MOTIVATION: Studying the genetic makeup of viruses and phages through genome analysis is crucial for comprehending their function in causing diseases, progressing medicine, tracing their evolutionary history, monitoring the environment, and creating innovative biotechnologies. However, accessing the necessary data can be challenging due to a lack of dedicated comparative genomic tools and viral and phage databases, which are often outdated. Moreover, many wet bench experimentalists may not have the computational proficiency required to manipulate large amounts of genomic data. RESULTS: We have developed VAPEX (Virus And Phage EXplorer), a web server which is supported by a database and features a user-friendly web interface. This tool enables users to easily perform various genomic analysis queries on all natural viruses and phages that have been fully sequenced and are listed in the NCBI compendium. VAPEX therefore excels in producing visual depictions of fully resolved synteny maps, which is one of its key strengths. VAPEX has the ability to exhibit a vast array of orthologous gene classes simultaneously through the use of symbolic representation. Additionally, VAPEX can fully analyze user-submitted viral and phage genomes, including those that have not yet been annotated. AVAILABILITY AND IMPLEMENTATION: VAPEX can be accessed from all current web browsers such as Chrome, Firefox, Edge, Safari, and Opera. VAPEX is freely accessible at https://archaea.i2bc.paris-saclay.fr/vapex/.

MOTIVATION: The retrieval of a single gene sequence and context from completely sequenced bacterial and archaeal genomes constitutes an intimidating task for the wet bench biologist. Existing web-based genome browsers are either too complex for routine use or only provide a subset of the available prokaryotic genomes. RESULTS: We have developed BAGET 2.0 (Bacterial and Archaeal Gene Exploration Tool), an updated web service granting access in just three mouse clicks to the sequence and synteny of any gene from completely sequenced bacteria and archaea. User-provided annotated genomes can be processed as well. BAGET 2.0 relies on a local database updated on a daily basis. AVAILABILITY AND IMPLEMENTATION: BAGET 2.0 befits all current browsers such as Chrome, Firefox, Edge, Opera and Safari. Internet Explorer 11 is supported. BAGET 2.0 is freely accessible at https://archaea.i2bc.paris-saclay.fr/baget/.

We introduce a new method that efficiently computes a set of viewpoints and trajectories for high-quality 3D reconstructions in outdoor environments. Our goal is to automatically explore an unknown area and obtain a complete 3D scan of a region of interest (e.g., a large building). Images from a commodity RGB camera, mounted on an autonomously navigated quadcopter, are fed into a multi-view stereo reconstruction pipeline that produces high-quality results but is computationally expensive. In this setting, the scanning result is constrained by the restricted flight time of quadcopters. To this end, we introduce a novel optimization strategy that respects these constraints by maximizing the information gain from sparsely sampled viewpoints while limiting the total travel distance of the quadcopter. At the core of our method lies a hierarchical volumetric representation that allows the algorithm to distinguish between unknown, free, and occupied space. Furthermore, our information gain-based formulation leverages this representation to handle occlusions in an efficient manner. In addition to the surface geometry, we utilize free-space information to avoid obstacles and determine collision-free flight paths. Our tool can be used to specify the region of interest and to plan trajectories. We demonstrate our method by obtaining a number of compelling 3D reconstructions, and we provide a thorough quantitative evaluation showing improvement over previous state-of-the-art and regular patterns.

We present a novel optimization-based algorithm for the design and fabrication of customized, deformable input devices, capable of continuously sensing their deformation. We propose to embed piezoresistive sensing elements into flexible 3D printed objects. These sensing elements are then utilized to recover rich and natural user interactions at runtime. Designing such objects is a challenging and hard problem if attempted manually for all but the simplest geometries and deformations. Our method simultaneously optimizes the internal routing of the sensing elements and computes a mapping from low-level sensor readings to user-specified outputs in order to minimize reconstruction error. We demonstrate the power and flexibility of the approach by designing and fabricating a set of flexible input devices. Our results indicate that the optimization-based design greatly outperforms manual routings in terms of reconstruction accuracy and thus interaction fidelity.

In this paper we propose a computational design tool that allows end-users to create advanced quadrotor trajectories with a variety of application scenarios in mind. Our algorithm allows novice users to create quadrotor based use-cases without requiring deep knowledge in either quadrotor control or the underlying constraints of the target domain. To achieve this goal we propose an optimization-based method that generates feasible trajectories which can be flown in the real world. Furthermore, the method incorporates high-level human objectives into the planning of flight trajectories. An easy to use 3D design tool allows for quick specification and editing of trajectories as well as for intuitive exploration of the resulting solution space. We demonstrate the utility of our approach in several real-world application scenarios, including aerial-videography, robotic light-painting and drone racing.

We present a tracking system based on ultra-wideband (UWB) radio tranceivers mounted on a robot and a target. In comparison to typical UWB localization systems with fixed UWB tranceivers in the environment we only require instrumentation of the target with a single UWB tranceiver. Our system works in GPS-denied environments and does not suffer from long-term drift and limited fields of view. This paper reports the localization algorithm and implementation details. Additionally, we demonstrate a quantitative evaluation of the accuracy (10cm average position error for a square with side-length of 4m) and application scenarios with a quadrotor flying in close proximity to a person and handling occlusion of the target. Finally, we release our implementation as open-source software.