24 research outputs found
OpenJML: Software verification for Java 7 using JML, OpenJDK, and Eclipse
OpenJML is a tool for checking code and specifications of Java programs. We
describe our experience building the tool on the foundation of JML, OpenJDK and
Eclipse, as well as on many advances in specification-based software
verification. The implementation demonstrates the value of integrating
specification tools directly in the software development IDE and in automating
as many tasks as possible. The tool, though still in progress, has now been
used for several college-level courses on software specification and
verification and for small-scale studies on existing Java programs.Comment: In Proceedings F-IDE 2014, arXiv:1404.578
SPEEDY: An Eclipse-based IDE for invariant inference
SPEEDY is an Eclipse-based IDE for exploring techniques that assist users in
generating correct specifications, particularly including invariant inference
algorithms and tools. It integrates with several back-end tools that propose
invariants and will incorporate published algorithms for inferring object and
loop invariants. Though the architecture is language-neutral, current SPEEDY
targets C programs. Building and using SPEEDY has confirmed earlier experience
demonstrating the importance of showing and editing specifications in the IDEs
that developers customarily use, automating as much of the production and
checking of specifications as possible, and showing counterexample information
directly in the source code editing environment. As in previous work,
automation of specification checking is provided by back-end SMT solvers.
However, reducing the effort demanded of software developers using formal
methods also requires a GUI design that guides users in writing, reviewing, and
correcting specifications and automates specification inference.Comment: In Proceedings F-IDE 2014, arXiv:1404.578
Demonstration of JML Tools
The Java Modeling language (JML) is a behavioral interface specification language tailored to Java. This demonstration presents some of the basic tools for generating and browsing documentation, runtime assertion checking, and unit testing
Applying SMT Solvers to the Test Template Framework
The Test Template Framework (TTF) is a model-based testing method for the Z
notation. In the TTF, test cases are generated from test specifications, which
are predicates written in Z. In turn, the Z notation is based on first-order
logic with equality and Zermelo-Fraenkel set theory. In this way, a test case
is a witness satisfying a formula in that theory. Satisfiability Modulo Theory
(SMT) solvers are software tools that decide the satisfiability of arbitrary
formulas in a large number of built-in logical theories and their combination.
In this paper, we present the first results of applying two SMT solvers, Yices
and CVC3, as the engines to find test cases from TTF's test specifications. In
doing so, shallow embeddings of a significant portion of the Z notation into
the input languages of Yices and CVC3 are provided, given that they do not
directly support Zermelo-Fraenkel set theory as defined in Z. Finally, the
results of applying these embeddings to a number of test specifications of
eight cases studies are analysed.Comment: In Proceedings MBT 2012, arXiv:1202.582
Alternative splicing of TIA-1 in human colon cancer regulates VEGF isoform expression, angiogenesis, tumour growth and bevacizumab resistance
© 2014 The Authors. The angiogenic capability of colorectal carcinomas (CRC), and their susceptibility to anti-angiogenic therapy, is determined by expression of vascular endothelial growth factor (VEGF) isoforms. The intracellular protein T-cell Intracellular Antigen (TIA-1) alters post-transcriptional RNA processing and binds VEGF-A mRNA. We therefore tested the hypothesis that TIA-1 could regulate VEGF-A isoform expression in colorectal cancers. TIA-1 and VEGF-A isoform expression was measured in colorectal cancers and cell lines. We discovered that an endogenous splice variant of TIA-1 encoding a truncated protein, short TIA-1 (sTIA-1) was expressed in CRC tissues and invasive K-Ras mutant colon cancer cells and tissues but not in adenoma cell lines. sTIA-1 was more highly expressed in CRC than in normal tissues and increased with tumour stage. Knockdown of sTIA-1 or over-expression of full length TIA-1 (flTIA-1) induced expression of the anti-angiogenic VEGF isoform VEGF-A 165 b. Whereas flTIA-1 selectively bound VEGF-A 165 mRNA and increased translation of VEGF-A 165 b, sTIA-1 prevented this binding. In nude mice, xenografted colon cancer cells over-expressing flTIA-1 formed smaller, less vascular tumours than those expressing sTIA-1, but flTIA-1 expression inhibited the effect of anti-VEGF antibodies. These results indicate that alternative splicing of an RNA binding protein can regulate isoform specific expression of VEGF providing an added layer of complexity to the angiogenic profile of colorectal cancer and their resistance to anti-angiogenic therapy
RNA Binding Protein CUGBP2/CELF2 Mediates Curcumin-Induced Mitotic Catastrophe of Pancreatic Cancer Cells
Curcumin inhibits the growth of pancreatic cancer tumor xenografts in nude mice; however, the mechanism of action is not well understood. It is becoming increasingly clear that RNA binding proteins regulate posttranscriptional gene expression and play a critical role in RNA stability and translation. Here, we have determined that curcumin modulates the expression of RNA binding protein CUGBP2 to inhibit pancreatic cancer growth.In this study, we show that curcumin treated tumor xenografts have a significant reduction in tumor volume and angiogenesis. Curcumin inhibited the proliferation, while inducing G2-M arrest and apoptosis resulting in mitotic catastrophe of various pancreatic cancer cells. This was further confirmed by increased phosphorylation of checkpoint kinase 2 (Chk2) protein coupled with higher levels of nuclear cyclin B1 and Cdc-2. Curcumin increased the expression of cyclooxygenase-2 (COX-2) and vascular endothelial growth factor (VEGF) mRNA, but protein levels were lower. Furthermore, curcumin increased the expression of RNA binding proteins CUGBP2/CELF2 and TIA-1. CUGBP2 binding to COX-2 and VEGF mRNA was also enhanced, thereby increasing mRNA stability, the half-life changing from 30 min to 8 h. On the other hand, silencer-mediated knockdown of CUGBP2 partially restored the expression of COX-2 and VEGF even with curcumin treatment. COX-2 and VEGF mRNA levels were reduced to control levels, while proteins levels were higher.Curcumin inhibits pancreatic tumor growth through mitotic catastrophe by increasing the expression of RNA binding protein CUGBP2, thereby inhibiting the translation of COX-2 and VEGF mRNA. These data suggest that translation inhibition is a novel mechanism of action for curcumin during the therapeutic intervention of pancreatic cancers
Reasoning with specifications containing method calls in JML and First-Order Provers
Allowing method invocations in program specifications increases modularity and comprehensibility and is as important in specifications as it is in the program itself. However, method invocations do not map neatly into the first-order logics that are often used for assuring the correctness of specifications. One problem is translating specifications in a way that acknowledges the potential for exceptional behavior. The ESC/Java2 tool has been able to achieve a practical translation of method invocations within the design constraints of its parent tool, ESC/Java. Furthermore, the techniques used are applicable to other specification constructs such as quantifiers and model variables
Reasoning with specifications containing method calls and model fields
Allowing abstraction in program specifications increases modularity and comprehensibility and is as important in specifications as it is in the program itself; two such abstraction mechanisms are method invocations and model fields. However, method invocations do not map neatly into the first-order logics that are often used for assuring the correctness of specifications. One problem is translating specifications in a way that acknowledges the potential for exceptional behavior. Furthermore, translating model fields into verification conditions exposes the non-trivial interactions between frame conditions and the model representations. The ESC/Java2 tool has been able to achieve a practical translation of method invocations and model fields within the design constraints of its parent tool, ESC/Java. Furthermore, the techniques used are applicable to other specification constructs such as generalized quantifiers