High Performance Computing of Gene Regulatory Networks using a Message-Passing Model

Gene regulatory network reconstruction is a fundamental problem in computational biology. We recently developed an algorithm, called PANDA (Passing Attributes Between Networks for Data Assimilation), that integrates multiple sources of 'omics data and estimates regulatory network models. This approach was initially implemented in the C++ programming language and has since been applied to a number of biological systems. In our current research we are beginning to expand the algorithm to incorporate larger and most diverse data-sets, to reconstruct networks that contain increasing numbers of elements, and to build not only single network models, but sets of networks. In order to accomplish these "Big Data" applications, it has become critical that we increase the computational efficiency of the PANDA implementation. In this paper we show how to recast PANDA's similarity equations as matrix operations. This allows us to implement a highly readable version of the algorithm using the MATLAB/Octave programming language. We find that the resulting M-code much shorter (103 compared to 1128 lines) and more easily modifiable for potential future applications. The new implementation also runs significantly faster, with increasing efficiency as the network models increase in size. Tests comparing the C-code and M-code versions of PANDA demonstrate that this speed-up is on the order of 20-80 times faster for networks of similar dimensions to those we find in current biological applications

Effectiveness of Dynamic Indicators of Basic Early Literacy Skills (DIBELS)

This research shows the effectiveness of Dynamic Indicators of Basic Early Literacy Skills (DIBELS) at identifying students in need of reading intervention compared to two other reading assessments, the Observation survey (OS) and Developmental Reading Assessment (DRA). The percent of time DIBELS agreed or disagreed with OS or DRA was used to determine the effectiveness. DIBELS was found to agree with the OS and DRA for the majority of the data. This shows that the school does not need to waste time and money on an assessment that is not needed. There were a few participants in which DIBELS determined the students to need an intervention when really they did not. This time and money on an unnecessary intervention could have been put towards interventions for students who need them and additional authentic resources. This school already has two authentic assessments that provide useful data to plan future instruction. A third assessment that tells the teachers the same thing while frustrating and confusing the students is not needed. The school would be better off providing the teachers with professional development regarding using the OS and DRA assessment data to guide instruction and plan interventions

Data reporting standards: making the things we use better

Genomic data often persist far beyond the initial study in which they were generated. But the true value of the data is tied to their being both used and useful, and the usefulness of the data relies intimately on how well annotated they are. While standards such as MIAME have been in existence for nearly a decade, we cannot think that the problem is solved or that we can ignore the need to develop better, more effective methods for capturing the essence of the meta-data that is ultimately required to guarantee utility of the data

Privatized v. Academic Online Tutoring: A Proposal to Determine the Effectiveness of the Mary G. Walsh Writing Center Compared to Pearson-Smarthinking

This proposal for an experiment (which is part of a larger study) will evaluate the effectiveness of the Mary G. Walsh Writing Center’s online tutoring system when compared to that of Pearson Education’s (known as Smarthinking Online Tutoring). This experiment is primarily interested in discerning which online system (PearsonSmarthinking or that of the Mary G. Walsh Writing Center) can provide the most complete virtual “tutor experience.

Fertile ruin

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