Background: Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader’s ability to evaluate critically the quality of the results presented or to repeat the experiments.

Content: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement.

Summary: Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.

/pdf/the-miqe-guidelines-minimum-information-for-publication-of-27m8n04lrd.pdf

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

物件導向軟體之架構(Object-Oriented Software Construction)探討

Many practical computing problems concern large graphs. Standard examples include the Web graph and various social networks. The scale of these graphs - in some cases billions of vertices, trillions of edges - poses challenges to their efficient processing. In this paper we present a computational model suitable for this task. Programs are expressed as a sequence of iterations, in each of which a vertex can receive messages sent in the previous iteration, send messages to other vertices, and modify its own state and that of its outgoing edges or mutate graph topology. This vertex-centric approach is flexible enough to express a broad set of algorithms. The model has been designed for efficient, scalable and fault-tolerant implementation on clusters of thousands of commodity computers, and its implied synchronicity makes reasoning about programs easier. Distribution-related details are hidden behind an abstract API. The result is a framework for processing large graphs that is expressive and easy to program.

/pdf/pregel-a-system-for-large-scale-graph-processing-30lgjenxxg.pdf

Pregel: a system for large-scale graph processing

The Unified Medical Language System (http:// umlsks.nlm.nih.gov) is a repository of biomedical vocabularies developed by the US National Library of Medicine. The UMLS integrates over 2 million names for some 900 000 concepts from more than 60 families of biomedical vocabularies, as well as 12 million relations among these concepts. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. In addition to data, the UMLS includes tools for customizing the Metathesaurus (MetamorphoSys), for generating lexical variants of concept names (lvg) and for extracting UMLS concepts from text (MetaMap). The UMLS knowledge sources are updated quarterly. All vocabularies are available at no fee for research purposes within an institution, but UMLS users are required to sign a license agreement. The UMLS knowledge sources are distributed on CD-ROM and by FTP.

/pdf/the-unified-medical-language-system-umls-integrating-e5vpeowaz8.pdf

The Unified Medical Language System (UMLS): integrating biomedical terminology

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Data scientists are usually interested in a subset of sources with properties that are most aligned to intended data use. The SOURCERY system supports interactive multi-criteria user-driven source selection. SOURCERY allows a user to identify criteria they consider of importance and indicate their relative importance, and seeks a source selection result aligned to the user-supplied criteria preferences. The user is given an overview of the properties of the sources that are selected along with visual analyses contextualizing the result in relation to what is theoretically possible and what is possible given the set of available sources. The system also enables a user to interactively perform iterative fine-tuning to explore how changes to preferences may impact results.

/pdf/sourcery-user-driven-multi-criteria-source-selection-24mf3qb4fw.pdf

SOURCERY: User Driven Multi-Criteria Source Selection

Dynamic Threshold Setting for VM Migration

Voyager: Data Discovery and Integration for Onboarding in Data Science

Traditionally, database management systems have been associated with high-cost, high-quality functionalities. That is, powerful capabilities are provided, but only in response to careful design, procurement, deployment and administration. This has been successful in many contexts, but in an environment in which data are available in increasing quantities under the management of a growing collection of distributed applications, and where effective use of available data often provides a competitive edge, there is a requirement for various benefits of a comprehensive data management infrastructure to be made available with rather fewer of the costs. If this requirement is to be met, automation will need to be deployed much more widely and systematically in data management platforms. This paper reviews recent results on autonomic data management, makes a case that current practice presents significant opportunities for further development and argues that comprehensive support for automation should be central to future data management infrastructures, whether centralized or distributed. Copyright © 2008 John Wiley & Sons, Ltd.

Norman W. Paton

Papers

SOURCERY: User Driven Multi-Criteria Source Selection

Dynamic Threshold Setting for VM Migration

Voyager: Data Discovery and Integration for Onboarding in Data Science

Autonomics and data management

Database programming languages : deductive, functional, persistent and object-orientated approaches