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This wiki collects information about tools and resources that can help scholars (particularly in the humanities and social sciences) conduct research more efficiently or creatively. Whether you need software to help you manage citations, author a multimedia work, or analyze texts, Digital Research Tools will help you find what you're looking for. We provide a directory of tools organized by research activity, as well as reviews of select tools in which we not only describe the tool's features, but also explore how it might be employed most effectively by researchers.

The Network Workbench Community Wiki is the part of Network Workbench (NWB) project. It provides descriptions for algorithms and datasets that have been integrated in the NWB Tool. It is also a place for users of the NWB Tool, the Cyberinfrastructure Shell, or any other CIShell based program to get, upload, and request algorithms & datasets to be used in the tool. This site is a sounding board to be used by the community to work together and create a tool which will meet their needs and the needs of the scientific community at large.

The present research analyses the 'social visualization' tool Sense.us, a commercial interactive Web application in which U.S. Census data are visualized. Sense.us was developed as a tool for social data exploration and interaction, in which it would be worthwhile to pay attention to the socio-cultural values that have driven the collection and categorization of the underlying U.S. Census datasets. It is argued that closer attention to value driven U.S. Census statistics would greatly enhance the social appeal of Sense.us, and would be a logical next step in the development of online social visualization tools. In order to allow for explicit socio-cultural values of statistics in online visualizations, three strategies are offered: pro-active annotation; more attention to visual aesthetics; and, a tighter integration of user profiles and represented data.

IBM® LanguageWare® is a set of run-time libraries and an easy-to-use Eclipse-based development environment for building custom text analyzers in various languages. Deployable in Apache UIMA, these analyzers can expose the information buried in text to any application. The Eclipse-based tools makes creating analyzers simple and fast, even for non-technical users. The tools make it easy to build dictionaries, ontologies, and rules for identifying key information, relationships and meaning.

The Gibeo Network is a new online service built by Gibeo. It's a rapidly growing community, a web annotation service, a open content-enhancing platform, an amazingly simple and useful tool for browsing and sharing the web. The Internet is still a fundamentally changing environment and this is the latest evolution in powerful online services. Simply browse the web by adding .gibeo.net to the end of any site, and it will be transparently enhanced by adding any community annotations and highlights to the page as well as enable the menu of personal tools available.

Picturing to Learn (PtL) is founded on the following core premises: one From a student's perspective: undergraduate students can clarify their own understanding of scientific concepts and processes by creating drawings that explain these concepts to non-experts. two From a teacher's perspective: drawings can be useful as: * assessment tools, allowing instructors to identify students' scientific understanding and pinpoint their misconceptions * educational tools, to help inform instructors' lecture preparation

The National Center for Biomedical Ontology is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods allowing scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our visionis that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that they are semantically interoperable and useful for improving biomedical science and clinical care. Our resources include the Open Biomedical Ontologies (OBO) library, the Open Biomedical Data (OBD) repositories, and tools for accessing and using this information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects to enable outside research and stimulate technology development in the Center. The Center undertakes outreach and educational activities (Biomedical Informatics Program) to train future researchers to use biomedical ontologies and related tools with the goal of enhancing scientific discovery.

This is the homepage for an ongoing research and development project named PATIKA - Pathway Analysis Tools for Integration and Knowledge Acquisition. Within this project so far, among others, an ontology has been defined; a pathway database (which integrates and interfaces with several public pathway databases) has been constructed; and some software tools have been developed for effective integration, querying, analysis, and manipulation of pathway data.

Lately I've posted on the need for the enterprise to not use email for everything, and the enabling tools that are more appropriate, especially network centric tools that add the dimension of getting things done via informal circles without relying on just your close colleagues and your hierarchy.

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.

"We don't think we have the right kind of tools to help decision makers plan for the future," said Jack Fellows, the vice president for corporate affairs of the University Corporation for Atmospheric Research, a consortium of 71 universities. Comment: this is an opportunity for improved sensemaking tools.

Systems Biology Linker (Sybil) is a platform for the integration of BioPAX and SBML. It is part of the Virtual Cell but also a useful tool for any SBML and BioPAX integration, in other words for any one who wants to use BioPAX with an SBML-capable platform or vice versa. While Sybil can be used as an intelligent conversion tool between SBML and BioPAX, it is primarily intended for building a joint repository for SBML and BioPAX data, where links between SBML elements and BioPAX objects are maintained by SBPAX. Sybil uses SYBREAM for most of the intelligent work involved in building the SBML-SBPAX-BioPAX joint repository.

ESSENCE: E-Science/Sensemaking/Climate Change is an immersive internet experiment, culminating in a face-face conference. We want to build a collective intelligence resource on the climate change debate. This is analogous to Wikipedia, but decidely not enforcing a "neutral point of view". We are going to put through their paces tools tuned for mapping the key issues, options, arguments and evidence on the different dillemmas - and reflect on how effective the current tools are.

MnM is an annotation tool which provides both automated and semi-automated support for annotating web pages with semantic contents. MnM integrates a web browser with an ontology editor and provides open APIs to link to ontology servers and for integrating information extraction tools.

BiOS is a response to inequities in food security, nutrition, health, natural resource management and energy. Our goal is to democratise problem solving to enable diverse solutions through decentralised innovation. Open Source We promote an innovation paradigm that focuses on a distinction between the tools of innovation and the products. We promote licenses that couple rights with responsibilities to foster efficient development, improvement, sharing and use of technology. Open Science We create and share new biological enabling technologies and platforms that can be used to deliver innovations. We develop new licensing and distributive collaboration mechanisms that have resonance with the open source software movement, but are tailored for biological innovation. Open Society We enhance the transparency, accessibility and capability to use all the tools of science, whether patented, open access or public domain.

Annotating is a pervasive element of scholarly practice for both the humanist and the scientist. It is a method by which scholars organize existing knowledge and facilitate the creation and sharing of new knowledge. It is used by individual scholars when reading as an aid to memory, to add commentary, and to classify. It can facilitate shared editing, scholarly collaboration, and pedagogy. Over time annotations can have scholarly value in their own right. Yet scholars remain dissatisfied with the options available for annotating digital resources. Scholars wanting to annotate have to learn different annotation clients for different content repositories, have no easy way to integrate annotations made on different systems or created by colleagues using other tools, and are often limited to simplistic and constrained models of annotation. The importance of annotating as a scholarly practice coupled with the real-world limitations of existing practices and tools supporting annotation of digital content has had a retarding effect on the growth of digital scholarship and the level of digital resource use by scholars.

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.

Patacritism is a project to develop interpretive tools for online humanities.

Faviki is a social bookmarking tool which allows you to tag webpages you want to remember with Wikipedia terms. This means that everybody uses the same names for tags from the world's largest collection of knowledge. Thanks to DBpedia, which extracts structured information from Wikipedia and represents it in a flexible data model, these tags are reference to objects which are categorized automatically, keeping your and your friend's bookmarks and interests well organized.

This is a resource page for CCL's Visual Explorer™ with descriptions of the tool and its multiple uses for creative conversations and dialogue. VE™ supports strategy making, visioning, culture transformation, creative problem solving, coaching, classroom facilitation, teambuilding, visual sensemaking, resolving complex challenges, and leadership development.