Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

Interprocedural Type Specialization of JavaScript Programs Without Type Analysis

Dynamically typed programming languages such as Python and JavaScript defer type checking to run time. VM implementations can improve performance by eliminating redundant dynamic type checks. However, type inference analyses are often costly and involve tradeoffs between compilation time and resulting precision. This has lead to the creation of increasingly complex multi-tiered VM architectures. Lazy basic block versioning is a simple JIT compilation technique which effectively removes redundant type checks from critical code paths. This novel approach lazily generates type-specialized versions of basic blocks on-the-fly while propagating context-dependent type information. This approach does not require the use of costly program analyses, is not restricted by the precision limitations of traditional type analyses. This paper extends lazy basic block versioning to propagate type information interprocedurally, across function call boundaries. Our implementation in a JavaScript JIT compiler shows that across 26 benchmarks, interprocedural basic block versioning eliminates more type tag tests on average than what is achievable with static type analysis without resorting to code transformations. On average, 94.3% of type tag tests are eliminated, yielding speedups of up to 56%. We also show that our implementation is able to outperform Truffle/JS on several benchmarks, both in terms of execution time and compilation time.Comment: 10 pages, 10 figures, submitted to CGO 201

Interoperability in the OpenDreamKit Project: The Math-in-the-Middle Approach

OpenDreamKit --- "Open Digital Research Environment Toolkit for the Advancement of Mathematics" --- is an H2020 EU Research Infrastructure project that aims at supporting, over the period 2015--2019, the ecosystem of open-source mathematical software systems. From that, OpenDreamKit will deliver a flexible toolkit enabling research groups to set up Virtual Research Environments, customised to meet the varied needs of research projects in pure mathematics and applications. An important step in the OpenDreamKit endeavor is to foster the interoperability between a variety of systems, ranging from computer algebra systems over mathematical databases to front-ends. This is the mission of the integration work package (WP6). We report on experiments and future plans with the \emph{Math-in-the-Middle} approach. This information architecture consists in a central mathematical ontology that documents the domain and fixes a joint vocabulary, combined with specifications of the functionalities of the various systems. Interaction between systems can then be enriched by pivoting off this information architecture.Comment: 15 pages, 7 figure

Slovenian Virtual Gallery on the Internet

The Slovenian Virtual Gallery (SVG) is a World Wide Web based multimedia collection of pictures, text, clickable-maps and video clips presenting Slovenian fine art from the gothic period up to the present days. Part of SVG is a virtual gallery space where pictures hang on the walls while another part is devoted to current exhibitions of selected Slovenian art galleries. The first version of this application was developed in the first half of 1995. It was based on a file system for storing all the data and custom developed software for search, automatic generation of HTML documents, scaling of pictures and remote management of the system. Due to the fast development of Web related tools a new version of SVG was developed in 1997 based on object-oriented relational database server technology. Both implementations are presented and compared in this article with issues related to the transion between the two versions. At the end, we will also discuss some extensions to SVG. We will present the GUI (Graphical User Interface) developed specially for presentation of current exhibitions over the Web which is based on GlobalView panoramic navigation extension to developed Internet Video Server (IVS). And since SVG operates with a lot of image data, we will confront with the problem of Image Content Retrieval

MHEG: An Interchange Format for Interactive Multimedia Presentations

This paper surveys the upcoming MHEG standard, as under development by the Multimedia Hypermedia Experts Group of ISO. It's scope is to define a system-independent encoding of the structure information which can be used for storing, exchanging, and executing of multimedia presentations in final form. We use a running example to describe the building blocks of an MHEG encoded presentation. To contribute our experience using MHEG in a networked multimedia kiosk environment, we present a complete MHEG run-time environment

Differential recruitment of brain networks following route and cartographic map learning of spatial environments.

An extensive neuroimaging literature has helped characterize the brain regions involved in navigating a spatial environment. Far less is known, however, about the brain networks involved when learning a spatial layout from a cartographic map. To compare the two means of acquiring a spatial representation, participants learned spatial environments either by directly navigating them or learning them from an aerial-view map. While undergoing functional magnetic resonance imaging (fMRI), participants then performed two different tasks to assess knowledge of the spatial environment: a scene and orientation dependent perceptual (SOP) pointing task and a judgment of relative direction (JRD) of landmarks pointing task. We found three brain regions showing significant effects of route vs. map learning during the two tasks. Parahippocampal and retrosplenial cortex showed greater activation following route compared to map learning during the JRD but not SOP task while inferior frontal gyrus showed greater activation following map compared to route learning during the SOP but not JRD task. We interpret our results to suggest that parahippocampal and retrosplenial cortex were involved in translating scene and orientation dependent coordinate information acquired during route learning to a landmark-referenced representation while inferior frontal gyrus played a role in converting primarily landmark-referenced coordinates acquired during map learning to a scene and orientation dependent coordinate system. Together, our results provide novel insight into the different brain networks underlying spatial representations formed during navigation vs. cartographic map learning and provide additional constraints on theoretical models of the neural basis of human spatial representation