a freely available database that has been transformed from a single gene storage facility recording mutations in the SOD1 gene to a multigene ALS bioinformatics repository and analytical instrument combining genotype, phenotype, and geographical information with associated analysis tools. These include a comparison tool to evaluate genes side by side or jointly with user configurable features, a pathogenicity prediction tool using a combination of computational approaches to distinguish variants with nonfunctional characteristics from disease-associated mutations with more dangerous consequences, and a credibility tool to enable ALS researchers to objectively assess the evidence for gene causation in ALS. Furthermore, integration of external tools, systems for feedback, annotation by users, and two-way links to collaborators hosting complementary databases further enhance the functionality of ALSoD.

TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data

Mass spectrometry coupled to high-performance liquid chromatography (HPLC-MS) is evolving more quickly than ever. A wide range of different instrument types and experimental setups are commonly used. Modern instruments acquire huge amounts of data, thus requiring tools for an efficient and automated data analysis. Most existing software for analyzing HPLC-MS data is monolithic and tailored toward a specific application. A more flexible alternative consists of pipeline-based tool kits allowing the construction of custom analysis workflows from small building blocks, e.g., the Trans Proteomics Pipeline (TPP) or The OpenMS Proteomics Pipeline (TOPP). One drawback, however, is the hurdle of setting up complex workflows using command line tools. We present TOPPAS, The OpenMS Proteomics Pipeline ASsistant, a graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction reduces to simple drag-and-drop of analysis tools and adding connections in between. Integration of external tools into these workflows is possible as well. Once workflows have been developed, they can be deployed in other workflow management systems or batch processing systems in a fully automated fashion. The implementation is portable and has been tested under Windows, Mac OS X, and Linux. TOPPAS is open-source software and available free of charge at http://www.OpenMS.de/TOPPAS .

Verifying the consistency of web-based technical documentations

A new framework for document verification is presented which covers the entire process from document analysis through information extraction, document modeling, representation of background knowledge about the domain of discourse, user level and formal representation of consistency criteria, verification by model checking, counterexample generation, and error reporting. Emphasis is placed on employing background knowledge to reduce the complexity and to increase the quality of results in each step. A rule-based approach to information extraction supports the concise definition of extraction rules for document formats based on XML or HTML. The expressiveness of the existing extraction methods is exceeded by supporting rule specialization, integration of external tools, and access to background knowledge represented in ontologies. As a formal basis for representing consistency criteria, the new temporal description logic ALC CTL is proposed. In contrast to the existing formalisms, criteria related to the coherence of content along individual paths of reading can be represented and verified efficiently. The adequacy, performance, and effectiveness of the proposed framework is demonstrated on a case study in technical documentation.

Introspection mechanisms for runtime verification in a system-level design environment

A new generation of computer-aided design (CAD) tools is mandatory to cope with the growing complexity of System-On-Chip. We believe that they should be built on top of a modern and standard framework. ESys.NET is a design environment based on the .NET Framework. It takes advantage of advanced programming features which facilitates the integration of external tools. This paper presents a runtime verification tool for ESys.NET. Introspection ability is emphasized together with its capabilities to cooperate with third party tools. Introspection is used to retrieve the state of the model during simulation and to check a set of user defined properties. Neither the model nor the simulator is modified by the verification process. Experimentations on an AMBA bus model highlight the effectiveness of this approach.