Reproducible Research: A Bioinformatics Case Study

While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has remained relatively stagnant. Publication is largely done in the same manner today as it was fifty years ago. Many journals have adopted electronic formats, however, their orientation and style is little different from a printed document. The documents tend to be static and take little advantage of computational resources that might be available. Recent work, Gentleman and Temple Lang (2004), suggests a methodology and basic infrastructure that can be used to publish documents in a substantially different way. Their approach is suitable for the publication of papers whose message relies on computation. Stated quite simply, Gentleman and Temple Lang propose a paradigm where documents are mixtures of code and text. Such documents may be self-contained or they may be a component of a compendium which provides the infrastructure needed to provide access to data and supporting software. These documents, or compendiums, can be processed in a number of different ways. One transformation will be to replace the code with its output -- thereby providing the familiar, but limited, static document. In this paper we apply these concepts to a seminal paper in bioinformatics, namely The Molecular Classification of Cancer, Golub et al. (1999). The authors of that paper have generously provided data and other information that have allowed us to largely reproduce their results. Rather than reproduce this paper exactly we demonstrate that such a reproduction is possible and instead concentrate on demonstrating the usefulness of the compendium concept itself.

Evaluating Integration. Research contributions for a gender sensitive migration policy: Research contributions for a gender sensitive migration policy

The integration of academic and non-academic knowledge is a key concern for researchers who aim at bridging the gap between research and policy. Researchers involved in the sustainability-oriented NCCR North-South programme have made the experience that linking different types of knowledge requires time and effort, and that methodologies are still lacking. One programme component was created at the inception of this transdisciplinary research programme to support exchange between researchers, development practitioners and policymakers. After 8 years of research, the programme is assessing whether research has indeed enabled a continuous communication across and beyond academic boundaries and has effected changes in the public policies of poor countries. In a first review of the data, we selected two case studies explicitly addressing the lives of women. In both cases – one in Pakistan, the other in Nepal – the dialogue between researchers and development practitioners contributed to important policy changes for female migration. In both countries, outmigration has become an increasingly important livelihood strategy. National migration policies are gendered, limiting the international migration of women. In Nepal, women were not allowed to migrate to specific countries such as the Gulf States or Malaysia. This was done in the name of positive discrimination, to protect women from potential exploitation and harassment in domestic work. However, women continued to migrate in many other and often illegal and more risky ways, increasing their vulnerability. In Pakistan, female labour migration was not allowed at all and male migration increased the vulnerability of the families remaining back home. Researchers and development practitioners in Nepal and Pakistan brought women’s shared experience of and exposure to the mechanisms of male domination into the public debate, and addressed the discriminating laws. Now, for the first time in Pakistan, the new draft policy currently under discussion would enable broadly-based female labour migration. What can we learn from the two case studies with regard to ways of relating experience- and research-based knowledge? The paper offers insights into the sequence of interactions between researchers, local people, development practitioners, and policy-makers, which eventually contributed to the formulation of a rights-based migration policy. The reflection aims at exploring the gendered dimension of ways to co-produce and share knowledge for development across boundaries. Above all, it should help researchers to better tighten the links between the spheres of research and policy in future.

Book Review of “Frontiers of Social Research: Japan and Beyond”. 351 pages, Trans Pacific Press, 2007, edited by Akira Furukawa

The title ‘Frontiers of Social Research’ implies a pioneering spirit, embarking upon unchartered territories. However, the most fascinating and insightful moments of this book are those which explore age-old Japanese research techniques and the potential for new methodologies to look to the old. The key theme of the work is the role of the researcher and the researcher’s relationships with research participants, the research audience and with knowledge itself.

Why Do We Think Practice Research is a Good Idea? Comments and Musings Inspired by the Salisbury Statement

In this paper I raise some questions about current understandings of practice research and whether they are worth pursuing. In particular, the notion of a gap between practice and research is examined in terms of how it constricts thinking about this issue. I also attempt to explicate some of the less examined assumptions associated with practice research. Finally, I suggest that we embrace multiplicity, not by trying to accommodate all views under the practice research umbrella, but by accepting that there will be many versions of practice research that will have differential appeal.

What is Practice Research in Social Work - Definitions, Barriers and Possibilities

Practice is subject to increasing pressure to demonstrate its ability to achieve outcomes required by public policy makers. As part of this process social work practice has to engage with issues around advancing knowledge-based learning processes in a close collaboration with education and research based perspectives. This has given rise to approaches seeking to combine research methodology, field research and practical experience. Practice research is connected to both “the science of the concrete” – a field of research oriented towards subjects more than objects and “mode 2 knowledge production” – an application-oriented research where frameworks and findings are discussed by a number of partners. Practice research is defined into two approaches: practice research – collaboration between practice and research – and practitioner research – processes controlled and accomplished by practitioners. The basic stakeholders in practice research are social workers, service users, administrators, management, organisations, politicians and researchers. Accordingly, practice research is necessarily collaborative, involving a meeting point for different views, interests and needs, where complexity and dilemmas are inherent. Instead of attempting to balance or reconcile these differences, it is important to respect the differences if collaboration is to be established. The strength of both practice and research in practice research is to address these difficult challenges. The danger for both fields is to avoid and reject them.

The door of the tomb is open: Participatory action research to assess the impact of strengthened community capacity on maternal health care in rural Mali

This participatory action-research project addressed the hypothesis that strengthened community and women's capacity for self-development will lead to action to address maternal health problems and the prevention of maternal morbidity and mortality in Mali. Research objectives were: (1) to undertake a comparative cross-sectional study of the association of community capacity with improved maternal health in rural areas of Sanando, Mali, where capacity building interventions have taken place in some villages but not in others. (2) to describe women's maternal health status, access to and use of maternal health services given their residence in program or comparison communities.^ The participatory action research project was an integrated qualitative and quantitative study using participatory rural appraisal exercises, semi-structured group interviews and a cross-sectional survey.^ Factors related to community capacity for self-development were identified: community harmony; an understanding of the benefits of self-development; dynamic leadership; and a structure to implement collective activities.^ A distinct difference between the program and comparison villages was the commitment to train and support traditional birth attendants (TBAs). The TBAs in the program villages work in the context of the wider, integrated self-development program and, 10 years after their initial training, the TBAs continue to practice.^ Many women experience labor and childbirth alone or are attended by an untrained relative in both program and comparison villages. Nevertheless a significant change is apparent, with more women in program villages than in comparison villages being assisted by the TBAs. The delivery practices of the TBAs reveal the positive impact of their training in the "three cleans" (clean hands of the assistant, clean delivery surface and clean cord-cutting). The findings of this study indicate a significant level of unmet need for child spacing methods in all villages.^ The training and support of TBAs in the program villages yielded significant improvements in their delivery practices, and resulting outcomes for women and infants. However, potential exists for further community action. Capacities for self-development have not yet been directed toward an action plan encompassing other Safe Motherhood interventions, including access to family planning services and emergency obstetric care services. ^

How Comprehensible, Interesting and Relevant is Current Research in Traditional Chinese Medicine for Practitioners?

Purpose: In traditional Chinese medicine (TCM) as in other fields of complementary medicine, research does not necessarily follow the sequence from in vitro studies via phase I to phase IV clinical trials, but all steps are being investigated simultaneously. Here, we aimed to investigate which kinds of studies were interesting and relevant for practitioners. Methods: Thirty abstracts from articles on TCM published between April and June 2012 were randomly chosen, including 5 abstracts each of in vitro studies, animal studies, case reports or series, studies with healthy volunteers, trials with patients, or reviews and meta-analyses. Six TCM practitioners (2 female, 5 non-medical, average age 46 years, average practical TCM experience 9 years) rated 10 abstracts each on a 5 point Likert scale (1=very poor to 5=very good) regarding comprehensibility, interest, relevance to practice, information for patients, and promoting reputation of TCM. Average ratings for each group of abstracts were calculated. Results: Comprehensibility of the abstracts was generally rated as good. Case reports/series, studies in healthy volunteers and trials with patients were rated interesting by the practitioners (average rating = 3.7, 3.8 and 3.7, respectively). Relevance to practice was mediocre for all types (2.5 to 3.5). In vitro studies and reviews/meta-analyses were not rated useful as information for patients (2.0). Reviews/Meta-analyses were considered negative for the reputation of TCM (2.2). Conclusions: Practitioners of TCM find abstracts of study results generally comprehensible and interesting. Case reports/series were rated in a similar way as trials with patients. Although TCM is commonly taught by means of case reports, practitioners seemed to value clinical trials. Abstracts of reviews/meta-analyses were rated rather uninformative, which was possibly due to several inconclusive results and the lack of detailed information in these abstracts.

Proper paraffin slide storage is crucial for translational research projects involving immunohistochemistry stains.

The use of paraffin slides and tissue microarrays (TMA) is indispensable for translational research. However, storage of paraffin slides over time has a substantial detrimental effect on the quality and reliability of immunohistochemistry stains. Particularly affected by this issue may be any collaborative efforts where paraffin slides or TMAs are shipped to central laboratories and then 'biobanked' for some time until use. This article summarizes some of the key issues affecting loss of antigenicity on paraffin slides and some simple storage solutions to help maintain high quality immunohistochemistry results when paraffin slides must be stored for a certain time prior to use.