Group items tagged

If required, entire databases can be downloaded from our FTP site in a variety of formats, from flat files to MySQL dumps. Please be aware that these files can run to many gigabytes of data. To facilitate storage and download all databases are GNU Zip (gzip, *.gz) compressed. Please note: Ensembl supports downloading of many correlation tables via the highly customisable BioMart data mining tool. You may find exploring this web-based data mining tool easier than extracting information from our database dumps.

This package of tools encompasses many of the common pieces of software required for the analysis of short read sequences produced by the Second Generation DNA sequencing machines. (eg. Illumina/Solexa sequencers, ABI SOLiD and 454). The focus of this project is on post-alignment analysis, thus the input for this process should be the files produced by sequence aligners such as MAQ, Eland or Exonerate. The output should be provided in several formats, including BED and WIG files which are readable by the UCSC Genome Browser.

PircBot is a Java framework for writing IRC bots quickly and easily. Its features include an event-driven architecture to handle common IRC events, flood protection, DCC resuming support, ident support, and more. Its comprehensive logfile format is suitable for use with pisg to generate channel statistics. Full documentation is included, and this page contains a 5-minute step-by-step guide to making your first IRC bot. PircBot allows you to perform a variety of fun tasks on IRC, but it is also used for more serious applications by the US Navy, the US Air Force, the CIA (unconfirmed), several national defence agencies, and inside the Azureus bittorrent client. But don't let that put you off - it's still easy to use!

BioMart is a query-oriented data management system developed jointly by the Ontario Institute for Cancer Research (OiCR) and the European Bioinformatics Institute (EBI). The system can be used with any type of data and is particularly suited for providing 'data mining' like searches of complex descriptive data. BioMart comes with an 'out of the box' website that can be installed, configured and customised according to user requirements. Further access is provided by graphical and text based applications or programmatically using web services or API written in Perl and Java. BioMart has built-in support for query optimisation and data federation and in addition can be configured to work as a DAS 1.5 Annotation server. The process of converting a data source into BioMart format is fully automated by the tools included in the package. Currently supported RDBMS platforms are MySQL, Oracle and Postgres. BioMart is completely Open Source, licensed under the LGPL, and freely available to anyone without restrictions.

SWAN (Semantic Web Applications in Neuromedicine) is a Web-based collaborative program that aims to organize and annotate scientific knowledge about Alzheimer disease (AD) and other neurodegenerative disorders. Its goal is to facilitate the formation, development and testing of hypotheses about the disease. The ultimate goal of this project is to create tools and resources to manage the evolving universe of data and information about AD in such a way that researchers can easily comprehend their larger context ("what hypothesis does this support or contradict?"), compare and contrast hypotheses ("where do these two hypotheses agree and disagree?"), identify unanswered questions and synthesize concepts and data into ever more comprehensive and useful hypotheses and treatment targets for this disease. The SWAN project is designed to allow the community of AD researchers to author, curate and connect a diversity of data and ideas about AD via secure personal and public SWAN workspaces, using the emerging Semantic Web paradigm for deep interconnection of data, information and knowledge. We are initially focusing on developing a fully public Web resource deployed as part of the Alzheimer Research Forum web site (www.alzforum.org). After the public resource has been launched, we will also develop secure personal workspaces (MySWAN) and semi-private lab workspaces (LabSWAN). An essential component of this project is development of an initial, core knowledge base within SWAN, which will provide immediate value to researchers at the time of deployment. This is a critically important part of our strategy to ensure that the SWAN system gains wide adoption and active participation by the AD research community. As part of our development strategy, we are also recruiting a "beta test" community of AD researchers to enter their own hypotheses, add commentaries and citations, and provide feedback on the technology and content. SWAN is being developed by a collaborative team from

Welcome to Manuscriptedit.com, your online partner for English language editing, proofreading, medical writing, formatting, design & development and publication support services. We offer a comprehensive manuscript editing service before its submission for publication as well as after acceptance by the peer review process.