LOMETS: A local meta-threading-server for protein structure prediction

We developed LOMETS, a local threading meta-server, for quick and automated predictions of protein tertiary structures and spatial constraints. Nine state-of-the-art threading programs are installed and run in a local computer cluster, which ensure the quick generation of initial threading alignments compared with traditional remote-server-based meta-servers. Consensus models are generated from the top predictions of the component-threading servers, which are at least 7% more accurate than the best individual servers based on TM-score at a t-test significance level of 0.1%. Moreover, side-chain and C-alpha (Cα) contacts of 42 and 61% accuracy respectively, as well as long- and short-range distant maps, are automatically constructed from the threading alignments. These data can be easily used as constraints to guide the ab initio procedures such as TASSER for further protein tertiary structure modeling. The LOMETS server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/LOMETS

Branch-coverage testability transformation for unstructured programs

Test data generation by hand is a tedious, expensive and error-prone activity, yet testing is a vital part of the development process. Several techniques have been proposed to automate the generation of test data, but all of these are hindered by the presence of unstructured control flow. This paper addresses the problem using testability transformation. Testability transformation does not preserve the traditional meaning of the program, rather it deals with preserving test-adequate sets of input data. This requires new equivalence relations which, in turn, entail novel proof obligations. The paper illustrates this using the branch coverage adequacy criterion and develops a branch adequacy equivalence relation and a testability transformation for restructuring. It then presents a proof that the transformation preserves branch adequacy

Semantics-based Automated Web Testing

We present TAO, a software testing tool performing automated test and oracle generation based on a semantic approach. TAO entangles grammar-based test generation with automated semantics evaluation using a denotational semantics framework. We show how TAO can be incorporated with the Selenium automation tool for automated web testing, and how TAO can be further extended to support automated delta debugging, where a failing web test script can be systematically reduced based on grammar-directed strategies. A real-life parking website is adopted throughout the paper to demonstrate the effectivity of our semantics-based web testing approach.Comment: In Proceedings WWV 2015, arXiv:1508.0338

CTGEN - a Unit Test Generator for C

We present a new unit test generator for C code, CTGEN. It generates test data for C1 structural coverage and functional coverage based on pre-/post-condition specifications or internal assertions. The generator supports automated stub generation, and data to be returned by the stub to the unit under test (UUT) may be specified by means of constraints. The typical application field for CTGEN is embedded systems testing; therefore the tool can cope with the typical aliasing problems present in low-level C, including pointer arithmetics, structures and unions. CTGEN creates complete test procedures which are ready to be compiled and run against the UUT. In this paper we describe the main features of CTGEN, their technical realisation, and we elaborate on its performance in comparison to a list of competing test generation tools. Since 2011, CTGEN is used in industrial scale test campaigns for embedded systems code in the automotive domain.Comment: In Proceedings SSV 2012, arXiv:1211.587

A Survey of Symbolic Execution Techniques

Many security and software testing applications require checking whether certain properties of a program hold for any possible usage scenario. For instance, a tool for identifying software vulnerabilities may need to rule out the existence of any backdoor to bypass a program's authentication. One approach would be to test the program using different, possibly random inputs. As the backdoor may only be hit for very specific program workloads, automated exploration of the space of possible inputs is of the essence. Symbolic execution provides an elegant solution to the problem, by systematically exploring many possible execution paths at the same time without necessarily requiring concrete inputs. Rather than taking on fully specified input values, the technique abstractly represents them as symbols, resorting to constraint solvers to construct actual instances that would cause property violations. Symbolic execution has been incubated in dozens of tools developed over the last four decades, leading to major practical breakthroughs in a number of prominent software reliability applications. The goal of this survey is to provide an overview of the main ideas, challenges, and solutions developed in the area, distilling them for a broad audience. The present survey has been accepted for publication at ACM Computing Surveys. If you are considering citing this survey, we would appreciate if you could use the following BibTeX entry: http://goo.gl/Hf5FvcComment: This is the authors pre-print copy. If you are considering citing this survey, we would appreciate if you could use the following BibTeX entry: http://goo.gl/Hf5Fv

Upside-down Deduction

Over the recent years, several proposals were made to enhance database systems with automated reasoning. In this article we analyze two such enhancements based on meta-interpretation. We consider on the one hand the theorem prover Satchmo, on the other hand the Alexander and Magic Set methods. Although they achieve different goals and are based on distinct reasoning paradigms, Satchmo and the Alexander or Magic Set methods can be similarly described by upside-down meta-interpreters, i.e., meta-interpreters implementing one reasoning principle in terms of the other. Upside-down meta-interpretation gives rise to simple and efficient implementations, but has not been investigated in the past. This article is devoted to studying this technique. We show that it permits one to inherit a search strategy from an inference engine, instead of implementing it, and to combine bottom-up and top-down reasoning. These properties yield an explanation for the efficiency of Satchmo and a justification for the unconventional approach to top-down reasoning of the Alexander and Magic Set methods

A methodology for producing reliable software, volume 1

An investigation into the areas having an impact on producing reliable software including automated verification tools, software modeling, testing techniques, structured programming, and management techniques is presented. This final report contains the results of this investigation, analysis of each technique, and the definition of a methodology for producing reliable software