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.

Midday measurements of leaf water potential and stomatal conductance are highly correlated with daily water use of Thompson Seedless grapevines

A study was conducted to determine the relationship between midday measurements of vine water status and daily water use of grapevines measured with a weighing lysimeter. Water applications to the vines were terminated on August 24th for 9 days and again on September 14th for 22 days. Daily water use of the vines in the lysimeter (ETLYS) was approximately 40 L vine−1 (5.3 mm) prior to turning the pump off, and it decreased to 22.3 L vine−1 by September 2nd. Pre-dawn leaf water potential (ΨPD) and midday Ψl on August 24th were −0.075 and −0.76 MPa, respectively, with midday Ψl decreasing to −1.28 MPa on September 2nd. Leaf g s decreased from ~500 to ~200 mmol m−2 s−1 during the two dry-down periods. Midday measurements of g s and Ψl were significantly correlated with one another (r = 0.96) and both with ETLYS/ETo (r = ~0.9). The decreases in Ψl, g s, and ETLYS/ETo in this study were also a linear function of the decrease in volumetric soil water content. The results indicate that even modest water stress can greatly reduce grapevine water use and that short-term measures of vine water status taken at midday are a reflection of daily grapevine water use

Rural tourism quality in Spain. The "Q" mark.

The Spanish tourism stakchoiders (State Tourism Administration, public tourism agencies, hospitality sector, recreational sector, travel operators, other touristic business, etc.) have developed a very powerful and practical quality certification system for all the actors in the tourism sector, including all those actors and activities in the rural tourism sector, which traditionally do not have a proper tourism system. In this framework the Institute for Spanish Tourism Quality (ICTE) administers, manages and monitors the "Spanish Tourism Quality" "Q" Mark, as an exclusive brand that announces the quality of the activity and service provided by the certified tourist business.

A governação de territórios metropolitanos. Contexto institucional e de planeamento nas regiões de Madrid, Barcelona, Paris e Lisboa / The regional metropolitan governance. Institutional mark and planning in Madrid, Barcelona, Paris and Lisbon

Resumo Em resposta aos desafios atuais de muitas grandes cidades, o contexto institucional e o planeamento territorial formam dimensões para melhorar a governação metropolitana. No quadro das regiões capitais do sudoeste europeu, quais poderão ser as inovações e diferenças nos seus modelos e processos em curso? Este artigo propõe uma investigação aplicada para apresentar a análise da governação metropolitana. Através do método de estudos de caso em perspectiva comparada, vários elementos e entrevistas são ponderados qualitativamente nas regiões de Madrid, Barcelona, Paris e Lisboa. As conclusões encontram uma tendência para o equilíbrio entre os esforços dessas duas dimensões da governação territorial metropolitana, não impedindo registrar os seus diferentes percursos: por exemplo Ile-de-France desenvolveu boas iniciativas em matéria de planeamento, que então pedem alguns ajustamentos no quadro político, enquanto Madrid teve “menos actividade” nos últimos anos, em resultado da sua grande estabilidade institucional. A região de Lisboa permanece talvez numa “posição intermédia”, com uma dinâmica de evolução pouco previsível. Mas de acordo com este argumento, admite-se que os seus processos podem levar a melhorias graduais no sistema de governação, com o seu próprio percurso, implementando acções que devem respeitar, em particular, a geografia do território. Abstract Addressing the running challenges of several greater cities, the institutional mark and regional planning are dimensions for improving metropolitan governance. Regarding the southwest European capital regions, what can be the innovations and differences in their currently processes and models? This paper proposes an applied framework to present the metropolitan governance analysis. Through a comparative case study methodology, various elements and interviews are qualitatively measured in the regions of Madrid, Barcelona, Paris and Lisbon. The conclusions find a tendency to balance between the efforts on those two regional metropolitan governance dimensions, which does not prevent to register their different paths: for example Ile-de-France has developed good initiatives in terms of planning, which then require some adjustments in the political mark, while Madrid had in recent years “less activity”, in result of his institutional stability. The Lisbon region maybe stays in an “intermediate position” with a dynamic evolution that is difficult to predict. But according to that argument, it’s possible to admit that his processes can gradually lead to small improvements in his governance system, with his own path, implementing actions that must respect, in particularly, the geography of the territory.