The rule-based model approach. A Kappa model for hepatic stellate cells activation by TGFB1

International audienc

Spray: programming with a persistent distributed heap

We introduce a programming paradigm for distributed applications based on a persistent distributed heap. A proof-of-concept implementation is provided as a Javascript library, together with several examples that embody popular patterns for web applications

Fundamental Approaches to Software Engineering

This open access book constitutes the proceedings of the 24th International Conference on Fundamental Approaches to Software Engineering, FASE 2021, which took place during March 27–April 1, 2021, and was held as part of the Joint Conferences on Theory and Practice of Software, ETAPS 2021. The conference was planned to take place in Luxembourg but changed to an online format due to the COVID-19 pandemic. The 16 full papers presented in this volume were carefully reviewed and selected from 52 submissions. The book also contains 4 Test-Comp contributions

Exploring C semantics and pointer provenance

The semantics of pointers and memory objects in C has been a vexed question for many years. C values cannot be treated as either purely abstract or purely concrete entities: the language exposes their representations, but compiler optimisations rely on analyses that reason about provenance and initialisation status, not just runtime representations. The ISO WG14 standard leaves much of this unclear, and in some respects differs with de facto standard usage - which itself is difficult to investigate. In this paper we explore the possible source-language semantics for memory objects and pointers, in ISO C and in C as it is used and implemented in practice, focussing especially on pointer provenance. We aim to, as far as possible, reconcile the ISO C standard, mainstream compiler behaviour, and the semantics relied on by the corpus of existing C code. We present two coherent proposals, tracking provenance via integers and not; both address many design questions. We highlight some pros and cons and open questions, and illustrate the discussion with a library of test cases. We make our semantics executable as a test oracle, integrating it with the Cerberus semantics for much of the rest of C, which we have made substantially more complete and robust, and equipped with a web-interface GUI. This allows us to experimentally assess our proposals on those test cases. To assess their viability with respect to larger bodies of C code, we analyse the changes required and the resulting behaviour for a port of FreeBSD to CHERI, a research architecture supporting hardware capabilities, which (roughly speaking) traps on the memory safety violations which our proposals deem undefined behaviour. We also develop a new runtime instrumentation tool to detect possible provenance violations in normal C code, and apply it to some of the SPEC benchmarks. We compare our proposal with a source-language variant of the twin-allocation LLVM semantics proposal of Lee et al. Finally, we describe ongoing interactions with WG14, exploring how our proposals could be incorporated into the ISO standard

Tools and Algorithms for the Construction and Analysis of Systems

This open access two-volume set constitutes the proceedings of the 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2021, which was held during March 27 – April 1, 2021, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2021. The conference was planned to take place in Luxembourg and changed to an online format due to the COVID-19 pandemic. The total of 41 full papers presented in the proceedings was carefully reviewed and selected from 141 submissions. The volume also contains 7 tool papers; 6 Tool Demo papers, 9 SV-Comp Competition Papers. The papers are organized in topical sections as follows: Part I: Game Theory; SMT Verification; Probabilities; Timed Systems; Neural Networks; Analysis of Network Communication. Part II: Verification Techniques (not SMT); Case Studies; Proof Generation/Validation; Tool Papers; Tool Demo Papers; SV-Comp Tool Competition Papers

Modular Collaborative Program Analysis

With our world increasingly relying on computers, it is important to ensure the quality, correctness, security, and performance of software systems. Static analysis that computes properties of computer programs without executing them has been an important method to achieve this for decades. However, static analysis faces major chal- lenges in increasingly complex programming languages and software systems and increasing and sometimes conflicting demands for soundness, precision, and scalability. In order to cope with these challenges, it is necessary to build static analyses for complex problems from small, independent, yet collaborating modules that can be developed in isolation and combined in a plug-and-play manner. So far, no generic architecture to implement and combine a broad range of dissimilar static analyses exists. The goal of this thesis is thus to design such an architecture and implement it as a generic framework for developing modular, collaborative static analyses. We use several, diverse case-study analyses from which we systematically derive requirements to guide the design of the framework. Based on this, we propose the use of a blackboard-architecture style collaboration of analyses that we implement in the OPAL framework. We also develop a formal model of our architectures core concepts and show how it enables freely composing analyses while retaining their soundness guarantees. We showcase and evaluate our architecture using the case-study analyses, each of which shows how important and complex problems of static analysis can be addressed using a modular, collaborative implementation style. In particular, we show how a modular architecture for the construction of call graphs ensures consistent soundness of different algorithms. We show how modular analyses for different aspects of immutability mutually benefit each other. Finally, we show how the analysis of method purity can benefit from the use of other complex analyses in a collaborative manner and from exchanging different analysis implementations that exhibit different characteristics. Each of these case studies improves over the respective state of the art in terms of soundness, precision, and/or scalability and shows how our architecture enables experimenting with and fine-tuning trade-offs between these qualities

Cautiously Optimistic Program Analyses for Secure and Reliable Software

Modern computer systems still have various security and reliability vulnerabilities. Well-known dynamic analyses solutions can mitigate them using runtime monitors that serve as lifeguards. But the additional work in enforcing these security and safety properties incurs exorbitant performance costs, and such tools are rarely used in practice. Our work addresses this problem by constructing a novel technique- Cautiously Optimistic Program Analysis (COPA). COPA is optimistic- it infers likely program invariants from dynamic observations, and assumes them in its static reasoning to precisely identify and elide wasteful runtime monitors. The resulting system is fast, but also ensures soundness by recovering to a conservatively optimized analysis when a likely invariant rarely fails at runtime. COPA is also cautious- by carefully restricting optimizations to only safe elisions, the recovery is greatly simplified. It avoids unbounded rollbacks upon recovery, thereby enabling analysis for live production software. We demonstrate the effectiveness of Cautiously Optimistic Program Analyses in three areas: Information-Flow Tracking (IFT) can help prevent security breaches and information leaks. But they are rarely used in practice due to their high performance overhead (>500% for web/email servers). COPA dramatically reduces this cost by eliding wasteful IFT monitors to make it practical (9% overhead, 4x speedup). Automatic Garbage Collection (GC) in managed languages (e.g. Java) simplifies programming tasks while ensuring memory safety. However, there is no correct GC for weakly-typed languages (e.g. C/C++), and manual memory management is prone to errors that have been exploited in high profile attacks. We develop the first sound GC for C/C++, and use COPA to optimize its performance (16% overhead). Sequential Consistency (SC) provides intuitive semantics to concurrent programs that simplifies reasoning for their correctness. However, ensuring SC behavior on commodity hardware remains expensive. We use COPA to ensure SC for Java at the language-level efficiently, and significantly reduce its cost (from 24% down to 5% on x86). COPA provides a way to realize strong software security, reliability and semantic guarantees at practical costs.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/170027/1/subarno_1.pd

Fundamental Approaches to Software Engineering

This open access book constitutes the proceedings of the 25th International Conference on Fundamental Approaches to Software Engineering, FASE 2022, which was held during April 4-5, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 17 regular papers presented in this volume were carefully reviewed and selected from 64 submissions. The proceedings also contain 3 contributions from the Test-Comp Competition. The papers deal with the foundations on which software engineering is built, including topics like software engineering as an engineering discipline, requirements engineering, software architectures, software quality, model-driven development, software processes, software evolution, AI-based software engineering, and the specification, design, and implementation of particular classes of systems, such as (self-)adaptive, collaborative, AI, embedded, distributed, mobile, pervasive, cyber-physical, or service-oriented applications