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The Distributed Annotation System (DAS) defines a communication protocol used to exchange biological annotations. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities.

Triplify provides a building block for the semantification of Web applications. Triplify is a small plugin for Web applications, which converts database content into RDF or JSON feeds and provides a Linked Data interface.

This is a list of repositories and databases for open data.

This habitat of excellence is designed and maintained by scientists for scientists from various disciplines e.g. veterinary and human virology, bioinformatics, epidemiology, immunology and clinical analysis etc. From here on, you will find a series of services, starting with our EpiFlu Database (led by the Swiss Institute of Bioinformatics) providing secure storage and the analysis of genetic, epidemiological and clinical data.

Human Proteinpedia is a community portal for sharing and integration of human protein data. It allows research laboratories to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information in the context of an individual protein. All the public data contributed to Human Proteinpedia can be queried, viewed and downloaded.

Trends in programming language development and adoption point to Python as the high-level systems integration language of choice. Python leverages a vast developer-base external to the Neuroscience community, and promises leaps in simulation complexity and maintainability to any neural simulator which adopts it. As more and more simulators support Python, model development times can be drastically reduced by promoting code sharing and reuse across simulator communities. As a result, modellers can devote their software development time to innovating new simulation tools such as network topology databases, stimulus programming, analysis and visualisation tools, and simulation accounting, to name a few.

Welcome to OmegaWiki. This project is many things to many people. The initial aim is to provide information on all words of all languages. As a consequence of the origin of OmegaWiki, it includes both lexical, terminological and ontological information. Our data is available in a relational database, as a result it is possible to use the data for many purposes.

A new Species-Environment Relations (SER) modeling approach depicts key ecological functions (KEFs) and key environmental correlates (KECs) of terrestrial plant and animal species, as part of a regional assessment of the Interior Columbia Basin Ecosystem Management Project. Assessing KEFs of species is one facet of understanding management effects and ecological integrity of ecosystems. A relational database was developed that ties species' KEFs with their key habitats, KECs, and distribution maps. In this way, potential management activities can be evaluated for how they influence: habitats and environmental correlates; associated plant, invertebrate, and vertebrate species; the array of ecological functions associated with those species; geographic functional ecology; and potential effects on ecosystem productivity, diversity, and sustainability.

Glasshouse by Green Phosphor is a gateway which can take a database query or a spreadsheet and place a 3D representation of it into a virtual world. Users can see data, and drill into it; re-sort it; explore it interactively - all from within a virtual world. Glasshouse produces graphs which are avatars of the data itself.

To manage information quality (IQ) effectively, one needs to know how IQ changes over time, what causes it to change, and whether the changes can be predicted. In this paper we analyze the structure of IQ change in Wikipedia, an open, collaborative general encyclopedia. We found several patterns in Wikipedia's IQ process trajectories and linked them to article types. Drawing on the results of our analysis, we develop a general model of IQ change that can be used for reasoning about IQ dynamics in many different settings, including traditional databases and information repositories.

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit.

This is the official community gathering place and information resource for the OpenDocument Format (ODF) OASIS Standard (ISO/IEC 26300). Suitable for text, spreadsheets, charts, graphs, presentations, and databases, ODF frees documents from their applications-of-origin, enabling them to be exchanged, retrieved, and edited with any OpenDocument-compliant software or tool. This is a community-driven site, and the public is encouraged to contribute content.

(aka YALE) data mining, machine learning, knowledge discovery, business intelligence in Java. 400+ operators: data mining incl. Weka,learning,preprocessing,validation,visualization. GUI,API,XML,analysis,knowledge discovery,databases,business intelligenc

The Lemur Toolkit is a open-source toolkit designed to facilitate research in language modeling and information retrieval. Lemur supports a wide range of industrial and research language applications such as ad-hoc retrieval, site-search, and text mining. The toolkit supports indexing of large-scale text databases, the construction of simple language models for documents, queries, or subcollections, and the implementation of retrieval systems based on language models as well as a variety of other retrieval models. The system is written in the C and C++ languages, and is designed as a research system to run under Unix operating systems, although it can also run under Windows.

Cloudera presents the MapReduce bull case

A system and method for organizing knowledge in such a way that humans can find knowledge, learn from it, and add to it as needed is disclosed. The exemplary system has four components: a knowledge base, a learning model and an associated tutor, a set of user tools, and a backend system. The invention also preferably comprises a set of application programming interfaces (APIs) that allow these components to work together, so that other people can create their own versions of each of the components. In the knowledge web a community of people with knowledge to share put knowledge in the database using the user tools. The knowledge may be in the form of documents or other media, or it may be a descriptor of a book or other physical source. Each piece of knowledge is associated with various types of meta-knowledge about what the knowledge is for, what form it is in, and so on. The information in the knowledge base can be created specifically for the knowledge base, but it can also consist of information converted from other sources, such as scientific documents, books, journals, Web pages, film, video, audio files, and course notes. The initial content of the knowledge web comprises existing curriculum materials, books and journals, and those explanatory pages that are already on the World Wide Web. These existing materials already contain most of the information, examples, problems, illustrations, even lesson plans, that the knowledge web needs. The knowledge base thus represents the core content (online documents or references to online or offline documents); the meta-knowledge that was created at the time of entry; and a number of user annotations and document metadata that accumulate over time about the usefulness of the knowledge, additional user opinions, certifications of its veracity and usefulness, commentary, and connections between various units of knowledge.

The Lemur Toolkit is a open-source toolkit designed to facilitate research in language modeling and information retrieval. Lemur supports a wide range of industrial and research language applications such as ad-hoc retrieval, site-search, and text mining. The toolkit supports indexing of large-scale text databases, the construction of simple language models for documents, queries, or subcollections, and the implementation of retrieval systems based on language models as well as a variety of other retrieval models. The system is written in the C and C++ languages, and is designed as a research system to run under Unix operating systems, although it can also run under Windows.

Sensing importance across a sea of dynamic systems with constantly changing data requires the accumulation and persistence of context. (I am using the term persistence here to mean storing/saving what one has observed and learned - in a database for example.)

Linked Environments for Atmospheric Discovery (LEAD) makes meteorological data, forecast models, and analysis and visualization tools available to anyone who wants to interactively explore the weather as it evolves. The LEAD Portal brings together all the necessary resources at one convenient access point

Welcome to ITIS, the Integrated Taxonomic Information System! Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world