MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

<p>Abstract</p> <p>Background</p> <p>Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server.</p> <p>Results</p> <p>MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only.</p> <p>Conclusions</p> <p>An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at <url>http://www.metnetonline.org/api</url>.</p

A survey of visualization tools for biological network analysis

The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology. Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data. There are a wide variety of graph representations available, which most often map the data on 2D graphs to visualize biological interactions. These methods are applicable to a wide range of problems, nevertheless many of them reach a limit in terms of user friendliness when thousands of nodes and connections have to be analyzed and visualized. In this study we are reviewing visualization tools that are currently available for visualization of biological networks mainly invented in the latest past years. We comment on the functionality, the limitations and the specific strengths of these tools, and how these tools could be further developed in the direction of data integration and information sharing

The Ego Conquiro as the Paradigm of Modern Imperialism and its Violence Against the Struggle for Epistemic Justice

This article begins with a discussion of the implications of Enrique Dussel’s “I conquer, therefore I am” (ego conquiro) thesis as the paradigm of modern imperialism. According to Dussel, underlying the “myth of modernity” (mito de la modernidad) is an epistemological structure of a substantive ego that naturalizes European colonial expansion. Dussel admits that the “I conquer, therefore, I am” thesis began earlier than Descartes’s account of the cogito, which was theorized after the Spanish colonization of the Americas, but the substantive “I” that constitutes the ego conquiro nonetheless represents a theory of knowledge that served and continues to serve the political domination of bodies that have been historically victimized. Couched within the epistemic structure of Descartes’s cogito is a duality between soul and matter, where the former represents an immortal substance detached from the body, taken to be the recipe for rational truth, while the latter is reduced to a quantifiable object occupying a “zero-point” geometrical space. But the cogito became the epistemological standpoint that allowed for the justification of the many hidden forms of domination around the world, because it masks the social, economic, and geopolitical contexts and their history to the modern subject. This article will investigate the ego conquiro thesis and its link to epistemic violence, namely, epistemic racism and epistemicide, and will argue as a concluding point for a method of resistance that foregrounds philosophical pluralism to disrupt the internalization of the epistemologies of the Global North as the common-sense position(s) of today

CamiTK: a Modular Framework Integrating Visualization, Image Processing and Biomechanical Modeling

International audienceIn this paper, we present CamiTK, a specific modular framework that helps researchers and clinicians to collaborate in order to prototype Computer Assisted Medical Intervention (CAMI) applications by using the best knowledge and know-how during all the required steps. CamiTK is an open-source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations. This paper first gives an overview of CamiTK core architecture and how it can be extended to fit particular scientific needs. The MML extension is then presented: it is an environment for comparing and evaluating soft-tissue simulation models and algorithms. Specifically designed as a soft-tissue simulation benchmark and a reference database for validation, it can compare models and algorithms built from different modeling techniques or biomechanical software. This article demonstrates the use of CamiTK on a textbook but complete example, where the medical image and MML extensions are collaborating in order to process and analyze MR brain images, reconstruct a patient-specific mesh of the brain, and simulate a basic brain-shift with different biomechanical models from ANSYS, SOFA and ArtiSynth