IMP: a pipeline for reproducible referenceindependent integrated metagenomic and metatranscriptomic analyses

in Genome Biology (2016), 17

Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the ... [more ▼]

Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license). [less ▲]

An Empirical Analysis of Vulnerabilities in OpenSSL and the Linux Kernel

in 2016 Asia-Pacific Software Engineering Conference (APSEC) (2016, December)

Vulnerabilities are one of the main concerns faced by practitioners when working with security critical applications. Unfortunately, developers and security teams, even experienced ones, fail to identify ... [more ▼]

Vulnerabilities are one of the main concerns faced by practitioners when working with security critical applications. Unfortunately, developers and security teams, even experienced ones, fail to identify many of them with severe consequences. Vulnerabilities are hard to discover since they appear in various forms, caused by many different issues and their identification requires an attacker’s mindset. In this paper, we aim at increasing the understanding of vulnerabilities by investigating their characteristics on two major open-source software systems, i.e., the Linux kernel and OpenSSL. In particular, we seek to analyse and build a profile for vulnerable code, which can ultimately help researchers in building automated approaches like vulnerability prediction models. Thus, we examine the location, criticality and category of vulnerable code along with its relation with software metrics. To do so, we collect more than 2,200 vulnerable files accounting for 863 vulnerabilities and compute more than 35 software metrics. Our results indicate that while 9 Common Weakness Enumeration (CWE) types of vulnerabilities are prevalent, only 3 of them are critical in OpenSSL and 2 of them in the Linux kernel. They also indicate that different types of vulnerabilities have different characteristics, i.e., metric profiles, and that vulnerabilities of the same type have different profiles in the two projects we examined. We also found that the file structure of the projects can provide useful information related to the vulnerabilities. Overall, our results demonstrate the need for making project specific approaches that focus on specific types of vulnerabilities. [less ▲]

Numerical methods for fracture/cutting of heterogeneous materials

Presentation (2016, December)

Nuclear Energy for Peaceful Purposes:

Presentation (2016, December)

Assessing Performance of Internet of Things-based Mobile Crowdsensing Systems for Sensing as a Service Applications in Smart Cities

in 8th IEEE International Conference on Cloud Computing Technology and Science (CloudCom) (2016, December)

The Internet of Things (IoT) paradigm makes the Internet more pervasive. IoT devices are objects equipped with computing, storage and sensing capabilities and they are interconnected with communication ... [more ▼]

The Internet of Things (IoT) paradigm makes the Internet more pervasive. IoT devices are objects equipped with computing, storage and sensing capabilities and they are interconnected with communication technologies. Smart cities exploit the most advanced information technologies to improve public services. For being effective, smart cities require a massive amount of data, typically gathered from sensors. The application of the IoT paradigm to smart cities is an excellent solution to build sustainable Information and Communication Technology (ICT) platforms and to produce a large amount of data following Sensing as a Service (S^2aaS) business models. Having citizens involved in the process through mobile crowdsensing (MCS) techniques unleashes potential benefits as MCS augments the capabilities of existing sensing platforms. To this date, it remains an open challenge to quantify the costs the users sustain to contribute data with IoT devices such as the energy from the batteries and the amount of data generated at city-level. In this paper, we analyze existing solutions, we provide guidelines to design a large-scale urban level simulator and we present preliminary results from a prototype. [less ▲]

On the Insecurity of a Method for Providing Secure and Private Fine-Grained Access to Outsourced Data

in Abstract book of 2016 IEEE 8th International Conference on Cloud Computing Technology and Science (CloudCom) (2016, December)

The protection of sensitive data stored in the cloud is paramount. Among the techniques proposed to provide protection, attribute-based access control, which frequently uses ciphertext-policy attribute ... [more ▼]

The protection of sensitive data stored in the cloud is paramount. Among the techniques proposed to provide protection, attribute-based access control, which frequently uses ciphertext-policy attribute-based encryption (CPABE), has received a lot of attention in the last years. Recently, Jahan et al.~(IEEE 40th Conference on Local Computer Networks, 2015) propose a scheme based on CPABE where users have reading and writing access to the outsourced data. We analyze the scheme by Jahan et al.\ and we show that it has several security vulnerabilities. For instance, the cloud server can get information about encrypted messages by using a stored ciphertext and an update of that ciphertext. As another example, users with writing access are able to decrypt all the messages regardless of their attributes. We discuss the security claims made by Jahan et al.\ and point out the reasons why they do not hold. We also explain that existing schemes can already provide the advantages claimed by Jahan et al. [less ▲]

Erinnerungen an die Zwangsrekrutierung im Großherzogtum Luxemburg

in Stroh, Frédéric; Quadflieg, Peter M. (Eds.) L’incorporation de force dans les territoires annexés par le IIIe Reich. Die Zwangsrekrutierung in den vom Dritten Reich annektierten Gebieten 1939-1945 (2016, December)

Tutorial Reproducible Research at the Cloud Era: Overview, Hands-on and Open challenges

Learning material (2016)

The term Reproducible Research (RR) refers to “the idea that the ultimate product of academic research is the paper along with the full computational environment used to produce the results in the paper ... [more ▼]

The term Reproducible Research (RR) refers to “the idea that the ultimate product of academic research is the paper along with the full computational environment used to produce the results in the paper such as the code, data, etc. that can be used to reproduce the results and create new work based on the research.” Source: Wikipedia. The need for reproducibility is increasing dramatically as data analyses become more complex, involving larger datasets and more sophisticated computations. Obviously, the advent of the Cloud Computing paradigm is expected to provide the appropriate means for RR. This tutorial is meant to provide an overview of sensible tools every researcher (in computer science but not only) should be aware of to enable RR in its own work. In particular, and after a general talk presenting RR and the existing associated tools and workflow, this tutorial will propose several practical exercises and hands-on meant to be performed on each attendee’s laptop, to cover the management of sharable Development environment using Vagrant. Resources of this tutorial will be available on Github. [less ▲]

Interpreting Finite Automata for Sequential Data

in Interpretable Machine Learning for Complex Systems: NIPS 2016 workshop proceedings (2016)

Cargo-Kulte. Magie im Zeitalter der Globalisierung.

in Zeitschrift für Interkulturelle Germanistik (2016), 2(2016), 80-89