Serafeim Chatzopoulos

DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Its eighth version is the first database indexing >1 million entries, corresponding to ∼670 000 unique miRNA-target pairs. The interactions are supported by >33 experimental methodologies, applied to ∼600 cell types/tissues under ∼451 experimental conditions. It integrates information on cell-type specific miRNA-gene regulation, while hundreds of thousands of miRNA-binding locations are reported. TarBase is coming of age, with more than a decade of continuous support in the non-coding RNA field. A new module has been implemented that enables the browsing of interactions through different filtering combinations. It permits easy retrieval of positive and negative miRNA targets per species, methodology, cell type and tissue. An incorporated ranking system is utilized for the display of interactions based on the robustness of their supporting methodologies. Statistics, pie-charts and interactive bar-plots depicting the database content are available through a dedicated result page. An intuitive interface is introduced, providing a user-friendly application with flexible options to different queries.

Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0.The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. More than 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in silico framework. These comprehensive data sets enable users to perform analyses based solely on experimentally supported information and to uncover central regulators within sequencing data: miRNAs controlling mRNAs and TFs regulating mRNA or miRNA expression. The server also supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4 species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement.

Due to the rapidly increasing number of scientific articles, finding valuable work for further research has become tedious and time consuming. To alleviate this issue, search engines have used citation-based article impact ranking. However, most engines rely on very simplistic impact measures (usually the citation count) and make the problematic assumption that there is a one-size-fits-all impact measure. To address these problems, we present BIP! Finder, a search engine that facilitates the identification of valuable articles by exploiting two different impact measures, each capturing a different aspect of the article impact. In addition, BIP! Finder provides many useful features (article comparison, intuitive visualisations, article bookmarking mechanism, etc.) making it a powerful addition to the researcher's toolbox.

Digitization is one of the most important issues in cultural heritage preservation. Several digitization projects, active today, will result in a massive amount of digital data representing the cultural heritage. This wealth of cultural information in digital form will be rendered useless in a digital universe without access. In this framework, virtual showrooms, exhibitions and museums that either work offline or via the Web are starting to gain appreciation as very important interfaces for data access to cultural content. In this work we present the technology framework for a dynamic and web-based virtual museum designed to host and present 3D digital models of musical instruments, which are the product of 3D digitization. INTRODUCTION Over the last years, the improvements that have been achieved in the Quality of Services provided through the Web in conjunction with a boost in multimedia technologies opened the floodgates for an increasing amount of Internet-based 3D applications concerning nearly every sector of interest. At the direction of the preservation of cultural heritage, many remarkable efforts regarding the implementation of 3D virtual exhibitions have already been addressed. A number of surveys regarding the issue of the usefulness of such 3D representations have demonstrated that, provided that they are carefully designed, real exhibitions that are accompanied by a respective virtual one have a greater impact on their visitors and encourage more people to visit the physical exhibitions (Di Blas et.al 2005, Thomas and Carey 2005). In all these 3D virtual museum efforts, novelties and standardized methods are being addressed, concerning the 3D museum construction, the digitization and the refinement of its exhibits (Corcoran et.al 2002, Tolva 2005), the creation of fully dynamic rooms, adjusted to the demands of the visitor (Ciabatti et.al 2005) and the implementation of complete applications of augmented reality for educational-oriented purposes (White et.al 2004). Common characteristics of all the above examples are the attractive interfaces, the capabilities of realistic navigation and the option for a detailed inspection of the exhibits. Alternatively, some other applications are designed for special purposes, like ∗ Work supported by the R&D project “POLYMNIA – Integrated System of Music Tools and Music Portal”, co-funded by the General Secretariat for Research and Technology and the European Union. Γ ∆ιeθνές Συνέδριο Μουσeιολογίας και eτήσιο Συνέδριο της eπιτροπής AVICOM, Μυτιλήνη, 5-9 Ιουνίου 2006 G. Pavlidis, D. Tsiafakis, G. Provopoulos, S. Chatzopoulos, F. Arnaoutoglou, C. Chamzas _____________________________________________________________________ _____________________________________________________________________ 2/3 the use of PDAs equipped with intelligent user-adaptive interfaces (Jaen et.al 2005), while others are more concerned about educating the visitor to the proper behavior when visiting an exhibition (Larson and Sincero 2005). Others are focusing in methods of indexing and description of the exhibits in such ways that they accelerate the procedures of retrieving the desirable information (Addis et.al 2005). Taking all these works on the subject into consideration, we have developed a webbased 3D virtual exhibition tool with main advantages in the simplicity of usage and administration, and the limited demands for computer and network resources while preserving a fully dynamic character regarding the provided information as well as the interoperability and cross-platform compliance. The specific implementation is a virtual museum of traditional Greek musical instruments (named MOMI) that have been digitized in three dimensions. An implementation of the museum can be found in http://www.ipet.gr/momi/ THE MUSEUM OF MUSICAL INSTRUMENTS (MOMI) The virtual museum of musical instruments or the MOMI is based on a technological framework developed in our Institute to support dynamic and web-based virtual showrooms able to host and present 3D digital models of musical instruments, which can be the product of 3D digitization. The virtual museum is content-dynamic in a sense that all exhibits are stored in a database along with the accompanied metadata. The dynamic character of the infrastructure is exploited in order to provide an online and easy to use administration interface. The functional requirements imposed at the beginning of this work were: • 3D visualization, navigation and interaction: the interface should be able to provide 3D representations with appropriate interaction capabilities to navigate and access the content • Web-based: the system should be able to work online • Dynamic content: the technological framework should support the visualization of dynamic content that would be stored in a multimedia database • Web-based administration: the system should provide easy, user-friendly and web-enabled administration of the placement of the content within the showrooms The dynamic character of the system is based on the usage of a database that includes all the information for the museum exhibits: • general information/descriptions • specific information and links • multimedia content, and • the file location of the 3D models of the exhibit Due to bandwidth limitations, in order to be able to provide a 3D representation of the exhibits within the museum, the models of the musical instruments had to be scaled down both in size and quality in order to fit the museum geometry and the network transportation capabilities. Thus, the models are provided in two forms: one that represents the preview quality within the virtual showroom and the one that represents the finer quality and actual dimensions of the virtual instruments. Γ ∆ιeθνές Συνέδριο Μουσeιολογίας και eτήσιο Συνέδριο της eπιτροπής AVICOM, Μυτιλήνη, 5-9 Ιουνίου 2006 G. Pavlidis, D. Tsiafakis, G. Provopoulos, S. Chatzopoulos, F. Arnaoutoglou, C. Chamzas _____________________________________________________________________ _____________________________________________________________________ 3/3 Administration of the exhibition is provided through a specifically designed web interface. The options that this interface provides include the management of: • the total number of exhibits that will be presented • the exhibits’ content (3D models, information, links) • Insert/edit/remove content, links, the exhibit itself • the exhibits’ positions in the museum • the position of the pedestals: movement of an exhibit is controlled by the movement of the corresponding pedestal