SBMLToolbox: an SBML toolbox for MATLAB users

We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML

Autonomously Calibrating a Quadrupole Mass Spectrometer

A computer program autonomously manages the calibration of a quadrupole ion mass spectrometer intended for use in monitoring concentrations and changes in concentrations of organic chemicals in the cabin air of the International Space Station. The instrument parameters calibrated include the voltage on a channel electron multiplier, a discriminator threshold, and an ionizer current. Calibration is achieved by analyzing the mass spectrum obtained while sweeping the parameter ranges in a heuristic procedure, developed by mass spectrometer experts, that involves detection of changes in signal trends that humans can easily recognize but cannot necessarily be straightforwardly codified in an algorithm. The procedure includes calculation of signal-to-noise ratios, signal-increase rates, and background-noise-increase rates; finding signal peaks; and identifying peak patterns. The software provides for several recovery-from-error scenarios and error-handling schemes. The software detects trace amounts of contaminant gases in the mass spectrometer and notifies associated command- and-data-handling software to schedule a cleaning. Furthermore, the software autonomously analyzes the mass spectrum to determine whether the parameters of a radio-frequency ramp waveform are set properly so that the peaks of the mass spectrum are at expected locations

Semi-Automated Identification of Rocks in Images

Rock Identification Toolkit Suite is a computer program that assists users in identifying and characterizing rocks shown in images returned by the Mars Explorer Rover mission. Included in the program are components for automated finding of rocks, interactive adjustments of outlines of rocks, active contouring of rocks, and automated analysis of shapes in two dimensions. The program assists users in evaluating the surface properties of rocks and soil and reports basic properties of rocks. The program requires either the Mac OS X operating system running on a G4 (or more capable) processor or a Linux operating system running on a Pentium (or more capable) processor, plus at least 128MB of random-access memory

Measuring Organizational Member Involvement In Physical Activity Coalitions Across the United States

Physical inactivity has been labeled a global pandemic with enormous economic, social, environmental, and public health consequences. The vast majority of American adults and youth are insufficiently physically active. Increasing population-levels of physical activity (PA) requires broad social and environmental change. PA coalitions provide the structure through which such broad change can be achieved. An extensive literature on health-based coalitions suggests that coalition success is impacted by coalition members. Coalitions are generally comprised of member organizations. Little is known about the characteristics of PA coalitions and less is known about organizational member involvement in PA coalitions. The purpose of this dissertation was to develop a survey instrument for measuring organizational member involvement in PA coalitions. The dissertation also provides descriptive characteristics of local-, state-, and national-level PA coalitions across the United States. Additionally, the dissertation provides descriptive characteristics of organizational members of PA coalitions across the U.S. Finally, the dissertation examines whether or not there is an association between organizational member involvement and physical activity coalition success as perceived by representatives of member organizations. The dissertation used a cross-sectional design and applied both qualitative and quantitative methods. The objective of the first study was to expand our knowledge of factors related to organizations\u27 decisions to join and remain committed to the coalition that developed and launched the U.S. National Physical Activity Plan (NPAP). Qualitative semi-structured phone interviews were conducted with fourteen key informants representing thirteen of the NPAP coalition\u27s partner organizations. Five primary factors for organizational membership emerged: (1) Strategic Alignment; (2) Organizational Alignment; (3) Providing Input; (4) Seminal Event; and (5) Cost/Benefit Ratio. The second study was conducted in three phases and resulted in a psychometrically sound instrument for measuring organizational member involvement in PA coalitions. The study\u27s three phases were: (1) Development of a draft survey based on the qualitative analysis of organizational members from the NPAP coalition; (2) Assessment of the content validity of the draft survey to produce a final survey; and (3) Conduct of an exploratory factor analysis to assess the final survey\u27s psychometric properties. The final survey was administered to 120 individuals who represent organizations that were members of PA coalitions across the U.S. The exploratory factor analysis yielded a three-factor model with the following subscales: Strategic Alignment, Organizational Alignment, and Providing Input. Each of the survey\u27s three subscales demonstrated high internal consistency reliability as follows: Strategic Alignment (Cronbach\u27s alpha = 0.94); Organizational Alignment (Cronbach\u27s alpha = 0.83); and Providing Input (Cronbach\u27s alpha = 0.88). Each of the subscales also demonstrated sufficient construct validity, being significantly positively correlated with two previously validated subscales (Coalition Satisfaction, Coalition Outcome Efficacy) for which a positive correlation should theoretically exist. The third study described the characteristics of PA coalitions and their organizational members, and investigated the association between factors for organizational membership and coalition success. Overall, PA coalitions were found to be working in a diverse range of settings including: Schools (78%); Built environment (58%); Workplace (58%); and Public Health (53%). Those coalitions were reported to have pursued a broad range of initiatives including: Advocacy to promote active living (78%); Changes to/formation of policy (71%); and Expanding their network of partners (52%). Most types organizational members of PA coalitions were Government agencies (48%) or Non-profit organizations (40%). Organizational members worked across a variety of settings including: Public Health (41%); Education (21%); Health Care (15%). Overall, mean scale scores for Strategic Alignment, Organizational Alignment, and Providing Input were high for all types of organizational members though some differences by organizational member type were noted. Factors for organizational membership were associated with coalition success. Pooled t-tests revealed statistically significant differences between each factor for organizational membership (Strategic Alignment, Organizational Alignment, and Providing Input) and high and low levels of perceived coalition success (Coalition Satisfaction, and Coalition Outcome Efficacy). In summary, this dissertation produced a psychometrically sound survey instrument for measuring key aspects of organizational membership in PA coalitions. This project shows that building and maintaining successful PA coalitions may hinge upon the ability to understand and demonstrate how organizational members benefit from: strategically aligning with the coalition; aligning with the coalition\u27s other organizational members; and providing input on the coalition\u27s activities

LibSBML: an API library for SBML

LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software

Mobile Thread Task Manager

The Mobile Thread Task Manager (MTTM) is being applied to parallelizing existing flight software to understand the benefits and to develop new techniques and architectural concepts for adapting software to multicore architectures. It allocates and load-balances tasks for a group of threads that migrate across processors to improve cache performance. In order to balance-load across threads, the MTTM augments a basic map-reduce strategy to draw jobs from a global queue. In a multicore processor, memory may be "homed" to the cache of a specific processor and must be accessed from that processor. The MTTB architecture wraps access to data with thread management to move threads to the home processor for that data so that the computation follows the data in an attempt to avoid L2 cache misses. Cache homing is also handled by a memory manager that translates identifiers to processor IDs where the data will be homed (according to rules defined by the user). The user can also specify the number of threads and processors separately, which is important for tuning performance for different patterns of computation and memory access. MTTM efficiently processes tasks in parallel on a multiprocessor computer. It also provides an interface to make it easier to adapt existing software to a multiprocessor environment

Injecting Artificial Memory Errors Into a Running Computer Program

Single-event upsets (SEUs) or bitflips are computer memory errors caused by radiation. BITFLIPS (Basic Instrumentation Tool for Fault Localized Injection of Probabilistic SEUs) is a computer program that deliberately injects SEUs into another computer program, while the latter is running, for the purpose of evaluating the fault tolerance of that program. BITFLIPS was written as a plug-in extension of the open-source Valgrind debugging and profiling software. BITFLIPS can inject SEUs into any program that can be run on the Linux operating system, without needing to modify the program s source code. Further, if access to the original program source code is available, BITFLIPS offers fine-grained control over exactly when and which areas of memory (as specified via program variables) will be subjected to SEUs. The rate of injection of SEUs is controlled by specifying either a fault probability or a fault rate based on memory size and radiation exposure time, in units of SEUs per byte per second. BITFLIPS can also log each SEU that it injects and, if program source code is available, report the magnitude of effect of the SEU on a floating-point value or other program variable

Major Constituents Analysis for the Vehicle Cabin Atmosphere Monitor

Vehicle Cabin Atmosphere Monitor (VCAM) can provide a means for monitoring the air within enclosed environments such as the International Space Station, the Crew Exploration Vehicle (CEV), a Lunar habitat, or another vehicle traveling to Mars. The software processes a sum total spectra (counts vs. mass channel) with the intention of computing abundance ratios for N2, O2, CO2, Ar2, and H2O. A brute-force powerset expansion compares a library of expected mass lines with those found within the data. Least squares error is combined with a penalty term for using small peaks