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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
NASA NTRS1996

GRASP/Ada 95: Reverse Engineering Tools for Ada

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped an algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD), and a new visualization for a fine-grained complexity metric called the Complexity Profile Graph (CPG). By synchronizing the CSD and the CPG, the CSD view of control structure, nesting, and source code is directly linked to the corresponding visualization of statement level complexity in the CPG. GRASP has been integrated with GNAT, the GNU Ada 95 Translator to provide a comprehensive graphical user interface and development environment for Ada 95. The user may view, edit, print, and compile source code as a CSD with no discernible addition to storage or computational overhead. The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis has been on the automatic generation of the CSD from Ada 95 source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. The current update has focused on the design and implementation of a new Motif compliant user interface, and a new CSD generator consisting of a tagger and renderer. The Complexity Profile Graph (CPG) is based on a set of functions that describes the context, content, and the scaling for complexity on a statement by statement basis. When combined graphicafly, the result is a composite profile of complexity for the program unit. Ongoing research includes the development and refinement of the associated functions, and the development of the CPG generator prototype. The current Version 5.0 prototype provides the capability for the user to generate CSDs and CPGs from Ada 95 source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application. This report provides an overview of the GRASP/Ada project with an emphasis on the current update.

Cross, James H., II↗
DOE OSTI2011

Reverse Engineering Adverse Outcome Pathways

The toxicological effects of many stressors are mediated through unknown, or poorly characterized, mechanisms of action. We describe the application of reverse engineering complex interaction networks from high dimensional omics data (gene, protein, metabolic, signaling) to characterize adverse outcome pathways (AOPs) for chemicals that disrupt the hypothalamus-pituitary-gonadal endocrine axis in fathead minnows. Gene expression changes in fathead minnow ovaries in response to 7 different chemicals, over different times, doses, and in vivo versus in vitro conditions were captured in a large data set of 868 arrays. We examined potential AOPs of the antiandrogen flutamide using two mutual information theory methods, ARACNE and CLR to infer gene regulatory networks and potential adverse outcome pathways. Representative networks from these studies were used to predict a network path from stressor to adverse outcome as a candidate AOP. The relationship of individual chemicals to an adverse outcome can be determined by following perturbations through the network in response to chemical treatment leading to the nodes associated with the adverse outcome. Identification of candidate pathways allows for formation of testable hypotheses about key biologic processes, biomarkers or alternative endpoints, which could be used to monitor an adverse outcome pathway. Finally, we identify the unique challenges facing the application of this approach in ecotoxicology, and attempt to provide a road map for the utilization of these tools. Key Words: mechanism of action, toxicology, microarray, network inference

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

GRASP/Ada: Graphical Representations of Algorithms, Structures, and Processes for Ada. The development of a program analysis environment for Ada: Reverse engineering tools for Ada, task 2, phase 3

The main objective is the investigation, formulation, and generation of graphical representations of algorithms, structures, and processes for Ada (GRASP/Ada). The presented task, in which various graphical representations that can be extracted or generated from source code are described and categorized, is focused on reverse engineering. The following subject areas are covered: the system model; control structure diagram generator; object oriented design diagram generator; user interface; and the GRASP library.

Cross, James H., II↗
NASA NTRS2002

Using a Formal Approach for Reverse Engineering and Design Recovery to Support Software Reuse

This document describes 3rd year accomplishments and summarizes overall project accomplishments. Included as attachments are all published papers from year three. Note that the budget for this project was discontinued after year two, but that a residual budget from year two allowed minimal continuance into year three. Accomplishments include initial investigations into log-file based reverse engineering, service-based software reuse, and a source to XML generator.

Gannod, Gerald C.↗
NASA NTRS2008

Revitalizing the Space Shuttle's Thermal Protection System with Reverse Engineering and 3D Vision Technology

The Space Shuttle is protected by a Thermal Protection System (TPS) made of tens of thousands of individually shaped heat protection tile. With every flight, tiles are damaged on take-off and return to earth. After each mission, the heat tiles must be fixed or replaced depending on the level of damage. As part of the return to flight mission, the TPS requirements are more stringent, leading to a significant increase in heat tile replacements. The replacement operation requires scanning tile cavities, and in some cases the actual tiles. The 3D scan data is used to reverse engineer each tile into a precise CAD model, which in turn, is exported to a CAM system for the manufacture of the heat protection tile. Scanning is performed while other activities are going on in the shuttle processing facility. Many technicians work simultaneously on the space shuttle structure, which results in structural movements and vibrations. This paper will cover a portable, ultra-fast data acquisition approach used to scan surfaces in this unstable environment.

Wilson, Brad↗
NASA NTRS2008

Revitalizing the Space Shuttle's Thermal Protection System with Reverse Engineering and 3D Vision Technology

The Space Shuttle is protected by a Thermal Protection System (TPS) made of tens of thousands of individually shaped heat protection tile. With every flight, tiles are damaged on take-off and return to earth. After each mission, the heat tiles must be fixed or replaced depending on the level of damage. As part of the return to flight mission, the TPS requirements are more stringent, leading to a significant increase in heat tile replacements. The replacement operation requires scanning tile cavities, and in some cases the actual tiles. The 3D scan data is used to reverse engineer each tile into a precise CAD model, which in turn, is exported to a CAM system for the manufacture of the heat protection tile. Scanning is performed while other activities are going on in the shuttle processing facility. Many technicians work simultaneously on the space shuttle structure, which results in structural movements and vibrations. This paper will cover a portable, ultra-fast data acquisition approach used to scan surfaces in this unstable environment.

Wilson, Brad↗
NASA NTRS1998

Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

Liang, Shoudan↗
NASA NTRS2000

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering

Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

Dhaeseleer, Patrik↗
DOE OSTI2016

Brain in situ hybridization maps as a source for reverse-engineering transcriptional regulatory networks: Alzheimer's disease insights

Microarray data have been a valuable resource for identifying transcriptional regulatory relationships among genes. As an example, brain region-specific transcriptional regulatory events have the potential of providing etiological insights into Alzheimer Disease (AD). However, there is often a paucity of suitable brain-region specific expression data obtained via microarrays or other high throughput means. The Allen Brain Atlas in situ hybridization (ISH) data sets (Jones et al., 2009) represent a potentially valuable alternative source of high-throughput brain region-specific gene expression data for such purposes. In this study, Allen BrainAtlasmouse ISH data in the hippocampal fields were extracted, focusing on 508 genes relevant to neurodegeneration. Transcriptional regulatory networkswere learned using three high-performing network inference algorithms. Only 17% of regulatory edges from a network reverse-engineered based on brain region-specific ISH data were also found in a network constructed upon gene expression correlations inmousewhole brain microarrays, thus showing the specificity of gene expression within brain sub-regions. Furthermore, the ISH data-based networks were used to identify instructive transcriptional regulatory relationships. Ncor2, Sp3 and Usf2 form a unique three-party regulatory motif, potentially affecting memory formation pathways. Nfe2l1, Egr1 and Usf2 emerge among regulators of genes involved in AD (e.g. Dhcr24, Aplp2, Tia1, Pdrx1, Vdac1, andSyn2). Further, Nfe2l1, Egr1 and Usf2 are sensitive to dietary factors and could be among links between dietary influences and genes in the AD etiology. Thus, this approach of harnessing brain region-specific ISH data represents a rare opportunity for gleaning unique etiological insights for diseases such as AD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Reverse engineering nuclear properties from rare earth abundances in the r process

The bulk of the rare earth elements are believed to be synthesized in the rapid neutron capture process or r process of nucleosynthesis. The solar r-process residuals show a small peak in the rare earths around $A\sim 160$, which is proposed to be formed dynamically during the end phase of the r process by a pileup of material. This abundance feature is of particular importance as it is sensitive to both the nuclear physics inputs and the astrophysical conditions of the main r process. Here, we explore the formation of the rare earth peak from the perspective of an inverse problem, using Monte Carlo studies of nuclear masses to investigate the unknown nuclear properties required to best match rare earth abundance sector of the solar isotopic residuals. When nuclear masses are changed, we recalculate the relevant β-decay properties and neutron capture rates in the rare earth region. The feedback provided by this observational constraint allows for the reverse engineering of nuclear properties far from stability where no experimental information exists. We investigate a range of astrophysical conditions with this method and show how these lead to different predictions in the nuclear properties influential to the formation of the rare earth peak. Finally, we conclude that targeted experimental campaigns in this region will help to resolve the type of conditions responsible for the production of the rare earth nuclei, and will provide new insights into the longstanding problem of the astrophysical site(s) of the r process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1994

Automation of reverse engineering process in aircraft modeling and related optimization problems

During the year of 1994, the engineering problems in aircraft modeling were studied. The initial concern was to obtain a surface model with desirable geometric characteristics. Much of the effort during the first half of the year was to find an efficient way of solving a computationally difficult optimization model. Since the smoothing technique in the proposal 'Surface Modeling and Optimization Studies of Aerodynamic Configurations' requires solutions of a sequence of large-scale quadratic programming problems, it is important to design algorithms that can solve each quadratic program in a few interactions. This research led to three papers by Dr. W. Li, which were submitted to SIAM Journal on Optimization and Mathematical Programming. Two of these papers have been accepted for publication. Even though significant progress has been made during this phase of research and computation times was reduced from 30 min. to 2 min. for a sample problem, it was not good enough for on-line processing of digitized data points. After discussion with Dr. Robert E. Smith Jr., it was decided not to enforce shape constraints in order in order to simplify the model. As a consequence, P. Dierckx's nonparametric spline fitting approach was adopted, where one has only one control parameter for the fitting process - the error tolerance. At the same time the surface modeling software developed by Imageware was tested. Research indicated a substantially improved fitting of digitalized data points can be achieved if a proper parameterization of the spline surface is chosen. A winning strategy is to incorporate Dierckx's surface fitting with a natural parameterization for aircraft parts. The report consists of 4 chapters. Chapter 1 provides an overview of reverse engineering related to aircraft modeling and some preliminary findings of the effort in the second half of the year. Chapters 2-4 are the research results by Dr. W. Li on penalty functions and conjugate gradient methods for quadratic programming problems.

Li, W.↗
DOE OSTI2021

Reverse-Engineering Strain in Nanocrystallites by Tracking Trimerons

Although strain underpins the behavior of many transition-oxide-based magnetic nanomaterials, it is elusive to quantify. Since the formation of orbital molecules is sensitive to strain, a metal–insulator transition should be a window into nanocrystallite strain. Using three sizes of differently strained Fe 3 O 4 polycrystalline nanorods, the impact of strain on the Verwey transition and the associated formation and dissolution processes of quasiparticle trimerons is tracked. In 40 and 50 nm long nanorods, increasing isotropic strain results in Verwey transitions going from T V ≈ 60 K to 20 K. By contrast, 700 nm long nanorods with uniaxial strain along the (110) direction have T V ≈ 150 K—the highest value reported thus far. A metal–insulator transition, like T V in Fe 3 O 4 , can be used to determine the effective strain within nanocrystallites, thus providing new insights into nanoparticle properties and nanomagnetism.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Reverse engineering the ancient ceramic technology based on X-ray fluorescence spectromicroscopy

We present results of X-ray fluorescence (XRF) microprobe analyses of ancient ceramic cross-sections aiming at deciphering the different firing protocols used for their production. Micro-focused XRF elemental mapping, Fe chemical mapping and Fe K-edge X-ray absorption near edge structure spectroscopy were performed on pre-sigillata ceramics from southern Gaul, and terra Sigillata vessels from Italy and southern Gaul. Pieces from the different workshops and regions showed significant difference in the starting clay material, clay conditioning and kiln firing condition. By contrast, sherds from the same workshop exhibited more subtle differences and possible misfirings. Understanding the precise firing conditions and protocols would allow recreation of kilns for various productions. Furthermore, evolution and modification of kiln design would shed some light on how ancient potters devised solutions to diverse technological problems they encountered.

99 GENERAL AND MISCELLANEOUS↗