Michael Travers

A Melanoma Molecular Disease Model

While advanced melanoma remains one of the most challenging cancers, recent developments in our understanding of the molecular drivers of this disease have uncovered exciting opportunities to guide personalized therapeutic decisions. Genetic analyses of melanoma have uncovered several key molecular pathways that are involved in disease onset and progression, as well as prognosis. These advances now make it possible to create a “Molecular Disease Model” (MDM) for melanoma that classifies individual tumors into molecular subtypes (in contrast to traditional histological subtypes), with proposed treatment guidelines for each subtype including specific assays, drugs, and clinical trials. This paper describes such a Melanoma Molecular Disease Model reflecting the latest scientific, clinical, and technological advances.

A visual representation for knowledge structures

Knowledge-based systems often represent their knowledge as a network of interrelated units. Such networks are commonly presented to the user as a diagram of nodes connected by lines. These diagrams have provided a powerful visual metaphor for knowledge representation. However, their complexity can easily become unmanageable as the knowledge base (KB) grows. This paper describes an alternate visual representation for navigating knowledge structures, based on a virtual museum metaphor. This representation uses nested boxes rather than linked nodes to represent relations. The intricate structure of the knowledge base is conveyed by a combination of position, size, color, and font cues, MUE (Museum Unit Editor) was implemented using this representation to provide a graphic front end for the Cyc knowledge base.

BioLingua: a programmable knowledge environment for biologists

UNLABELLED BioLingua is an interactive, web-based programming environment that enables biologists to analyze biological systems by combining knowledge and data through direct end-user programming. BioLingua embeds a mature symbolic programming language in a frame-based knowledge environment, integrating genomic and pathway knowledge about a class of similar organisms. The BioLingua language provides interfaces to numerous state-of-the-art bioinformatic tools, making these available as an integrated package through the novel use of web-based programmability and an integrated Wiki-based community code and data store. The pilot instantiation of BioLingua, which has been developed in collaboration with several cyanobacteriologists, integrates knowledge about a subset of cyanobacteria with the Gene Ontology, KEGG and BioCyc knowledge bases. We introduce the BioLingua concept, architecture and language, and give several examples of its use in complex analyses. AVAILABILITY Extensive documentation is available online at http://nostoc.stanford.edu/Docs/index.html CONTACT JShrager@Stanford.edu

Recursive interfaces for reactive objects

LiveWorld is a graphical environment designed to support research into programming with active objects. It offers novice users a world of manipulable objects, with graphical objects and elements of the programs that make them move integrated into a single framework. LiveWorld is designed to support a style of programming based on rule-like agents that allow objects to be responsive to their environment. In order to make this style of programming accessible to novices, computational objects such as behavioral rules need to be just as concrete and accessible as the graphic objects. LiveWorld fills this need by using a novel object system, Framer, in which the usual structures of an objectoriented system (classes, objects, and slots) are replaced with a single one, the frame, that has a simple and intuitive graphic representation. This unification enables the construction of an interface that achieves elegance, simplicity and power. Allowing graphic objects and internal computational objects to be manipulated through an integrated interface can provide a conceptual scaffolding for novices to enter into programming.

LiveWorld: a construction kit for animate systems

LiveWorld is a graphical environment designed to support research into programming with active objects. It offers novice users a world of manipulable objects, with graphical objects and elements of the programs that make them move integrated into a single framework. LiveWorld is designed to support a style of programming based on rule-like agents that allow objects to be responsive to their environment. In order to make this style of programming accessible to novices, computational objects such as behavioral rules need to be just as concrete and accessible as the graphic objects. LiveWorld fills this need by using a novel object system, Framer, in which the usual structures of an objectoriented system (classes, objects, and slots) are replaced with a single one, the@ne, that has a simple and intuitive graphic qm3sentation. This unifkation enables the construction of an interface that achieves elegance, simplicity and power. Allowing graphic objects and internal computational objects to be manipulated through an integrated interface can provide a conceptual scaffolding for novices to enler into programming.

Programming with characters

Programs are hard to build, and even harder to understand after they are built. We lack intuitive interfaces for visualizing and manipulating many parts of programs and the ways in which these parts interact. Constraint systems have addressed these problems. We generalize some of the notions inherent in constraint systems to agent-based systems, and explore the use of animated characters as interface representations of agents. In particular, conflict detection and resolution is dramatized by the use of characters and their emotions. The history of their interactions is presented as a narrative using video and storyboard techniques. Building programs out of agents and enabling users to manipulate program parts by interacting with simple animated characters can aid relatively unskilled users in understanding and modifying complex systems.