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GFBio WP1 - Portal

Environmental and biological research is becoming central to major societal challenges related to the Earth’s ecosystems and climate dynamics. To handle the scale and complexity of the scientific questions being addressed, there is a strong need to integrate knowledge because biological data are currently scattered and difficult to share. The overall goal of the ‘German Federation for the Curation of Biological Data’ (GFBio) is to provide a sustainable, service oriented, national data infrastructure facilitating data sharing and stimulating data intensive science in the fields of biological and environmental research. Services provided by the GFBio will cover the full life cycle of research data from field or real time data acquisition to long term archiving and publication as well as analysis and re-use of these data. The project consists of a large consortium, bringing together national archives, history collections, universities and other research institutions. It is funded by the German Research Foundation (DFG). Our task is to build up a portal, which will be the central fully-customizable platform mediating the communication between data archives, services, and science, respectively users of GFBio via attractive web interfaces. The platform on the one hand will supply a powerful search engine and tools for accessing, analyzing, and visualizing all registered and published data from related archives which are either part of GFBio or external ones (e.g., accessible via international networks). On the other hand it will be the technical base supplying individual support for archiving and publishing data as well as for all data management requests.
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AquaDiva INFRA 1 – semantic technologies for scientific data management and text mining

The Collaborative Research Centre AquaDiva (CRC 1076), funded by the German Research Foundation (DFG), focuses on the important roles of water (Aqua) and biodiversity (Diva) for shaping the structure, properties and functions of the subsurface. This project aims to answer fundamental questions about the Earth’s Critical Zone (CZ) that begins below the highest density of plant roots (~0.3 meters) and extends down into the first aquifers (~100 meters): What biota live there? How do they interact with and reflect their environment? and How do they reflect surface properties? In cooperation with the research group of Prof. Dr. Udo Hahn ( ) we are responsible for the subproject INFRA 1 – semantic technologies for scientific data management and text mining. Taking into account the fact that scientific data today appear in a structured form (e.g. scientific databases, spreadsheets) and in an unstructured form (e.g. scientific publications, reports), our primary goal within INFRA1 is to make structured as well as unstructured data semantically homogeneous so that their diverse origins and heterogeneous formats are no longer obstacles to common use. Therefore, we will provide a commonly shared platform for the storage of and the personalized access to the data produced by the other CRC AquaDiva subprojects (scientific data management). We will combine heterogeneous collections of structured data in a hitherto non-existing homogeneous way (data integration) in order to structure the information contained in unstructured publications and to provide a semantically transparent integration of both structured and (once) unstructured data (data interoperability). Our final goal is to supply researchers with a semantically driven scientific problem solving platform which allows extensive semantic computing over integrated quantitative and qualitative data. This will allow researchers to derive novel facts and new evidence from the underlying data that take into account the data’s uncertainty, credibility, etc.   Please visit the official AquaDiva website for more information:
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iDiv- Biodiversity Informatics Unit (BDU)

The German Centre for Integrative Biodiversity Research (iDiv) funded by the  German Research Foundation (DGF) , is a hub for international biodiversity science whose central mission is to promote theory-driven synthesis and data-driven theory. The concept of iDiv encompasses detection and quantification of biodiversity, understanding its existence and emergence, exploring it’s consequences for ecosystem functions and services, and developing new strategies to safeguard biodiversity. No single institution – not even a whole generation of scientists – possesses the intellectual capacity to exploit the potential of the data it generates and assembles. Without efficient data storage and sharing within iDiv, between iDiv and the outside, and between current and future generations of scientists, much of these valuable and expensive data will be prone to deterioration and eventually lost. At the same time, data is gaining an ever increasing role in scientific progress and, in particular, constitute the raw material for the research groups. In view of this the iDiv's Biodiversity Informatics Unit (BDU) has been established in the  Friedrich Schiller University Jena (FSU) and its main tasks and responsibilities are – Design and develop iDiv’s data management portal using the modular and scalable  BExIS ++ framework as the foundation. Cater to sDiv workshop requirements related to biodiversity data management, integration and storage. Ensure safe, long-term storage and back-ups of the data. In consultation with the stakeholders within iDiv consortium develop biodiversity data-sharing policy, enforcement strategies and mechanisms to provide incentives for data sharing. Develop and implement plans to encourage biodiversity data paper publications for facilitating data discovery and dissemination. Technical and organisational integration of the unit’s work in national and international networks. Teaching biodiversity data management courses at iDiv’s graduate school ( yDiv ). Coordinating the biodiversity informatics unit’s work with that of the bioinformatics and biodiversity synthesis within iDiv
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The CoSRe project of the Friedrich-Schiller-University of Jena investigates how computers can support the entire scientific life cycle. Today in each science computers are needed, not only for the storage of experimental data, but also for generating simulation data and futhermore for the analysis of different kinds of data. Over the internet scientists can work together and can share their results. This collaboration leads to new knowledge and new challenges. To deal with this "flood of information" the complete scientific cycle has to be supported by computers. For more information about CoSRe - please visit the project website
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Biodiversity Exploratories - Core Project 4: Data Management

The Central Data Management Project of the Biodiversity Exploratories Research provides the platform for data storage and information exchange between the different working groups. Most of the services are delivered through its online platform called BExIS (Biodiversity Exploratory Information System). BExIS is the data repository and information exchange platform of the Biodiversity Exploratories project. The Biodiversity Exploratories started in 2006 and is funded by the German Science Foundation (DFG) as a long-term, interdisciplinary open research platform. The goal is to advance biodiversity research in Germany and further the understanding of the relationship between biodiversity of different taxa and levels, the role of land use and management for biodiversity, and the role of biodiversity for ecosystem processes. At present 61 working groups with more than 330 researchers work on 300 research plots of two landuse types in three regions in Germany. The interchange of data among projects is considered crucial for the success of the project. The diversity among the involved projects is mirrored by the diversity of file formats, -syntax and, semantics. BExIS supports file formats common among its researchers and allows data ingestion of flexible syntax, determined in collaboration with all field researchers. BExIS has a web-based interface to a platform for storage and management of all project data in a database. It has a fine grained user and rights management and offers upload, update, and online edit of data. BExIS supports different structured data types and unstructured data. Support of flexible data syntax is ensured by use of XML based metadata schemas and datastructure mapping. BExIS provides further project desired functionalities, e.g. to organize and document field work, for visualising and editing common data on maps, managing publications, and provides the use of statistical analysis also for online merged data sets.
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Mercury is a joint project between the Institute of Computer Science at FSU Jena and the IBM Deutschland Research & Development GmbH in Boeblingen. The main objective of this project is to develop a system that combines the user centric device and service processing. Since the integrated system of utilizing a heterogeneous infrastructure of simple sensors and actuators is complicated for average users, we aim to overcome the complexity of this system integration.
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Adaptive Semantic Assistants in Online Applications

The rapid growth rate of available textual documents underlines a prominent need for novel approaches to overcome the information overload that knowledge workers are faced with. In such situations, new information filtering and analysis techniques are required to provide end users with information related to their context and task at hand. In cooperation with the Semantic Software Lab at Concordia University in Montréal, Canada ( ), we have been developing a new generation of portals that automatically adapt to their users context using novel techniques from the Natural Language Processing (NLP) and Semantic Computing domains. The vision is to extend an existing open source portal such that it can adjust its content according to its users interests and seamlessly provide them with NLP capabilities within their working environment. These NLP capabilities are provided by the Semantic Assistants framework as assistants that collaboratively work with the portal users on analyzing textual content, while the personalization is realized through using the visualization component, developed at the Heinz-Nixdorf Stiftungslehrstuhl of the Friedrich-Schiller-University of Jena (FSU). In addition, we intend to enable portal users to have full control over their user profile, meaning that they can view, modify, or delete their interests. The funding for this project was generously provided by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the German Academic Exchange Service (DAAD).
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Completed Projects

Minerva Portals

Minerva Portals is a joint effort of the Institute of Computer Science at the University of Jena and the IBM Deutschland Entwicklung GmbH in Boeblingen. The overall goal of this project is provide an architectural solution for the next generation Web portals.
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OPOSSum (Online POrtal for Semantic Services ) is a portal dedicated to collaboratively build a public test collection of semantic web services. Despite significant research efforts in the field of semantic web services, real tools and applications using them are still rare. One of the main obstacles for improvements in this direction is the lack of sufficiently large and high-quality collections to test and evaluate tools and algorithms for semantic web services. Such collections cannot be built by any single group but only in a collaborative way by the community as a whole. The purpose of OPOSSum is to equip the community with the means to do so. OPOSSum has been designed to make it easy to collect, share and compare semantic service descriptions across various formalisms.
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01.06.2009 - 30.04.2012
For the security forces and rescue workers engaged in a major operation, no integrative information and communication tool is available up until now. Today such coordination is carried out by personal consultation at the site, via official radio channels or by means of paper-based documentation. In the case of scenarios such as mass casualty incidents, however, personal consultations or the procurement and dispatch of documents are virtually impossible to manage. Processes are inefficient and precious time is lost as a result: factors that, in the worst case, raise the number of victims. In this BMBF-funded project, this problem is tackled from two perspectives: SpeedUp Practice and SpeedUp Technology. SpeedUp Practice focuses on the development of interaction and communication models for the emergency forces and on methods for structuring and describing the situation. This can then serve as a basis for assessing the situation and options and their impacts. At the same time, the results serve as specifications and a benchmark for the future technical implementation, the SpeedUp Technology. SpeedUp Technology as IT solution will be designed to support rescue workers in all required actions through additional information, processed sensor data and flexible communication structures. This will enable faster and higher quality action in a disaster and make it possible to save more lives.
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06.08.2009 - 06.02.2012
The aim of the  "MOPS"  project is the development of solutions for the transfer of formerly static business processes into the world of mobile data devices. The project under the title "Adaptive Planung und sichere Ausführung mobiler Prozesse in dynamischen Szenarien (MOPS)"  (Adaptive Planning and Secure Execution of Mobile Processes in Dynamic Scenarios) is funded by the “Thüringer Aufbaubank” and began on the 06.08.2009. The whole project runs 30 months and has a volume of 2.2 million euros. For this purpose financial resources from European Regional Development Fund (ERDF) are used. The project consortium includes TU Ilmenau, FH Erfurt, Navimatix, NetSys.IT, the Agent Factory and Godyo AG (coordinator).
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Power to the People: Business Users Drive Application Development for Portal Websites

30.11.2007 - 31.12.2010
Portals are the next generation application systems, offering personalized, seamless integration of diverse applications. The vision is that in the future, business users without programming expertise will build their own portal based environments. The Heinz-Nixdorf Endowed Chair at the University of Jena plans to extend its current research activities in these directions. This could be well done on the basis of former work and the group's experience in areas like portal technology (gained within the context of JSR 286) and (semantic) web services.

DIANE - Services in ad hoc Networks

08.05.2002 - 31.12.2010
In the DIANE project, we aim at developing and evaluating concepts that will allow integrated, efficient and effective usage of services offered in open and dynamic environments like ad-hoc networks. To achieve these goals, we propose mechanisms to address a number of questions: How can service search be facilitated in decentralized, dynamic environments? How can services be described, automatically found, and selected? How can services be efficiently executed? How can fairness be ensured in open environments? We propose mechanisms to describe, find and select services as well as methods including overlays and replication mechanisms to efficiently process such queries. Additionally, we develop reputation systems to ensure fair service exchange. This way the whole process of service usage including discovery, matchmaking, negotiation, binding and invocation can be fully automated. In German, our project name, DIANE, is the acronym of Services in Ad-hoc Networks.
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Pluto / JSR 286

29.11.2005 - 12.06.2008
Apache Pluto Project - Java Portlet Specifikation 2 in cooperation with the IBM research labs in Böblingen, Stuttgart
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