Approaches to Interpreter Composition

In this paper, we compose six different Python and Prolog VMs into 4 pairwise compositions: one using C interpreters; one running on the JVM; one using meta-tracing interpreters; and one using a C interpreter and a meta-tracing interpreter. We show that programs that cross the language barrier frequently execute faster in a meta-tracing composition, and that meta-tracing imposes a significantly lower overhead on composed programs relative to mono-language programs.Comment: 33 pages, 1 figure, 9 table

Rigorous Validation of Systems Security Engineering Analytics

In response to the asymmetric advantage that attackers enjoy over defenders in cyber systems, the cyber community has generated a steady stream of cybersecurity-related frameworks, methodologies, analytics, and “best practices” lists. However, these artifacts almost never under-go rigorous validation of their efficacy but instead tend to be accepted on faith, to, we suggest, our collective detriment based on evidence of continued attacker success. But what would rigorous validation look like, and can we afford it? This paper describes the design and estimates the cost of a controlled experiment whose goal is to deter-mine the effectiveness of an exemplar systems security analytic. Given the significant footprint that humans play in cyber systems (e.g., their design, use, attack, and defense), any such experiment must necessarily take into account and control for variable human behavior. Thus, the paper reinforces the argument that cybersecurity can be understood as a hybrid discipline with strong technical and human dimensions

The Truth, the Whole Truth, and Nothing but the Truth: A Pragmatic Guide to Assessing Empirical Evaluations

An unsound claim can misdirect a field, encouraging the pursuit of unworthy ideas and the abandonment of promising ideas. An inadequate description of a claim can make it difficult to reason about the claim, for example to determine whether the claim is sound. Many practitioners will acknowledge the threat of un- sound claims or inadequate descriptions of claims to their field. We believe that this situation is exacerbated and even encouraged by the lack of a systematic approach to exploring, exposing, and addressing the source of unsound claims and poor exposition. This paper proposes a framework that identifies three sins of reasoning that lead to unsound claims and two sins of exposition that lead to poorly described claims. Sins of exposition obfuscate the objective of determining whether or not a claim is sound, while sins of reasoning lead directly to unsound claims. Our framework provides practitioners with a principled way of critiquing the integrity of their own work and the work of others. We hope that this will help individuals conduct better science and encourage a cultural shift in our research community to identify and promulgate sound claims

Expresión diferencial del GASH/Sal tras estimulación sonora

Trabajo de Fin de Máster del Máster en Neurociencias, curso 2018-2019[ES] La línea de hámster dorado o sirio (Mesocricetus Auratus) GASH/Sal es un modelo de epilepsia audiógena de origen genético cuyo foco epileptógeno es el colículo inferior (CI). Objetivos. Analizar el transcriptoma del CI para obtener un perfil de expresión de los genes relevantes en la línea GASH/Sal que podría usarse para buscar un vínculo común con la epilepsia humana. Metodología. Utilizando la técnica de ARN-Seq en la plataforma Illumina 75bp Single-End, se han obtenido dos tipos de transcriptomas de los CIs de hámsteres controles y de la línea GASH/Sal, ambos sometidos a estimulación auditiva, alineándolos con dos genomas de referencia distintos, el del hámster chino (Cricetulus griseus) y el del propio hámster sirio. Posterior análisis comparativo de los dos transcriptomas con ambos genomas de referencia, nos permitió obtener un conjunto de genes diferencialmente expresados y, seguidamente, en base a los criterios de la diferencia del nivel de expresión (Fold Change, |FC| >1.5), p valor (p 1.5 ), p value (p <0.05) and False Discovery Rate (FDR), select a small group of genes that were validated by quantitative PCR (qPCR). Results. We determined 41 and 33 differentially expressed genes using the Syrian hamster genome and the Chinese hamster genome, respectively, being the first of them, which presented a better alignment by base, coverage, percentage of homology and greater sensitivity in the detection of transcripts. The comparison between both groups of genes showed that 12 genes were coincident and 9 of them (Atp2a3, C6, Egr1, Egr2, Egr3, Fos, Rxfp2, Slc28a1 and Ttr) were used in the validation of the variations of gene expression detected by the qPCR technique. Conclusion The results show genes differentially expressed in the IC of the Syrian hamster line GASH / Sal that can serve as a starting point to look for the epileptogenic mechanisms in this animal model and possible correlations with human epilepsy

Fine-Grained Workflow Interoperability in Life Sciences

In den vergangenen Jahrzehnten führten Fortschritte in den Schlüsseltechnologien der Lebenswissenschaften zu einer exponentiellen Zunahme der zur Verfügung stehenden biologischen Daten. Um Ergebnisse zeitnah generieren zu können werden sowohl spezialisierte Rechensystem als auch Programmierfähigkeiten benötigt: Desktopcomputer oder monolithische Ansätze sind weder in der Lage mit dem Wachstum der verfügbaren biologischen Daten noch mit der Komplexität der Analysetechniken Schritt zu halten. Workflows erlauben diesem Trend durch Parallelisierungsansätzen und verteilten Rechensystemen entgegenzuwirken. Ihre transparenten Abläufe, gegeben durch ihre klar definierten Strukturen, ebenso ihre Wiederholbarkeit, erfüllen die Standards der Reproduzierbarkeit, welche an wissenschaftliche Methoden gestellt werden. Eines der Ziele unserer Arbeit ist es Forschern beim Bedienen von Rechensystemen zu unterstützen, ohne dass Programmierkenntnisse notwendig sind. Dafür wurde eine Sammlung von Tools entwickelt, welche jedes Kommandozeilenprogramm in ein Workflowsystem integrieren kann. Ohne weitere Anpassungen kann unser Programm zwei weit verbreitete Workflowsysteme unterstützen. Unser modularer Entwurf erlaubt zudem Unterstützung für weitere Workflowmaschinen hinzuzufügen. Basierend auf der Bedeutung von frühen und robusten Workflowentwürfen, haben wir außerdem eine wohl etablierte Desktop–basierte Analyseplattform erweitert. Diese enthält über 2.000 Aufgaben, wobei jede als Baustein in einem Workflow fungiert. Die Plattform erlaubt einfache Entwicklung neuer Aufgaben und die Integration externer Kommandozeilenprogramme. In dieser Arbeit wurde ein Plugin zur Konvertierung entwickelt, welches nutzerfreundliche Mechanismen bereitstellt, um Workflows auf verteilten Hochleistungsrechensystemen auszuführen—eine Aufgabe, die sonst technische Kenntnisse erfordert, die gewöhnlich nicht zum Anforderungsprofil eines Lebenswissenschaftlers gehören. Unsere Konverter–Erweiterung generiert quasi identische Versionen desselben Workflows, welche im Anschluss auf leistungsfähigen Berechnungsressourcen ausgeführt werden können. Infolgedessen werden nicht nur die Möglichkeiten von verteilten hochperformanten Rechensystemen sowie die Bequemlichkeit eines für Desktopcomputer entwickelte Workflowsystems ausgenutzt, sondern zusätzlich werden Berechnungsbeschränkungen von Desktopcomputern und die steile Lernkurve, die mit dem Workflowentwurf auf verteilten Systemen verbunden ist, umgangen. Unser Konverter–Plugin hat sofortige Anwendung für Forscher. Wir zeigen dies in drei für die Lebenswissenschaften relevanten Anwendungsbeispielen: Strukturelle Bioinformatik, Immuninformatik, und Metabolomik.Recent decades have witnessed an exponential increase of available biological data due to advances in key technologies for life sciences. Specialized computing resources and scripting skills are now required to deliver results in a timely fashion: desktop computers or monolithic approaches can no longer keep pace with neither the growth of available biological data nor the complexity of analysis techniques. Workflows offer an accessible way to counter against this trend by facilitating parallelization and distribution of computations. Given their structured and repeatable nature, workflows also provide a transparent process to satisfy strict reproducibility standards required by the scientific method. One of the goals of our work is to assist researchers in accessing computing resources without the need for programming or scripting skills. To this effect, we created a toolset able to integrate any command line tool into workflow systems. Out of the box, our toolset supports two widely–used workflow systems, but our modular design allows for seamless additions in order to support further workflow engines. Recognizing the importance of early and robust workflow design, we also extended a well–established, desktop–based analytics platform that contains more than two thousand tasks (each being a building block for a workflow), allows easy development of new tasks and is able to integrate external command line tools. We developed a converter plug–in that offers a user–friendly mechanism to execute workflows on distributed high–performance computing resources—an exercise that would otherwise require technical skills typically not associated with the average life scientist's profile. Our converter extension generates virtually identical versions of the same workflows, which can then be executed on more capable computing resources. That is, not only did we leverage the capacity of distributed high–performance resources and the conveniences of a workflow engine designed for personal computers but we also circumvented computing limitations of personal computers and the steep learning curve associated with creating workflows for distributed environments. Our converter extension has immediate applications for researchers and we showcase our results by means of three use cases relevant for life scientists: structural bioinformatics, immunoinformatics and metabolomics

Performance Test Selection Using Machine Learning and a Study of Binning Effect in Memory Allocators

Performance testing is an essential part of the development life cycle that must be done in a timely fashion. However, checking for performance regressions in software can be time-consuming, especially for complex systems containing multiple lengthy tests cases. The first part of this thesis presents a technique to performance test selection using machine learning. In our approach, we build features using information extracted from the previous software versions to train classifiers that assist developers in deciding whether or not to execute a performance test on a new version. Our results show that the classifiers can be used as a mechanism that aids test selection and consequently avoids unnecessary testing. The second part of this work investigates the binning effect on user-space memory allocators. First, we examine how binning events can be a source of performance outliers in Redis and CPython object allocators. Second, we implement a \textit{Pintool} to detect the occurrence of binning on Python programs. The tool performs dynamic binary instrumentation on the interpreter and outputs information that helps developers in performing code optimizations. Finally, we use our tool to investigate the presence of binning in various widely used Python libraries

Transactional Sapphire: Lessons in High Performance, On-the-fly Garbage Collection

Constructing a high-performance garbage collector is hard. Constructing a fully concurrent 'on-the-fly', compacting collector is much more so. We describe our experience of implementing the Sapphire algorithm as the first on-the-fly, parallel, replication copying, garbage collector for the Jikes RVM Java virtual machine. In part, we explain our innovations such as copying with hardware and software transactions, on-the-fly management of Java's reference types and simple, yet correct, lock-free management of volatile fields in a replicating collector. We fully evaluate, for the first time, and using realistic benchmarks, Sapphire's performance and suitability as a low latency collector. An important contribution of this work is a detailed description of our experience of building an on-the-fly copying collector for a complete JVM with some assurance that it is correct. A key aspect of this is model checking of critical components of this complicated and highly concurrent system