Structuring research methods and data with the research object model: genomics workflows as a case study

Background: One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. Results: We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as “which particular data was input to a particular workflow to test a particular hypothesis?”, and “which particular conclusions were drawn from a particular workflow?”. Conclusions: Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well.

Health survey research methods : third biennial conference.

Mode of access: Internet.

Interdisciplinary team research: methods and problems.

Includes bibliography.

Range research methods : a symposium, Denver, Colorado, May 1962 /

Includes bibliographical references (p. 155-172).

Comparisons of physical separation methods of Kunjin virus-induced membranes

The two sets of connected membranes induced in Kunjin virus-infected cells are characterized by the presence of NS3 helicase/protease in both, and by RNA-dependent RNA polymerase (RdRp) activity plus the associated double-stranded RNA (dsRNA) template in vesicle packets (VP), or by the absence of both the VP-specific markers in the convoluted membranes/paracrystalline arrays (CM/PC). Attempts were made to separate flavivirus-induced membranes by sedimentation or flotation analyses in density gradients of sucrose or iodixanol, respectively, after treatment of cell lysates by sonication, osmotic shock, or tryptic digestion. Only osmotic shock treatment provided suggestive evidence of separation. This was explored by flow cytometry analysis (FCA) of RdRp active membrane fractions from a sucrose gradient, using dual fluorescent labelling via antibodies to NS3 and dsRNA. FCA revealed the presence of a dual labelled membrane population indicative of VP, and in a faster sedimenting fraction a membrane population able to be labelled only in NS3, representative of CM/PC and associated (R)ER. It was postulated that osmotic shock ruptured the bounding membrane of the VP, releasing the enclosed small vesicles associated with the Kunjin virus replication complex characterized previously. Notably, the presence of the full spectrum of nonstructural proteins in some membrane fractions was not a reliable marker for RdRp activity. These experiments may provide the opportunity for isolation of relatively pure flavivirus replication complexes in their native membrane-associated state by fluorescence-activated cell sorting. (C) 2004 Elsevier B.V. All rights reserved.

A discussion of ethnographic research methods and their relevance for the translation process

In recent years, technologically advanced methodologies such as Translog have gained a lot of ground in translation process research. However, in this paper it will be argued that quantitative research methods can be supplemented by ethnographic qualitative ones so as to enhance our understanding of what underlies the translation process. Although translation studies scholars have sometimes applied an ethnographic approach to the study of translation, this paper offers a different perspective and considers the potential of ethnographic research methods for tapping cognitive and behavioural aspects of the translation process. A number of ethnographic principles are discussed and it is argued that process researchers aiming to understand translators’ perspectives and intentions, how these shape their behaviours, as well as how translators reflect on the situations they face and how they see themselves, would undoubtedly benefit from adopting an ethnographic framework for their studies on translation processes.

New business histories! Plurality in business history research methods

We agree with de Jong et al.'s argument that business historians should make their methods more explicit and welcome a more general debate about the most appropriate methods for business historical research. But rather than advocating one ‘new business history’, we argue that contemporary debates about methodology in business history need greater appreciation for the diversity of approaches that have developed in the last decade. And while the hypothesis-testing framework prevalent in the mainstream social sciences favoured by de Jong et al. should have its place among these methodologies, we identify a number of additional streams of research that can legitimately claim to have contributed novel methodological insights by broadening the range of interpretative and qualitative approaches to business history. Thus, we reject privileging a single method, whatever it may be, and argue instead in favour of recognising the plurality of methods being developed and used by business historians – both within their own field and as a basis for interactions with others.

Identifying frames:a comparison of research methods

Framing plays an important role in public policy. Interest groups strategically highlight some aspects of a policy proposal while downplaying others in order to steer the policy debate in a favorable direction. Despite the importance of framing, we still know relatively little about the framing strategies of interest groups due to methodological difficulties that have prevented scholars from systematically studying interest group framing across a large number of interest groups and multiple policy debates. This article therefore provides an overview of three novel research methods that allow researchers to systematically measure interest group frames. More specifically, this article introduces a word-based quantitative text analysis technique, a manual, computer-assisted content analysis approach and face-to-face interviews designed to systematically identify interest group frames. The results generated by all three techniques are compared on the basis of a case study of interest group framing in an environmental policy debate in the European Union.