Group items tagged

Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust. This site provides free access to all the data and software from the Ensembl project. Click on a species name to browse the data.

Trends in programming language development and adoption point to Python as the high-level systems integration language of choice. Python leverages a vast developer-base external to the Neuroscience community, and promises leaps in simulation complexity and maintainability to any neural simulator which adopts it. As more and more simulators support Python, model development times can be drastically reduced by promoting code sharing and reuse across simulator communities. As a result, modellers can devote their software development time to innovating new simulation tools such as network topology databases, stimulus programming, analysis and visualisation tools, and simulation accounting, to name a few.

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit.

"The semantic web proposes to inject machine meaningful data into the existing human language oriented web. As part of this effort, on the semantic web, URIs are used to identify entities. But there is currently no standard way to specify what it is that any given URI is to identify, or to whom, or when. Recent work in linguistics offers ideas for a solution to this lack. It focuses on the pragmatics of actual language use among ensembles of people. Also, the World Wide Web provides a set of technologies, in the form of socially constructed web sites, that could be employed to provide a solution. In this paper, I suggest how such socially constructed web sites could be used to address the problem of establishing common ground among a community of machines of the referent of a URI used on the semantic web. The result is a proposal to automate social meaning by creating societies of machines that share knowledge representations identified by URIs."

What tagging does point to convincingly is the social aspect of naming. In a given natural language, many sorts of identifiers, such as common words, are socially centralized. Other sorts of identifiers, such as proper names, are socially decentralized, varying from local context to local context. Black has noticed a correspondence between this socially grounded identification process and the use of socially constructed Web sites.