Visualisation Methods of Hierarchical Biological Data: A Survey and Review

The sheer amount of high dimensional biomedical data requires machine learning, and advanced data visualization techniques to make the data understandable for human experts. Most biomedical data today is in arbitrary high dimensional spaces, and is not directly accessible to the human expert for a visual and interactive analysis process. To cope with this challenge, the application of machine learning and knowledge extraction methods is indispensable throughout the entire data analysis workflow. Nevertheless, human experts need to understand and interpret the data and experimental results. Appropriate understanding is typically supported by visualizing the results adequately, which is not a simple task. Consequently, data visualization is one of the most crucial steps in conveying biomedical results. It can and should be considered as a critical part of the analysis pipeline. Still as of today, 2D representations dominate, and human perception is limited to this lower dimension to understand the data. This makes the visualization of the results in an understandable and comprehensive manner a grand challenge. This paper reviews the current state of visualization methods in a biomedical context. It focuses on hierarchical biological data as a source for visualization, and gives a comprehensiv

Teamwork collaboration around CAE models in an industrial context

2015 - 2016Medium and Large Companies must compete every day in a global context. To achieve greater efficiency in their products/processes they are forced to globalize by opening multiple locations in geographically distant places. In this context, people from the same team or different teams must work together regardless of the time zone and where they are located. Therefore, a "virtual" team consists of groups of geographically distant people who can coordinate with the help of new technologies. The tools and methodologies supporting "Computer Supported Cooperative Work" (CSCW) can facilitate collaboration by reducing distance and time related issues. The main goals CSCW aims to achieve within a complex organization are listed below: • Schedule, track, and chart the steps in a project as it is being completed (Project Management) • Share, review, approve or reject project proposals from other workgroup members (Authoring Systems) • Collaborative management of tasks and documents within a knowledge-based business process (Workflow Management) • Collect, organize, manage, and share various forms of information (Knowledge Management) • Collaborative bookmarking engine to tag, organize, share, and search enterprise data (Enterprise Bookmarking) • Collect, organize, manage and share information associated with the delivery of a project (Extranet Systems) • Quickly share company information to members within a company via Internet (Intranet Systems) • Organize social relations of groups (Social Network) • Collaborate and share structured data and information (Online SpreadSheet) This work is based on the main objectives outlined through a specific research experience that verifies compliance and ensures its applicability. The real context consists of virtual team of engineers and the way they cooperate within the automotive industry. The research “iter” can be summarized as follows: (1) the main collaborative and engineering requirements have been identified by referring to a real use case within Fiat Chrysler Automobiles; (2) each requirement has been met by implementing an integrated, modular and extensible architecture; (3) Floasys platform for collecting, centralizing and sharing simulations has been designed, implemented and tested; (4) a tool called ExploraTool has been designed to visually explore a simulation repository within Floasys; (5) the possible extension of the platform has been identified in terms of multidisciplinarity and multisectorality; (6) downstream of the whole process, all the requirements a CSCW intended to meet were verified. The initial phase of the work has focused on collecting collaborative requirements and related needs that emerge when different virtual teams find themselves collaborating to pursue a common result. The collaborative requirements identified to support collaboration between geographically remote teams are: centralizing simulation data, providing annotation and adding metadata to files, providing a search engine for simulations completed by other analysts, providing data versioning and support their sharing. In line with the requirements identified, a collaborative platform prototype (CSCW) called Floasys was developed. Floasys customers are all industries using CAE simulations to design their products, so the automotive, aeronautical and naval industries, etc. Floasys collects simulation data, stores them in open XML format and centralizes them into a shared repository; It also provides additional services on collected data stored in open format, such as the ability to annotate files or search within the repository regardless of the simulator with which they were generated. It is extremely useful to be able to retrieve simulations from other members of the same team or different teams in order to compare the performance of a current project. In order to provide these services, various aspects must be considered: surely the services listed above must be immersed in an existing business environment with existing practices, workflows and software systems. To bring a concrete example, the only centralization of simulation data involves communication with existing simulation software by mitigating the problem of Vendor Lock-In, which is the strong dependence on the simulators themselves. From an architectural point of view, Floasys meets the non-functional extensibility and modularity requirements. This way the system can be tailored to the needs of customers, open to meet future needs and be used in other departments. The modular and extensible Floasys architecture was obtained based on the concept of plug-in. Although the research activity directly concerns the automotive industry, the requirements and the difficulties described are common to other sectors as described in the literature. So many of the considerations made in this work and the solutions adopted can be reused for other types of simulation as well as for data obtained from experiments. Finally, within Floasys, an interactive tool called "ExploraTool" was integrated for viewing, exploring, and querying simulation repositories. Although the idea of this tool was born in the context of simulation repository navigation, it is generic and can be used with any dataset. The tool is based on Eulero-Venn diagrams. The universe is the set of all simulations stored in one or more repositories. Simulation groups are represented by grafted ellipses. Using this tool, analysts can explore the repository through drill-down and roll-up operations to get more or less detail. Going down in the hierarchy, the user filters the items within the dataset and performs a graphical query. In this way, the user explores the repository by finally obtaining two or more simulations to be compared. After the design, implementation and implementation phase, the tool was tested with real users to gain data on its usability. [edited by author]XV n.s

Teamwork collaboration around simulation data in an industrial context

2013 - 2014Nowadays even more small, medium and large enterprises are world-wide and com- pete on a global market. In order to face the new challenges, industries have multiple co-located and geographically dispersed teams that work across time, space, and organ- isational boundaries. A virtual team or a dispersed team is a group of geographically, organisationally and/or time dispersed knowledge workers who coordinate their work using electronic technologies to accomplish a common goal. The advent of Internet and Computer Supported Cooperative Work (CSCW) technologies can reduce the distances between these teams and are used to support the collaboration among them. The topic of this thesis concerns the engineering dispersed teams and their collaboration within enterprises. In this context, the contributions of this thesis are the following: I was able to (1) identify the key collaborative requirements analysing a real use case of two engineering dispersed teams within Fiat Chrysler Automobiles; (2) address each of them with an integrated, extensible and modular architecture; (3) implement a working in- dustrial prototype called Floasys to collect, centralise, search, and share simulations as well as automate repetitive, error-prone and time-consuming tasks like the document generation; (4) design a tool called ExploraTool to visually explore a repository of sim- ulations provided by Floasys, and (5) identify the possible extensions of this work to other contexts (like aeronautic, rail and naval sectors). The rst research aim of this work is the analysis of the key collaborative require- ments within a real industrial use case of geographically dispersed teams. In order to gather these requirements, I worked closely with two geographically separated en- gineering teams in Fiat Chrysler Automobiles (FCA): one team located in Pomigliano D'Arco (Italy) and the other one in Torino (Italy). Both teams use computer numerical Computational Fluid Dynamic (CFD) simulations to design vehicle products simulating physical phenomenons, such as vehicle aerodynamic and its drag coefficient, or the in- ternal ow for the passengers thermal comfort. The applied methodology to collect the collaborative and engineering requirements is based on an extensive literature review, on site directly observations, stakeholders' interviews and an user survey. The identi ed key collaborative requirements as actions to perform to improve the collaboration among dispersed teams are: centralise simulation data, provide metadata over simulation data, provide search facility, simulation data versioning, and data sharing... [edited by Author]XIII n.s