NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various cell mechanisms. It is difficult to explore these large maps, to comment their content and to maintain them. Though there exist several tools addressing these problems individually, the scientific community still lacks an environment that combines these three capabilities together. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. NaviCell combines three features: (1) efficient map browsing based on Google Maps engine; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting the community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of their interest in the context of signaling pathways and cross-talks between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive fashion due to an imbedded blogging system. NaviCell provides an easy way to explore large-scale maps of molecular interactions, thanks to the Google Maps and WordPress interfaces, already familiar to many users. Semantic zooming used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization meaningful to the user. In addition, NaviCell provides a framework for community-based map curation.Comment: 20 pages, 5 figures, submitte

A HIERACHICAL MODEL FOR MEDICAL REGISTRATIONS

The aim of this paper is to improve solutions for developing and improving medical and pharmaceutical services. We made a SWOT analyze of SIUI in order to build a document management system and create medical registration papers, based on collaborative editing and international medical standard. This model was focused on hierarchical decomposition of PHR and EHR records, using modular solution, which stores all data in XML files. It requires a system that is simple to use and allows users to focus their efforts on the content rather that on the technology used to create it. This approach allows a great flexibility in handling document and user interaction.medical registrations, HME standards, PHR, SIUI, hierarchical decomposition

Challenges in identifying and interpreting organizational modules in morphology

Form is a rich concept that agglutinates information about the proportions and topological arrangement of body parts. Modularity is readily measurable in both features, the variation of proportions (variational modules) and the organization of topology (organizational modules). The study of variational modularity and of organizational modularity faces similar challenges regarding the identification of meaningful modules and the validation of generative processes; however, most studies in morphology focus solely on variational modularity, while organizational modularity is much less understood. A possible cause for this bias is the successful development in the last twenty years of morphometrics, and specially geometric morphometrics, to study patters of variation. This contrasts with the lack of a similar mathematical framework to deal with patterns of organization. Recently, a new mathematical framework has been proposed to study the organization of gross anatomy using tools from Network Theory, so‐called Anatomical Network Analysis (AnNA). In this essay, I explore the potential use of this new framework—and the challenges it faces in identifying and validating biologically meaningful modules in morphological systems—by providing working examples of a complete analysis of modularity of the human skull and upper limb. Finally, I suggest further directions of research that may bridge the gap between variational and organizational modularity studies, and discuss how alternative modeling strategies of morphological systems using networks can benefit from each other

Development of a model-based algorithm for the assessment of the Obsessive-Compulsive Disorder

Questa tesi presentata AAS-PD (Sistema di Assessment Adattivo per i disturbi psicologici), un sistema computerizzato di assessment psicologico adattivo per il Disturbo Ossessivo-Compulsivo (DOC). Tale sistema software è basato su una rappresentazione forma del DOC, chiamata Formal Psychological Assessment (FPA), e rappresenta una novità nel campo della psicologia clinica. AAS-PD prende una struttura di conoscenza (struttura clinica), ed esegue l'assessment facendo inferenze probabilistiche su tale struttura, usando come criterio di stop la misura dell'entropia della struttura. I risultati mostrano che AAS-PD assegna correttamente pattern di risposta a stati clinici, evidenziando inoltre alcuni miglioramenti del modello formale da fare. Sviluppi futuri comportano lo sviluppo di un vero e proprio software capace di supportare il clinico nell'assessment dei principali disturbi psicologici / This thesis presents AAS-PD (Adaptive Assessment System for psychological disorders), a computerized adaptive psychological assessment system for the Obsessive-Compulsive Disorder (OCD). This software system is based on a formal representation of the OCD called Formal Psychological Assessment (FPA), and represents an innovation in the field of clinical psychology. AAS-PD requires a knowledge structure (clinical structure), and performs the assessment by making probabilistic inferences of such a structure, using as stop criterion the measure of entropy of the structure. The results show that PD-AAS properly assigns response patterns to clinical states, and note some improvements of the formal model to do. Future developments will involve the development of a real software that supports the clinician in the assessment of the major psychological disordersope