27,648 research outputs found
Dynamic Influence Networks for Rule-based Models
We introduce the Dynamic Influence Network (DIN), a novel visual analytics
technique for representing and analyzing rule-based models of protein-protein
interaction networks. Rule-based modeling has proved instrumental in developing
biological models that are concise, comprehensible, easily extensible, and that
mitigate the combinatorial complexity of multi-state and multi-component
biological molecules. Our technique visualizes the dynamics of these rules as
they evolve over time. Using the data produced by KaSim, an open source
stochastic simulator of rule-based models written in the Kappa language, DINs
provide a node-link diagram that represents the influence that each rule has on
the other rules. That is, rather than representing individual biological
components or types, we instead represent the rules about them (as nodes) and
the current influence of these rules (as links). Using our interactive DIN-Viz
software tool, researchers are able to query this dynamic network to find
meaningful patterns about biological processes, and to identify salient aspects
of complex rule-based models. To evaluate the effectiveness of our approach, we
investigate a simulation of a circadian clock model that illustrates the
oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres
eXamine: a Cytoscape app for exploring annotated modules in networks
Background. Biological networks have growing importance for the
interpretation of high-throughput "omics" data. Statistical and combinatorial
methods allow to obtain mechanistic insights through the extraction of smaller
subnetwork modules. Further enrichment analyses provide set-based annotations
of these modules.
Results. We present eXamine, a set-oriented visual analysis approach for
annotated modules that displays set membership as contours on top of a
node-link layout. Our approach extends upon Self Organizing Maps to
simultaneously lay out nodes, links, and set contours.
Conclusions. We implemented eXamine as a freely available Cytoscape app.
Using eXamine we study a module that is activated by the virally-encoded
G-protein coupled receptor US28 and formulate a novel hypothesis about its
functioning
Exploring user types and what users seek in an open content based educational resource
The OpenLearn site is an example of an Open Educational Resource (OER) providing units for free study and for re-use under the Creative Commons license. The primary focus of the site is content but it also offers social tools such as forums, personal journals, presence, and videoconferencing. The content can also support interactivity such as quizzes, opportunities for reflection, and interactive diagrams. This paper discusses desirable attributes for a learning environment suited to OERs and considers OpenLearn in the light of the four types of learning focus suggested by Bransford et al (2002) namely: learner, knowledge, community and assessment centred. A study of user views of OpenLearn is reviewed using cluster analysis to identify possible user types. The needs of these user types are then considered with a focus on assessment issues and possible responses suggested in the case of OpenLearn to help bring in assessment to informal learning resources
Leveraging Citation Networks to Visualize Scholarly Influence Over Time
Assessing the influence of a scholar's work is an important task for funding
organizations, academic departments, and researchers. Common methods, such as
measures of citation counts, can ignore much of the nuance and
multidimensionality of scholarly influence. We present an approach for
generating dynamic visualizations of scholars' careers. This approach uses an
animated node-link diagram showing the citation network accumulated around the
researcher over the course of the career in concert with key indicators,
highlighting influence both within and across fields. We developed our design
in collaboration with one funding organization---the Pew Biomedical Scholars
program---but the methods are generalizable to visualizations of scholarly
influence. We applied the design method to the Microsoft Academic Graph, which
includes more than 120 million publications. We validate our abstractions
throughout the process through collaboration with the Pew Biomedical Scholars
program officers and summative evaluations with their scholars
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