DEEC Projects

Linux based Server for BNCD
Start Date: April 1 2006
Investigator: BNCD Core faculty, DEEC
Status: Active

The Linux based server for BNCD has been upgraded to provide new functionality to DEEC and all BNCD researchers. The upgrade has been conducted with the goal of facilitating collaboration among BNCD researchers, and making it easier for researchers to disseminate information to others. We hope that the server can be used as a model for other centers or small research labs.

There are numerous Linux distributions that could have been used for upgrading the server. The Fedora Core 5 Linux distribution was chosen because of the large open source development group that has grown around this project. The Fedora Linux software distributions offer a very broad array of programs that are easily configured for a desktop or, as in our case, a server environment. Fedora also has an excellent and growing implementation of the Xen virtual machine.

The Xen virtual machine is a new open source project that enables multiple operating systems to be run simultaneously on one computer with negligible performance penalties. Although our current Dell Poweredge server can’t run Microsoft Operating systems under Xen, it is worthy to note that Microsoft XP SP2 can be run under Xen with a CPU that has VT technology from Intel, or similar virtualization technology from AMD. We installed Xen for the following reasons:

a. We have a powerful server with multiple network connections. Due to the relatively small size of our group, the server has the capability of being used for additional purposes without hurting performance. Xen gives us more flexibility in choosing the operating system these applications can run on.

b. In general it is a good security practice to run only one type of server on a platform. Xen makes it possible to isolate different servers to different virtual machines and therefore run multiple servers on one computer. In most cases if a server is compromised the affected virtual machine can be reinstalled without disturbing the other virtual machines.

c. We can run both a test server and an online server on one computer. Changes to a server can be tested without affecting the online server.

d. A software application may be easiest to install, compile, or configure in a particular operating system. In many cases Xen allows us to install the needed operating system either permanently or temporarily for testing.

The Plone Content Management System (CMS) was installed to:

a. Allow DEEC to better maintain software project documentation.

b. Simplify Communication among project members.

c. Allow for dissemination of information and software to remote groups.

d. Permit online training of BNCD researchers.

As the Plone Content Management system becomes familiar to BNCD researchers we expect that numerous uses for collaboration and dissemination of information will be discovered.

Subversion is an open source version control system. It has clients that work with Microsoft Windows, MAC, or Linux operating systems. DEEC uses a Subversion repository to maintain the source code, and releases for all new projects. Older software projects are being added to the repository.

A version control system is an obvious tool to be used by software developers, but it may also be very useful for researchers in general. DEEC is investigating how Subversion may be used by other BNCD investigators, and will be training those interested in its use. Subversion is ideal to handle documents that may have multiple authors, several revisions, and possibly many related branches such as journal papers, grant proposals, and procedural documentation.

The Apache 2 HTTP server can be used to serve web pages. In our case we use it to serve the Plone CMS site, and the Subversion repository. SSL is used to encrypt all information (including passwords) to or from our sites. We also use an Apache 2 HTTP server to test projects that have online interfaces, before deploying these applications on a campus server.

Web-interface “calculator” based on a child corpus
Start Date: March 6 2006
Investigator: Dr. Holly Storkel, DEEC
Status: Active

The Child Corpus Calculator is a program where individuals can input a letter string representing the pronunciation of one or more words or nonsense words, specify the calculations they would like performed, and the type of output they would like returned. The program calculates word frequency, word length, phonotactic probability (including positional segment frequency and biphone frequency), and neighborhood density.

To speed software development time an initial version of the Child Corpus Calculator was written in LabVIEW and the first release, Version 0.6, was packaged and installed. Testing is currently underway and the feedback will be used to improve the next version.

Oral Stiffness Measurement
Start Date: September 1 2005
Investigator: Dr. Steven M.Barlow, CNL, DEEC
Status: Active

The OROSTIFF program is designed to interface with a device developed by Dr. Steven Barlow, which produces an interangle stretch of the oral angle at the commissural plane during a rest (non-participatory, passive) condition. The device will be used in studies of patients undergoing pharmacologic and/or neurosurgical intervention for advanced Parkinson’s disease (collaboration with Drs. Raj Pahwa and Kelly Lyons, KU Medical School, Department of Neurology), in patients who have ustained missile or shrapnel wounds to the head and neck (collaboration with Walter Reed Army Medical Center), or experimental cheiloplasty for revision of cleft lip (collaboration with University of North Carolina Dental School).

The device uses an air cylinder to stretch the lips. A subminiature differential variable reluctance transducer (s-DVRT, MicroStrain) is used to measure displacement of the lips, and a pressure transducer is used to derive the reactive force (lip tissue recoil). The device is very small and mobile because actuation is accomplished by pressurizing the air cylinder with a small syringe instead of a large electromechanical servo-controlled pump as used in previous work.

The OROSTIFF program is written in LabVIEW and uses NI-DAQmx drivers to interface with the National Instruments PCI-6052E multifunction data acquisition card. Pressure and displacement signals are acquired and displayed in real-time. A stiffness coefficient is also calculated and displayed in real-time. A second part of the program is used for analysis of collected data.

The data acquisition portion of the OROSTIFF program has been written in such a way that most of the code will be easily eused in future programs. Documentation is being created so that this program can serve as part of a DEEC created LabVIEW tutorial.

The data analysis portion of the software has undergone many changes. We have been endeavoring to produce a data analysis product that will help ensure repeatability of results. As the mechanical device is refined the analysis software will be changed, and then a new release created.

Matlab application to plot NNS Fast Fourier Transform plots.
Start Date: Mar 28 2005
Investigator: Dr. Steven M.Barlow, Atulya Deekonda
Status: Completed

An application was developed to create three-dimensional surface plots of non-nutritive suck (NNS) Fast Fourier Transforms FFT) using MatLab. Previously, this was carried out using Minitab, but was deemed too limiting and prone to scaling and plot errors. The new MatLab application provided efficient data array input functions, and a variety of display functions to permit flexible modification of the FFT surface plots. Additional scaling features were developed to allow the investigator to characterize the FFT magnitude in real world physical units (cmH 2O) or scaled to a reference signal and expressed in decibels. Gestational age was encoded into this display program and parameterized along the Z-axis, permitting the user to visualize trends in motor development in the frequency domain. This program provides the user with zoom and rotation functions for improved data visualization and hardcopy output functions.

Subthalamic Nucleus DBS 3-D Electrode Reconstruction in Parkinson's Disease
Start Date: Jan 24 2005
Investigator: Dr. Steven M.Barlow, Lalit K. Venkatesan
Status: Completed

The most effective surgery for advanced Parkinson's disease is known as subthalamic nucleus deep brain stimulation. Usually, this procedure is performed bilaterally to provide a neurotherapeutic stimulation of the STN and/or fibers of passage, or on both sides of the brain simultaneously.

The subthalamic nucleus is a small, almond shaped structure, which is located deep in the brain, adjacent to the substantia nigra, which is the area which contains dopamine cells, which predominantly degenerate in Parkinson's disease. As a result of the dopamine deficiency, there is over activity of the subthalamic nucleus. This over activity is important in the generation of Parkinsonism. Reduction in this over activity with the use of deep brain stimulation results in significant improvement in Parkinsonism. The key element of the deep brain stimulating system is a multipolar electrode, which has 4 programmable ontacts. The electrode itself is placed proximal to the subthalamic nucleus during a precise stereotactic neurosurgical procedure .

Turbo CAD was used to develop graphical models of the subthalamic and red nuclei bilaterally in relation to DBS electrodes localized in Tailarach coordinates via post-operative MRI. Clinical outcome is being used to develop the model for the placement of the DBS electrodes and the effectiveness of the DBS electrodes in PD patients.

Dual task costs to production by older and young adults
Start Date: Dec 20 2004
Investigator: Dr. Susan Kemper, DEEC
Status: Active

The objective of this project was to develop a computerized pursuit rotor to monitor the dual task costs of speaking. The project onsists of an oval track over which a circular ball rotates at a speed set by the experimenter. The total time the mouse pointer is over the ball is recorded for every 100ms interval and is plotted with respect to time. The project has been divided into two experiments; one experiment evaluates the appropriate rotor speed for a particular subject, and having obtained the appropriate rotor speed, the rotor speed is then used in the second experiment which validates the use of pursuit rotor tracking accuracy as a measure of cognitive processing costs associated with language production. The second experiment involves tracking the rotor ball along with speech analysis. The results of the experiments are obtained in terms of graphs of Percentage Accuracy, Pointer to Rotor Distance and Speech Amplitude, all with respect to Time in milliseconds. The entire project has been carried out in Visual Basic 6 application software

DEEC has made three new releases of the Speech-Rotor project and is planning the release of Version 1.0. Version 0.7 fixed several bugs and made a small functional change. Version 0.8 added the ability to record baseline data and access this data from each subject’s record. Version 0.9 was created to allow the program to be used with very slow rotation speeds. A question dialog is now shown after the experiment has either completed one rotation or a minute has elapsed.

Peak picking algorithms in identifying specific ERP components
Start Date: Sep 1 2004
Investigator: Dr. Mabel Rice, Lalit K. Venkatesan
Status: Completed

As part of the Developmental Neurolinguistics Lab, Dr. Rice will be conducting an ERP study investigating the neural processing (i.e., EEG waveforms) of semantic and syntactic information in children with and without specific language impairment. For the data analysis procedures, DEEC developed peak picking algorithms, using MATLAB, for use in identifying the specific ERP components expected to be elicited as part of this study. A customized Graphical User Interface (GUI), with a variety of functions and features, was developed, to analyze and display the data.

Linux based Samba File Server for BNCD
Start Date: Mar 25 2004
Investigator: Dr. Mabel Rice, Schiefelbusch Institute for Life Span Studies
Status: Active

Samba is an Open Source/Free Software suite that provides seamless file and print services to SMB/CIFS clients. Samba is freely available under the GNU General Public License.
Samba provides file and print services for Microsoft Windows/MAC OS clients. These services may be hosted off any TCP/IP-enabled platform. The original deployment platforms were UNIX and Linux, though today it is in common use across a broad variety of systems.
The Samba project includes not only an impressive feature set in file and print serving capabilities, but has been extended to include client functionality, utilities to ease migration to Samba, tools to aid interoperability with Microsoft Windows, and administration tools.
RAID Server:
DELL PowerEdge 2600 series server is used for the File Server. It is a Dual Xeon Processor Mainstream 5U Tower and is great for Local and distributed workgroup applications where availability, performance and expandability are important.
Redundant Array of Independent (or Inexpensive) Disks, a category of disk drives that employ two or more drives in combination for fault tolerance and performance.
Here a RAID 5 category server is used. RAID 5 provides excellent performance and good fault tolerance. Also data striping at the byte level and stripe error correction information is provided.
The RAID 5 server is a high end computer running RedHat 9.0 (linux) operating system. A dual symmetric multiprocessor system is proposed for providing good response times for file or database processing. The running and maintaining a Linux based system provides a very cost effective approach, since the need for buying licences per client is unnecessary.

Clients:
The client computers can be Microsoft Windows based or MAC OS based or Linux based. The server can service all these irrespective of their configuration. The setup changes on the client computers are minimal. A small tutorial on DEEC’s website should be helpful in configuring and setting up clients for file sharing operations.

The following are some of the salient features of the proposed system:
• Relablility, Integrity – Miminal unscheduled down time, correctness of data.
• Efficient - Linux will run on low-specification hardware. Processor utilization is low in normal running.
• Secure – Data encryption using 128bit SSH2 algorithm, Remote access via SSH (Secure Shell) and not FTP.
• Shared, group and individual disk space on the file server.
• IP Address based filtering of clients: Users can be allowed secure access based on the client IP Address (Ex: Allow only KU Clients – 129.237.xxx.xxx)
• NO Viruses, Service updates: Linux has no known viruses, does not need constant service pack updates. (Note: Antivirus packages on server can cause significant performance degradation)

All the network lines are based on 100Mbps Ethernet standard. A dual interface card for the server is proposed to split the incoming traffic into two parts, for load balancing.

N-Trainer
Start Date: Jan1 2004
Investigator: Dr.Steven Barlow, SPLH, CNL, DEEC

Design and development of an adaptive database and control system for entrainment of centrally patterned motor behavior in human neonates Premature birth is associated with a variety of medical and developmental conditions that may disrupt central pattern generation (CPG) and motor skill acquisition, including nutritive and non-nutritive suck (NNS) behaviors which are presumed pivotal for later emergent activities including vocalization, babbling, and speech.
Computer synthesized nipple conformation stimuli generated by a specialized servo-controlled mechanical stimulus generator, known as the N-Trainer, are effective in driving the NNS CPG. Working collaboratively with the engineering staff in the Communication Neuroscience Laboratories, DEEC engineers will be charged with the design of a ‘kiosk-based’ interface that will be used by neonatal intensive care medical professionals to ‘login’ premature babies for neurotherapeutic sensorimotor training sessions. An MS-Access database will be used to maintain a record of the stimuli type and frequency of presentation to produce a log of sensorimotor experience for each infant that can be tracked as they progress through the NICU.

Conversion of The Observer file format (ODF) to SALT file format (SLT)
Start Date: Dec 10 2003
Investigator: Dr.Nancy Brady, Schiefelbusch Institute for Life Span Studies
Status: Active

Conversion of The Observer file format (ODF) to SALT file format (SLT)
The Observer is a professional system for the collection, analysis, presentation and management of observational data. It is used to record activities, postures, movements, positions, facial expressions, social interactions or any other aspect of human or animal behavior. This is an integrated solution for systematic observation with analysis reports that are available instantly. This provides objective and quantitative data for direct conclusions or further research.
In the project the researcher wished to refine and analyze the Observer File (ODF) using another program called The SALT (SLT File format).
DEEC developed a file parser to read the ODF file as input and generate the SLT file as output. The development environment was Visual Basic 6.0 and the latest Microsoft VB runtimes. The system would parse and filter the ODF file searching for specific keywords and sentences recorded using The Observer.

Curve Fitting Distortion Product Otoacoustic Emissions
Start Date: Aug 20 2003
Investigator: Dr.Mark Chertoff, KUMC
Status: Completed

This project aims to automate the process of curve fitting Otoacoustic Emissions data using Trust-Region Reflective Newton algorithm (improvement over Levenberg-Marquardt algorithm).

Integration of EPrime with Eyetracker software
Start Date: July 28 2003
Investigator: Dr.Susan Kemper, Psychology
Status: Active

E-Prime is a comprehensive suite of applications offering audited millisecond-timing precision, enabling researchers to develop a wide variety of paradigms that can be implemented with randomized or fixed presentation of text, pictures and sounds. GazeTracker is a multifunction eye-movement analysis application that allows analysis of user eye-responses to still images, videos and graphical user interfaces. The main idea of this project is to integrate EPrime's features with Gazetracker's functionality, automating the randomization of visual stimuli, and at the same time synchronizing with Gazetracker.

Graphical Interface for Analyzing Distortion Product Otoacoustic Emissions
Start Date: June 05 2003
Investigator: Dr.Mark Chertoff, KUMC
Status: Completed

The objective of the project was to generate plots of responses in the form of distortion products to signals sent to either ear of a chicken. The responses included the level of distortion product, noise floor, and system distortion. Previously, the plotting was done manually using MS-Excel. This consumed a considerable amount of time. The main purpose of our MATLAB program was to minimise the time for plot generation through the use of an automated command sequence to read data files and produce graphic output.