SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology

BACKGROUND: The biological information in genomic expression data can be understood, and computationally extracted, in the context of systems of interacting molecules. The automation of this information extraction requires high throughput management and analysis of genomic expression data, and integration of these data with other data types. RESULTS: SBEAMS-Microarray, a module of the open-source Systems Biology Experiment Analysis Management System (SBEAMS), enables MIAME-compliant storage, management, analysis, and integration of high-throughput genomic expression data. It is interoperable with the Cytoscape network integration, visualization, analysis, and modeling software platform. CONCLUSION: SBEAMS-Microarray provides end-to-end support for genomic expression analyses for network-based systems biology research

Nanopore Detector Feedback Control Using Cheminformatics Methods Integrated with Labview/Labwindows Tools

Single biopolymers (DNA, RNA, or polypeptide) can be examined using an alpha-hemolysin channel detector. When a biopolymer is present in an alpha-hemolysin channel it can produce a highly structured ionic current blockade pattern, where the lifetimes at various sub-blockade levels reveal information about the kinetics of the biopolymer. Here we describe integration of LabVIEW/LabWindows automation capabilities with the in-house Channel Current Cheminformatics (CCC) software. Data acquired with LabVIEW/LabWindows is passed to the CCC software, on a streaming real time basis, for analysis and classification. The classification results are then quickly returned to the LabVIEW/LabWindows automation software for experimental feedback control. The prototype signal processing architecture is designed to rapidly extract useful information from noisy blockade signals. A fast, specially designed, generic Hidden Markov Model can be used for the channel current feature extraction. Classification of feature vectors obtained by the HMM can then be done by Support Vector Machines

A unified view of data-intensive flows in business intelligence systems : a survey

Data-intensive flows are central processes in today’s business intelligence (BI) systems, deploying different technologies to deliver data, from a multitude of data sources, in user-preferred and analysis-ready formats. To meet complex requirements of next generation BI systems, we often need an effective combination of the traditionally batched extract-transform-load (ETL) processes that populate a data warehouse (DW) from integrated data sources, and more real-time and operational data flows that integrate source data at runtime. Both academia and industry thus must have a clear understanding of the foundations of data-intensive flows and the challenges of moving towards next generation BI environments. In this paper we present a survey of today’s research on data-intensive flows and the related fundamental fields of database theory. The study is based on a proposed set of dimensions describing the important challenges of data-intensive flows in the next generation BI setting. As a result of this survey, we envision an architecture of a system for managing the lifecycle of data-intensive flows. The results further provide a comprehensive understanding of data-intensive flows, recognizing challenges that still are to be addressed, and how the current solutions can be applied for addressing these challenges.Peer ReviewedPostprint (author's final draft

A question of trust: can we build an evidence base to gain trust in systematic review automation technologies?

Background Although many aspects of systematic reviews use computational tools, systematic reviewers have been reluctant to adopt machine learning tools. Discussion We discuss that the potential reason for the slow adoption of machine learning tools into systematic reviews is multifactorial. We focus on the current absence of trust in automation and set-up challenges as major barriers to adoption. It is important that reviews produced using automation tools are considered non-inferior or superior to current practice. However, this standard will likely not be sufficient to lead to widespread adoption. As with many technologies, it is important that reviewers see “others” in the review community using automation tools. Adoption will also be slow if the automation tools are not compatible with workflows and tasks currently used to produce reviews. Many automation tools being developed for systematic reviews mimic classification problems. Therefore, the evidence that these automation tools are non-inferior or superior can be presented using methods similar to diagnostic test evaluations, i.e., precision and recall compared to a human reviewer. However, the assessment of automation tools does present unique challenges for investigators and systematic reviewers, including the need to clarify which metrics are of interest to the systematic review community and the unique documentation challenges for reproducible software experiments. Conclusion We discuss adoption barriers with the goal of providing tool developers with guidance as to how to design and report such evaluations and for end users to assess their validity. Further, we discuss approaches to formatting and announcing publicly available datasets suitable for assessment of automation technologies and tools. Making these resources available will increase trust that tools are non-inferior or superior to current practice. Finally, we identify that, even with evidence that automation tools are non-inferior or superior to current practice, substantial set-up challenges remain for main stream integration of automation into the systematic review process

Web Data Extraction, Applications and Techniques: A Survey

Web Data Extraction is an important problem that has been studied by means of different scientific tools and in a broad range of applications. Many approaches to extracting data from the Web have been designed to solve specific problems and operate in ad-hoc domains. Other approaches, instead, heavily reuse techniques and algorithms developed in the field of Information Extraction. This survey aims at providing a structured and comprehensive overview of the literature in the field of Web Data Extraction. We provided a simple classification framework in which existing Web Data Extraction applications are grouped into two main classes, namely applications at the Enterprise level and at the Social Web level. At the Enterprise level, Web Data Extraction techniques emerge as a key tool to perform data analysis in Business and Competitive Intelligence systems as well as for business process re-engineering. At the Social Web level, Web Data Extraction techniques allow to gather a large amount of structured data continuously generated and disseminated by Web 2.0, Social Media and Online Social Network users and this offers unprecedented opportunities to analyze human behavior at a very large scale. We discuss also the potential of cross-fertilization, i.e., on the possibility of re-using Web Data Extraction techniques originally designed to work in a given domain, in other domains.Comment: Knowledge-based System

An ‘on-demand’ Data Communication Architecture for Supplying Multiple Applications from a Single Data Source: An Industrial Application Case Study

A key aspect of automation is the manipulation of feedback sensor data for the automated control of particular process actuators. Often in practice this data can be reused for other applications, such as the live update of a graphical user interface, a fault detection application or a business intelligence process performance engine in real-time. In order for this data to be reused effectively, appropriate data communication architecture must be utilised to provide such functionality. This architecture must accommodate the dependencies of the system and sustain the required data transmission speed to ensure stability and data integrity. Such an architecture is presented in this paper, which shows how the data needs of multiple applications are satisfied from a single source of data. It shows how the flexibility of this architecture enables the integration of additional data sources as the data dependencies grow. This research is based on the development of a fully integrated automation system for the test of fuel controls used on civil transport aircraft engines