E-BioFlow: Different Perspectives on Scientific Workflows

We introduce a new type of workflow design system called\ud e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows

Sticks, balls or a ribbon? Results of a formative user study with bioinformaticians

User interfaces in modern bioinformatics tools are designed for experts. They are too complicated for\ud novice users such as bench biologists. This report presents the full results of a formative user study as part of a\ud domain and requirements analysis to enhance user interfaces and collaborative environments for\ud multidisciplinary teamwork. Contextual field observations, questionnaires and interviews with bioinformatics\ud researchers of different levels of expertise and various backgrounds were performed in order to gain insight into\ud their needs and working practices. The analysed results are presented as a user profile description and user\ud requirements for designing user interfaces that support the collaboration of multidisciplinary research teams in\ud scientific collaborative environments. Although the number of participants limits the generalisability of the\ud findings, the combination of recurrent observations with other user analysis techniques in real-life settings\ud makes the contribution of this user study novel

New Interactions with Workflow Systems

This paper describes the evaluation of our early design ideas of an ad-hoc of workflow system. Using the teach-back technique, we have performed a hermeneutic analysis of the mockup implementation named NIWS to get corrective and creative feedback at the functional, dialogue and representation level of the new workflow system

Professionele ruimte en gespreid leiderschap

Professionele ruimte voor leraren staat hoog op de politieke agenda. Op dit moment is er een wetsvoorstel over dit thema in behandeling bij de Tweede Kamer. Professionele ruimte zou moeten leiden tot een grotere inhoudelijke ontwikkelingstaak van leraren, en tot meer reflectie en ideeënuitwisseling. Professionele ruimte is daarmee direct gekoppeld aan vraagstukken rond de professionele ontwikkeling van leraren. Hoe professionele ruimte vorm moet krijgen, is echter de vraag. Uit diverse onderzoeken blijkt dat de rol van de leidinggevende cruciaal is, maar hoe die rol er precies uitziet is onduidelijk. Er is behoefte aan een nieuw type onderzoek naar de wijze waarop leraren professionele ruimte krijgen en nemen.\ud Deze reviewstudie heeft als doel om het perspectief van gespreid leiderschap nader te duiden en in verband te brengen met de professionele ruimte die leraren ervaren in scholen. De literatuur rondom gespreid leiderschap en professionele ruimte wordt verkend en er wordt een conceptueel model voorgesteld om deze begrippen met elkaar in verband te brengen. Op basis hiervan wordt toegewerkt naar een ontwerp van een praktijknabij onderzoeksinstrument om dit verband inzichtelijk te maken

Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

BACKGROUND: There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. RESULTS: Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench. CONCLUSION: Taverna can be used by data analysis experts as a generic tool for composing ad hoc analyses of quantitative data by combining the use of scripts written in the R programming language with tools exposed as services in workflows. When these workflows are shared with colleagues and the wider scientific community, they provide an approach for other scientists wanting to use tools such as R without having to learn the corresponding programming language to analyse their own data.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Normalisation to Blood Activity Is Required for the Accurate Quantification of Na/I Symporter Ectopic Expression by SPECT/CT in Individual Subjects

The utilisation of the Na/I symporter (NIS) and associated radiotracers as a reporter system for imaging gene expression is now reaching the clinical setting in cancer gene therapy applications. However, a formal assessment of the methodology in terms of normalisation of the data still remains to be performed, particularly in the context of the assessment of activities in individual subjects in longitudinal studies. In this context, we administered to mice a recombinant, replication-incompetent adenovirus encoding rat NIS, or a human colorectal carcinoma cell line (HT29) encoding mouse NIS. We used 99mTc pertechnetate as a radiotracer for SPECT/CT imaging to determine the pattern of ectopic NIS expression in longitudinal kinetic studies. Some animals of the cohort were culled and NIS expression was measured by quantitative RT-PCR and immunohistochemistry. The radioactive content of some liver biopsies was also measured ex vivo. Our results show that in longitudinal studies involving datasets taken from individual mice, the presentation of non-normalised data (activity expressed as %ID/g or %ID/cc) leads to ‘noisy’, and sometimes incoherent, results. This variability is due to the fact that the blood pertechnetate concentration can vary up to three-fold from day to day. Normalisation of these data with blood activities corrects for these inconsistencies. We advocate that, blood pertechnetate activity should be determined and used to normalise the activity measured in the organ/region of interest that expresses NIS ectopically. Considering that NIS imaging has already reached the clinical setting in the context of cancer gene therapy, this normalisation may be essential in order to obtain accurate and predictive information in future longitudinal clinical studies in biotherapy