SPIKE – a database, visualization and analysis tool of cellular signaling pathways

<p>Abstract</p> <p>Background</p> <p>Biological signaling pathways that govern cellular physiology form an intricate web of tightly regulated interlocking processes. Data on these regulatory networks are accumulating at an unprecedented pace. The assimilation, visualization and interpretation of these data have become a major challenge in biological research, and once met, will greatly boost our ability to understand cell functioning on a systems level.</p> <p>Results</p> <p>To cope with this challenge, we are developing the SPIKE knowledge-base of signaling pathways. SPIKE contains three main software components: 1) A database (DB) of biological signaling pathways. Carefully curated information from the literature and data from large public sources constitute distinct tiers of the DB. 2) A visualization package that allows interactive graphic representations of regulatory interactions stored in the DB and superposition of functional genomic and proteomic data on the maps. 3) An algorithmic inference engine that analyzes the networks for novel functional interplays between network components.</p> <p>SPIKE is designed and implemented as a community tool and therefore provides a user-friendly interface that allows registered users to upload data to SPIKE DB. Our vision is that the DB will be populated by a distributed and highly collaborative effort undertaken by multiple groups in the research community, where each group contributes data in its field of expertise.</p> <p>Conclusion</p> <p>The integrated capabilities of SPIKE make it a powerful platform for the analysis of signaling networks and the integration of knowledge on such networks with <it>omics </it>data. </p

Action synopsis: Pose selection and illustration

Figure 1: Action synopsis analyzes the motion-curve embedded in a low dimensional space (a); super-positioning of carefully selected poses (b) vs. uniform sampling (c). (Images used courtesy of Moshe Mahler and Jessica Hodgins, copyright Carnegie Mellon University.) Illustrating motion in still imagery for the purpose of summary, abstraction and motion description is important for a diverse spectrum of fields, ranging from arts to sciences. In this paper, we introduce a method that produces an action synopsis for presenting motion in still images. The method carefully selects key poses based on an analysis of a skeletal animation sequence, to facilitate expressing complex motions in a single image or a small number of concise views. Our approach is to embed the high-dimensional motion curve in a low-dimensional Euclidean space, where the main characteristics of the skeletal action are kept. The lower complexity of the embedded motion curve allows a simple iterative method which analyzes the curve and locates significant points, associated with the key poses of the original motion. We present methods for illustrating the selected poses in an image as a means to convey the action. We applied our methods to a variety of motions of human actions given either as 3D animation sequences or as video clips, and generated images that depict their synopsis