BioCloud Search EnGene: Surfing Biological Data on the Cloud

The massive production and spread of biomedical data around the web introduces new challenges related to identify computational approaches for providing quality search and browsing of web resources. This papers presents BioCloud Search EnGene (BSE), a cloud application that facilitates searching and integration of the many layers of biological information offered by public large-scale genomic repositories. Grounding on the concept of dataspace, BSE is built on top of a cloud platform that severely curtails issues associated with scalability and performance. Like popular online gene portals, BSE adopts a gene-centric approach: researchers can find their information of interest by means of a simple “Google-like” query interface that accepts standard gene identification as keywords. We present BSE architecture and functionality and discuss how our strategies contribute to successfully tackle big data problems in querying gene-based web resources. BSE is publically available at: http://biocloud-unica.appspot.com/

Science of Digital Libraries(SciDL)

Our purpose is to ensure that people and institutions better manage information through digital libraries (DLs). Thus we address a fundamental human and social need, which is particularly urgent in the modern Information (and Knowledge) Age. Our goal is to significantly advance both the theory and state-of-theart of DLs (and other advanced information systems) - thoroughly validating our approach using highly visible testbeds. Our research objective is to leverage our formal, theory-based approach to the problems of defining, understanding, modeling, building, personalizing, and evaluating DLs. We will construct models and tools based on that theory so organizations and individuals can easily create and maintain fully functional DLs, whose components can interoperate with corresponding components of related DLs. This research should be highly meritorious intellectually. We bring together a team of senior researchers with expertise in information retrieval, human-computer interaction, scenario-based design, personalization, and componentized system development and expect to make important contributions in each of those areas. Of crucial import, however, is that we will integrate our prior research and experience to achieve breakthrough advances in the field of DLs, regarding theory, methodology, systems, and evaluation. We will extend the 5S theory, which has identified five key dimensions or onstructs underlying effective DLs: Streams, Structures, Spaces, Scenarios, and Societies. We will use that theory to describe and develop metamodels, models, and systems, which can be tailored to disciplines and/or groups, as well as personalized. We will disseminate our findings as well as provide toolkits as open source software, encouraging wide use. We will validate our work using testbeds, ensuring broad impact. We will put powerful tools into the hands of digital librarians so they may easily plan and configure tailored systems, to support an extensible set of services, including publishing, discovery, searching, browsing, recommending, and access control, handling diverse types of collections, and varied genres and classes of digital objects. With these tools, end-users will for be able to design personal DLs. Testbeds are crucial to validate scientific theories and will be thoroughly integrated into SciDL research and evaluation. We will focus on two application domains, which together should allow comprehensive validation and increase the significance of SciDL's impact on scholarly communities. One is education (through CITIDEL); the other is libraries (through DLA and OCKHAM). CITIDEL deals with content from publishers (e.g, ACM Digital Library), corporate research efforts e.g., CiteSeer), volunteer initiatives (e.g., DBLP, based on the database and logic rogramming literature), CS departments (e.g., NCSTRL, mostly technical reports), educational initiatives (e.g., Computer Science Teaching Center), and universities (e.g., theses and dissertations). DLA is a unit of the Virginia Tech library that virtually publishes scholarly communication such as faculty-edited journals and rare and unique resources including image collections and finding aids from Special Collections. The OCKHAM initiative, calling for simplicity in the library world, emphasizes a three-part solution: lightweightprotocols, component-based development, and open reference models. It provides a framework to research the deployment of the SciDL approach in libraries. Thus our choice of testbeds also will nsure that our research will have additional benefit to and impact on the fields of computing and library and information science, supporting transformations in how we learn and deal with information

A Data-Driven Approach to Measure Web Site Navigability

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Evaluation of Drum Rhythmspace in a Music Production Environment

In modern computer-based music production, vast musical data libraries are essential. However, their presentation via subpar interfaces can hinder creativity, complicating the selection of ideal sequences. While low-dimensional space solutions have been suggested, their evaluations in real-world music production remain limited. In this study, we focus on Rhythmspace, a two-dimensional platform tailored for the exploration and generation of drum patterns in symbolic MIDI format. Our primary objectives encompass two main aspects: first, the evolution of Rhythmspace into a VST tool specifically designed for music production settings, and second, a thorough evaluation of this tool to ascertain its performance and applicability within the music production scenario. The tool’s development necessitated transitioning the existing Rhythmspace, which operates in Puredata and Python, into a VST compatible with Digital Audio Workstations (DAWs) using the JUCE(C++) framework. Our evaluation encompassed a series of experiments, starting with a composition test where participants crafted drum sequences followed by a listening test, wherein participants ranked the sequences from the initial experiment. The results show that Rhythmspace and similar tools are beneficial, facilitating the exploration and creation of drum patterns in a user-friendly and intuitive manner, and enhancing the creative process for music producers. These tools not only streamline the drum sequence generation but also offer a fresh perspective, often serving as a source of inspiration in the dynamic realm of electronic music production

Combination of web usage, content and structure information for diverse web mining applications in the tourism context and the context of users with disabilities

188 p.This PhD focuses on the application of machine learning techniques for behaviourmodelling in different types of websites. Using data mining techniques two aspects whichare problematic and difficult to solve have been addressed: getting the system todynamically adapt to possible changes of user preferences, and to try to extract theinformation necessary to ensure the adaptation in a transparent manner for the users,without infringing on their privacy. The work in question combines information of differentnature such as usage information, content information and website structure and usesappropriate web mining techniques to extract as much knowledge as possible from thewebsites. The extracted knowledge is used for different purposes such as adaptingwebsites to the users through proposals of interesting links, so that the users can get therelevant information more easily and comfortably; for discovering interests or needs ofusers accessing the website and to inform the service providers about it; or detectingproblems during navigation.Systems have been successfully generated for two completely different fields: thefield of tourism, working with the website of bidasoa turismo (www.bidasoaturismo.com)and, the field of disabled people, working with discapnet website (www.discapnet.com)from ONCE/Tecnosite foundation

Genome visualisation and user studies in biologist-computer interaction

We surveyed a number of genome visualisation tools used in biomedical research. We recognised that none of the tools shows all the relevant data geneticists who look for candidate disease genes would like to see. The biological researchers we collaborate with would like to view integrated data from a variety of sources and be able to see both data overviews and details. In response to this need, we developed a new visualisation tool, VisGenome, which allows the users to add their own data or data downloaded from other sources, such as Ensembl. VisGenome visualises single and comparative representations of the rat, the mouse, and the human chromosomes, and can easily be used for other genomes. In the context of VisGenome development we made the following research contributions. We developed a new algorithm (CartoonPlus) which allows the users to see different kinds of data in cartoon scaling depending on a selected basis. Also, two user studies were conducted: an initial quantitative user study and a mixed paradigm user study. The first study showed that neither Ensembl nor VisGenome fulfil all user requirements and can be regarded as user-friendly, as the users make a significant number of mistakes during data navigation. To help users navigate their data easily, we improved existing visualisation techniques in VisGenome and added a new technique CartoonPlus. To verify if this solution was useful, we conducted a second user study. We saw that the users became more familiar with the tool, and found new ways to use the application on its own and in connection with other tools. They frequently used CartoonPlus, which allowed them to see small regions of their data in a way that was not possible before

The UCSC Genome Browser Database: update 2009

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs

Balancing automation and user control in a home video editing system

The context of this PhD project is the area of multimedia content management, in particular interaction with home videos. Nowadays, more and more home videos are produced, shared and edited. Home videos are captured by amateur users, mainly to document their lives. People frequently edit home videos, to select and keep the best parts of their visual memories and to add to them a touch of personal creativity. However, most users find the current products for video editing timeconsuming and sometimes too technical and difficult. One reason of the large amount of time required for editing is the slow accessibility caused by the temporal dimension of videos: a video needs to be played back in order to be watched or edited. Another reason of the limitation of current video editing tools is that they are modelled too much on professional video editing systems, including technical details like frame-by-frame browsing. This thesis aims at making home video editing more efficient and easier for the non-technical, amateur user. To accomplish this goal, an approach was taken characterized by two main guidelines. We designed a semi-automatic tool, and we adopted a user-centered approach. To gain insights on user behaviours and needs related to home video editing, we designed an Internet-based survey, which was answered by 180 home video users. The results of the survey revealed the facts that video editing is done frequently and is seen as a very time-consuming activity. We also found that users with low experience with PCs often consider video editing programs too complex. Although nearly all commercial editing tools are designed for a PC, many of our respondents said to be interested in doing video editing on a TV. We created a novel concept, Edit While Watching, designed to be user-friendly. It requires only a TV set and a remote control, instead of a PC. The video that the user inputs to the system is automatically analyzed and structured in small video segments. The editing operations happen on the basis of these video segments: the user is not aware anymore of the single video frames. After the input video has been analyzed and structured, a first edited version is automatically prepared. Successively, Edit While Watching allows the user to modify and enrich the automatically edited video while watching it. When the user is satisfied, the video can be saved to a DVD or to another storage medium. We performed two iterations of system implementation and use testing to refine our concept. After the first iteration, we discovered that two requirements were insufficiently addressed: to have an overview of the video and to precisely control which video content to keep or to discard. The second version of EditWhileWatching was designed to address these points. It allows the user to visualize the video at three levels of detail: the different chapters (or scenes) of the video, the shots inside one chapter, and the timeline representation of a single shot. Also, the second version allows the users to edit the video at different levels of automation. For example, the user can choose an event in the video (e.g. a child playing with a toy) and just ask the system to automatically include more content related to it. Alternatively, if the user wants more control, he or she can precisely select which content to add to the video. We evaluated the second version of our tool by inviting nine users to edit their own home videos with it. The users judged Edit While Watching as an easy to use and fast application. However, some of them missed the possibility of enriching the video with transitions, music, text and pictures. Our test showed that the requirements of overview on the video and control in the selection of the edited material are better addressed than in the first version. Moreover, the participants were able to select which video portions to keep or to discard in a time close to the playback time of the video. The second version of Edit While Watching exploits different levels of automation. In some editing functions the user only gives an indication about editing a clip, and the system automatically decides the start and end points of the part of the video to be cut. However, there are also editing functions in which the user has complete control on the start and end points of a cut. We wanted to investigate how to balance automation and user control to optimize the perceived ease of use, the perceived control, the objective editing efficiency and the mental effort. To this aim, we implemented three types of editing functions, each type representing a different balance between automation and user control. To compare these three levels, we invited 25 users to perform pre-defined tasks with the three function types. The results showed that the type of functions with the highest level of automation performed worse than the two other types, according to both subjective and objective measurements. The other two types of functions were equally liked. However, some users clearly preferred the functions that allowed faster editing while others preferred the functions that gave full control and a more complete overview. In conclusion, on the basis of this research some design guidelines can be offered for building an easy and efficient video editing application. Such application should automatically structure the video, eliminate the detail about single frames, support a scalable video overview, implement a rich set of editing functionalities, and should be preferably TV-based

Rice-Map: a new-generation rice genome browser

<p>Abstract</p> <p>Background</p> <p>The concurrent release of rice genome sequences for two subspecies (<it>Oryza sativa </it>L. ssp. <it>japonica </it>and <it>Oryza sativa </it>L. ssp. <it>indica</it>) facilitates rice studies at the whole genome level. Since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively.</p> <p>Description</p> <p>More than one hundred annotation tracks (81 for <it>japonica </it>and 82 for <it>indica</it>) have been compiled and loaded into Rice-Map. These pre-computed annotations cover gene models, transcript evidences, expression profiling, epigenetic modifications, inter-species and intra-species homologies, genetic markers and other genomic features. In addition to these pre-computed tracks, registered users can interactively add comments and research notes to Rice-Map as User-Defined Annotation entries. By smoothly scrolling, dragging and zooming, users can browse various genomic features simultaneously at multiple scales. On-the-fly analysis for selected entries could be performed through dedicated bioinformatic analysis platforms such as WebLab and Galaxy. Furthermore, a BioMart-powered data warehouse "Rice Mart" is offered for advanced users to fetch bulk datasets based on complex criteria.</p> <p>Conclusions</p> <p>Rice-Map delivers abundant up-to-date <it>japonica </it>and <it>indica </it>annotations, providing a valuable resource for both computational and bench biologists. Rice-Map is publicly accessible at <url>http://www.ricemap.org/</url>, with all data available for free downloading.</p