OGSA-DAI

Posted on September 28, 2010 by Dan Gezelter

OGSA-DAI is an open source framework for executing complex data management scenarios (including data access, update, transformation, integration and delivery) involving distributed databases. It supports relational, XML and file resources. The supported functionality, data resources and presentation layers can all be customised or replaced. OGSA-DAI has been used to build applications in astronomy, medicine, geo-location, social sciences, environment, and transportation amongst others. OGSA-DAI, managed by EPCC, The University of Edinburgh, is 100% Java and is freely available under an Apache 2.0 licence from SourceForge (http://sourceforge.net/projects/ogsa-dai)
Find OGSA-DAI at: http://www.ogsadai.org.uk

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Sysmo db

Posted on September 17, 2010 by Dan Gezelter

SysMO-DB is a web-based platform for finding, sharing and exchanging Data, Models and Processes in Systems Biology. It was designed to support the SysMO Consortium (Systems Biology for Micro-Organisms), but the principles and methods employed are equally applicable to other multi-site Systems Biology projects. The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that: * facilitates and maximises the potential for data exchange between SysMO research groups; * maximises the ‘shelf life’ and utility of data generated by SysMO; * provides an integrated platform for the dissemination of the results of the SysMO projects to the scientific community; and * facilitates standardisation of practices in Systems Biology for the interfacing of modelling and experimentation. We follow several key principles: * exploit what is already available, both within the consortium and outside it, and do not reinvent; * identify the least we can do to make a benefit and do this incrementally.
Find Sysmo db at: http://code.google.com/p/sysmo-db/

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myExperiment

Posted on September 17, 2010 by Dan Gezelter

myExperiment makes it easy to find, use and share scientific workflows and other Research Objects, and to build communities.
Find myExperiment at: http://www.myexperiment.org/

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MethodBox

Posted on September 17, 2010 by Dan Gezelter

Finding the variables you need to support a particular research question can be time consuming. Wading through hundreds of pages of PDF documents, codebooks and metadata and then trying to find the exact column in a huge spreadsheet can be very frustrating. MethodBox gets you to the variables faster and lets you download only the data you need. You can also share your scripts with others to allow them to adopt best practice quicker than before. MethodBox enables you to browse and download datasets, share methods and scripts, find fellow researchers with similar interests and share your knowledge. A deployed version of the methodbox code can be found at http://www.methodbox.org
Find MethodBox at: http://code.google.com/p/methodbox

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Biocatalogue

Posted on September 17, 2010 by Dan Gezelter

The BioCatalogue is a registry of biological Web Services. The BioCatalogue website is freely accessible to the world as it is searchable and indexable to search engines. It provides an open platform for biological Web Services registration, annotation and monitoring. Our Goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Provide a curated catalogue of life science web services * Providers, Expert curators and Users will provide oversight, monitor the catalogue and provide high quality annotations for services. * BioCatalogue as a place where the community can find, contact and meet the experts and maintainers of these services.
Find Biocatalogue at: http://www.biocatalogue.org/

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myExperiment

Posted on September 15, 2010 by Dan Gezelter

The myExperiment Virtual Research Environment enables you and your colleagues to share digital items associated with your research in particular it enables you to share and execute scientific workflows. You can use www.myexperiment.org to find publicly shared workflows. If you want further access, and the ability to upload and share workflows, you will need to sign up.
Find myExperiment at: http://www.myexperiment.org

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BioCatalogue – the Life Sciences Web Service Registry

Posted on September 15, 2010 by Dan Gezelter

The BioCatalogue is a registry of biological Web Services. The BioCatalogue website is freely accessible to the world as it is searchable and indexable to search engines. It provides an open platform for biological Web Services registration, annotation and monitoring.
Find BioCatalogue – the Life Sciences Web Service Registry at: http://www.biocatalogue.org

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Taverna Workbench and Server

Posted on September 15, 2010 by Dan Gezelter

Taverna is an open source domain independent Workflow Management System a suite of tools used to design and execute scientific workflows. Taverna has been created by the myGrid project and funded through the OMII-UK. Taverna has a guaranteed funding till 2014. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool that for a quick execution of workflows from a terminal without the overheads of the GUI. Taverna allows for the automation of experimental methods through the use of a number of different (local or remote) services from a very diverse set of domains biology, chemistry and medicine to music, meteorology and social sciences. Effectively, Taverna allows a scientist with limited computing background and limited technical resources and support to construct highly complex analyses over public and private data and computational resources, all from a standard PC, UNIX box or Apple computer.
Find Taverna Workbench and Server at: http://www.taverna.org.uk

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SciDAVis

Posted on August 17, 2010 by Dan Gezelter

SciDAVis is a free application for Scientific Data Analysis and Visualization. It combines a shallow learning curve and an intuitive, easy-to-use graphical user interface with powerful features such as scriptability and extensibility. SciDAVis runs on GNU/Linux, Windows and MacOS X; possibly also on other platforms like *BSD, although this is untested.
Find SciDAVis at: http://scidavis.sourceforge.net/

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Ascalaph

Posted on July 29, 2010 by Dan Gezelter

Package of molecular graphics and dynamics with an interface to quantum chemistry. GPL
Find Ascalaph at: http://www.biomolecular-modeling.com/Ascalaph/index.html

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Posted in Molecular Dynamics, Theoretical and Computational | Leave a comment