Morphological Homogeneity of Neurons: Searching for Outlier Neuronal Cells

We report a morphology-based approach for the automatic identification of outlier neurons, as well as its application to the NeuroMorpho.org database, with more than 5,000 neurons. Each neuron in a given analysis is represented by a feature vector composed of 20 measurements, which are then projected into a two-dimensional space by applying principal component analysis. Bivariate kernel density estimation is then used to obtain the probability distribution for the group of cells, so that the cells with highest probabilities are understood as archetypes while those with the smallest probabilities are classified as outliers. The potential of the methodology is illustrated in several cases involving uniform cell types as well as cell types for specific animal species. The results provide insights regarding the distribution of cells, yielding single and multi-variate clusters, and they suggest that outlier cells tend to be more planar and tortuous. The proposed methodology can be used in several situations involving one or more categories of cells, as well as for detection of new categories and possible artifacts.

STRUCTURE AND DYNAMICS: THE TRANSITION FROM NONEQUILIBRIUM TO EQUILIBRIUM IN INTEGRATE-AND-FIRE DYNAMICS

The transient and equilibrium properties of dynamics unfolding in complex systems can depend critically on specific topological features of the underlying interconnections. In this work, we investigate such a relationship with respect to the integrate-and-fire dynamics emanating from a source node and an extended network model that allows control of the small-world feature as well as the length of the long-range connections. A systematic approach to investigate the local and global correlations between structural and dynamical features of the networks was adopted that involved extensive simulations (one and a half million cases) so as to obtain two-dimensional correlation maps. Smooth, but diverse surfaces of correlation values were obtained in all cases. Regarding the global cases, it has been verified that the onset avalanche time (but not its intensity) can be accurately predicted from the structural features within specific regions of the map (i.e. networks with specific structural properties). The analysis at local level revealed that the dynamical features before the avalanches can also be accurately predicted from structural features. This is not possible for the dynamical features after the avalanches take place. This is so because the overall topology of the network predominates over the local topology around the source at the stationary state.

Introduction to E-Science

An introduction to computationally-enabled science, challenges, and opportunities.

Data Management Policies and Issues with Life Science Data

Data management and sharing are relatively new concepts in the health and life sciences fields. This presentation will cover some basic policies as well as the impediments to data sharing unique to health and life sciences data.

Overview of Data Management Planning Tools

These Data Management Plans are more comprehensive and complex than in the past. Libraries around the nation are trying to put together tools to help researchers write plans that conform to the new requirements. This session will look at some of these tools.

Compliance: E-Science Mandates and Policies

Data collected under federally funded research is subject to compliance rules and regulations. Policies affecting what you can and cannot do with your data, who is responsible, and what role your institution plays can vary with funding agencies and the type of data collected. This talk will address many of the compliance issues associated with research data, as well as funder mandates that you need to be aware of to ensure compliance.

April 25, 2012

Geneva Henry, Executive Director of the Center for Digital Scholarship, Rice University. Data rights and ownership of digital research data can impact how you use data, how others use data you've collected, and how rights are determined in collaborative research. Copyright rules governing data vary from one country to the next, making data ownership in international collaborations particularly murky. Licensing the use of data sets from the start is one way to address these issues early and provide a means for easily sharing datasets that can be cited and properly attributed. This talk with introduce issues associated with digital research data governance and how to protect your rights with data you work with.

Developing front-end Web 2.0 technologies to access services, content and things in the future Internet

The future Internet is expected to be composed of a mesh of interoperable web services accessible from all over the web. This approach has not yet caught on since global user?service interaction is still an open issue. This paper states one vision with regard to next-generation front-end Web 2.0 technology that will enable integrated access to services, contents and things in the future Internet. In this paper, we illustrate how front-ends that wrap traditional services and resources can be tailored to the needs of end users, converting end users into prosumers (creators and consumers of service-based applications). To do this, we propose an architecture that end users without programming skills can use to create front-ends, consult catalogues of resources tailored to their needs, easily integrate and coordinate front-ends and create composite applications to orchestrate services in their back-end. The paper includes a case study illustrating that current user-centred web development tools are at a very early stage of evolution. We provide statistical data on how the proposed architecture improves these tools. This paper is based on research conducted by the Service Front End (SFE) Open Alliance initiative.

Common motifs in scientific workflows: An empirical analysis

While workflow technology has gained momentum in the last decade as a means for specifying and enacting computational experiments in modern science, reusing and repurposing existing workflows to build new scientific experiments is still a daunting task. This is partly due to the difficulty that scientists experience when attempting to understand existing workflows, which contain several data preparation and adaptation steps in addition to the scientifically significant analysis steps. One way to tackle the understandability problem is through providing abstractions that give a high-level view of activities undertaken within workflows. As a first step towards abstractions, we report in this paper on the results of a manual analysis performed over a set of real-world scientific workflows from Taverna and Wings systems. Our analysis has resulted in a set of scientific workflow motifs that outline i) the kinds of data intensive activities that are observed in workflows (data oriented motifs), and ii) the different manners in which activities are implemented within workflows (workflow oriented motifs). These motifs can be useful to inform workflow designers on the good and bad practices for workflow development, to inform the design of automated tools for the generation of workflow abstractions, etc.

Research Objects

In the domain of eScience, investigations are increasingly collaborative. Most scientific and engineering domains benefit from building on top of the outputs of other research: By sharing information to reason over and data to incorporate in the modelling task at hand. This raises the need to provide means for preserving and sharing entire eScience workflows and processes for later reuse. It is required to define which information is to be collected, create means to preserve it and approaches to enable and validate the re-execution of a preserved process. This includes and goes beyond preserving the data used in the experiments, as the process underlying its creation and use is essential. This tutorial thus provides an introduction to the problem domain and discusses solutions for the curation of eScience processes.

FragFlow: automated fragment detection in scientific workflows

Scientific workflows provide the means to define, execute and reproduce computational experiments. However, reusing existing workflows still poses challenges for workflow designers. Workflows are often too large and too specific to reuse in their entirety, so reuse is more likely to happen for fragments of workflows. These fragments may be identified manually by users as sub-workflows, or detected automatically. In this paper we present the FragFlow approach, which detects workflow fragments automatically by analyzing existing workflow corpora with graph mining algorithms. FragFlow detects the most common workflow fragments, links them to the original workflows and visualizes them. We evaluate our approach by comparing FragFlow results against user-defined sub-workflows from three different corpora of the LONI Pipeline system. Based on this evaluation, we discuss how automated workflow fragment detection could facilitate workflow reuse.

Workflow reuse in practice: a study of neuroimaging pipeline users

Workflow reuse is a major benefit of workflow systems and shared workflow repositories, but there are barely any studies that quantify the degree of reuse of workflows or the practical barriers that may stand in the way of successful reuse. In our own work, we hypothesize that defining workflow fragments improves reuse, since end-to-end workflows may be very specific and only partially reusable by others. This paper reports on a study of the current use of workflows and workflow fragments in labs that use the LONI Pipeline, a popular workflow system used mainly for neuroimaging research that enables users to define and reuse workflow fragments. We present an overview of the benefits of workflows and workflow fragments reported by users in informal discussions. We also report on a survey of researchers in a lab that has the LONI Pipeline installed, asking them about their experiences with reuse of workflow fragments and the actual benefits they perceive. This leads to quantifiable indicators of the reuse of workflows and workflow fragments in practice. Finally, we discuss barriers to further adoption of workflow fragments and workflow reuse that motivate further work.

A Semantic Workflow Mechanism to Realize Experimental Goals and Constraints

Postprint

Influence apart from Adoption: How Interaction between Programming and Scientific Practices Shapes Modes of Inquiry in Four Oceanography Teams

Thesis (Ph.D.)--University of Washington, 2016-06