Abstract: Methods, systems and computer readable media for network-based identification of significant molecules, for which at least one biological network is provided to include significant molecules to be identified. A node in the network is identified. A member-specific sub-network containing nodes connected to the identified node is identified for L levels of nearest neighbors, wherein L is a positive integer, and a connectivity score is calculated for the molecule represented by the identified node based on significance scores of each node contained in the member-specific sub-network. These steps are repeated for other nodes in the network.

Abstract: Visualization techniques tools and systems for displaying network diagrams to convey both focus and context to a user of the display. Network diagrams may be displayed to emulate a three dimensional presentation. Network diagrams may be presented with items of interest in sharp definition and the remainder of a diagram or diagrams being blurred or having relative degrees of sharpness/blurriness.

Abstract: System, tools and methods for extracting the contents from a graphical image, such as the representation of a biological process, and converting the contents into a standardized, machine readable format. The standard format can be used to create editable graphical representations of images, such as biological models.

Abstract: Systems, methods and computer readable media for performing a domain-specific metasearch, and obtaining search results therefrom. A metasearch engine capable of accessing generic, web-based search engines and domain-relevant search engines is provided to receive one or more queries inputted by a user, and to search for documents on at least one the generic, web-based search engines and domain-relevant search engines which are relevant to the queries. Raw data search results are fetched in the form of text documents. Relevant data including semantic information are extracted from the raw data search results, and converted to a local format. The relevant data having been converted to the local format may be visualized as a network visualization. Additionally or alternatively, the raw data search results may be ranked and/or filtered based on the linking of the relevant data.

Abstract: Systems, methods and recordable media for facilitating user-guidance of computational analysis and knowledge extraction tools for use with biological data for disambiguation and determination of causation in representations of the data. Systems, methods, tools and computer readable media for user-guided expansion of biological networks and manipulations of the same. Tools for qualitative simulation of network models, for identifying interactions between multiple networks and form maintaining knowledge about multiple alternative biological networks. Combinations of portions of networks may be constructed to provide optimal networks. Networks may be evaluated against experimental data and networks of interest may be identified based on experimental data.

Abstract: Systems, tools, methods and recordable media for providing a visual grammar to be associated with a local format for creating interactive biological diagrams. Stencils are provided to represent higher level representations of associated entities and interactions are descriptively and unambiguously displayed. Additionally, information may be overlaid and compared with existing biological diagrams.

Abstract: Systems, methods and recordable media for interactively importing, creating, and manipulating biological diagrams. Such diagrams may be used for linking and navigating to other sources of biological information.

Abstract: Systems, tools, methods and recordable media for text mining textual documents and extracting and associating entities and interactions mined with other data formats, such as diagrammatic displays and experimental data, using a local format. Additionally, information may be overlaid and compared with existing biological diagrams.

Abstract: Methods, systems and computer readable media for visualizing multiple data values adjacent graphical representations of entities in a diagram representing biological relationships between the entities. A diagram of interconnected entities representing biological relationships between the entities is displayed. A data set having rows of data values, each row containing values representing a single entity is provided, wherein at least some of the entities are represented on the diagram. At least one row of data values from the dataset is overlaid on the displayed diagram such that the row of data values appears adjacent the entity on the diagram that matches the entity in the data set that the row of data characterizes. The display of the row of data values is scaled so that components of the display are dimensionally proportional to numerical values of the data values taken from the data set.

Abstract: Visualization techniques tools and systems for displaying network diagrams to convey both focus and context to a user of the display. Network diagrams may be displayed to emulate a three dimensional presentation. Network diagrams may be presented with items of interest in sharp definition and the remainder of a diagram or diagrams being blurred or having relative degrees of sharpness/blurriness.

Abstract: A system, tools, software and methods for importing data from multiple sources and of multiple formats and categories, extracting relevant data from the same, and representing the relevant data in a local format that can be used for direct comparisons of data across diverse data types or categories and for overlaying one or more data types over another. Reverse mapping of relevant data into a different data type or category can also be performed.

Abstract: System, tools and methods for extracting the contents from a graphical image, such as the representation of a biological process, and converting the contents into a standardized, machine readable format. The standard format can be used to create editable graphical representations of images, such as biological models.

Abstract: An extensible, generalized architecture, an application programming interface, software and methods for building data overlays, as well as software, a system, methods and interface for building specific data overlays, with particular relevance to biological data.

Abstract: An interactive software system provides a framework, methodology, and tools for organizing information during speculative phases of research using a narrative structure. The system provides interactive tools and techniques for organizing, sharing, and using diverse information at multiple levels of abstraction through coordinated multiple-view visualization in the process of hypothesis formation. Annotation and collaboration are supported.

Abstract: Narrative structure and a free-form database to support biological storytelling. An interactive software system provides a framework, methodology, and tools for organizing information during speculative phases of research using a narrative structure. The system provides interactive tools and techniques for organizing, sharing, and using diverse information at multiple levels of abstraction through coordinated multiple-view visualization in the process of hypothesis formation. Items are created or imported through an item manager and can be grouped into collections using a collection manager. Items and collections are combined in a narrative structure through pathway and story editors. Annotation and collaboration are supported.