A software used by the Life Science bioinformatician community distributed according to Open Source rules.
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InterMine is a powerful open source data warehouse system. Using InterMine, you can create databases of biological data accessed by sophisticated web query tools. InterMine can be used to create databases from a single data set or can integrate multiple sources of data. Support is provided for several common biological formats and there is a framework for adding your own data. InterMine includes an attractive, user-friendly web interface that works 'out of the box' and can be easily customised for your specific needs.
InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the sequence ontology and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an XML format to help import custom data.
A web application allows creation of custom queries, includes template queries (web forms to run 'canned' queries) and can upload and operate on lists of data. It is possible to configure/create widgets to analyse lists with graphs and enrichment statistics. An admin user can publish new
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases and searching in large networks. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.
Cytoscape was originally created at the Institute of Systems Biology in Seattle in 2002. Now, it is developed by an international consortium of open source developers. Cytoscape was initially made public in July, 2002 (v0.8); the second release (v0.9) was in November, 2002. and v1.0 was released in March 2003. Version 1.1.1 is the last stable release for the 1.0 series. Version 2.0 was initially released in 2004; Cytoscape 2.5 was released in July 2007. The last version is 2.8.3, released in May 2012.
The Cytoscape core developer team continues to work on this project and in the near future, is going to release next major version, Cytoscape 3.0. It will be a
BioMOBY is a registry of web services used in bioinformatics. It allows interoperability between biological data hosts and analytical services by annotating services with terms taken from standard ontologies.
The BioMoby project began at the Model Organism Bring Your own Database Interface Conference (MOBY-DIC), held in Emma Lake, Saskatchewan on September 21, 2001. It stemmed from a conversation between Mark D Wilkinson and Suzanna Lewis during a Gene Ontology developers meeting at the Carnegie Institute, Stanford, where the functionalities of the Genquire and Apollo genome annotation tools were being discussed and compared. The lack of a simple standard that would allow these tools to interact with the myriad of data-sources required to accurately annotate a genome was a critical need of both systems.
Funding for the BioMOBY project was subsequently adopted by Genome Prairie (2002-2005), Genome Alberta (2005-date), in part through Genome Canada , a not-for-profit institution leading the Canadian X-omic initiatives.
There are two main branches of the BioMOBY project. One is a web-service-based approach, while the other utilizes Semantic Web technologies. This article will refer
BioRuby is a package of Open Source Ruby code, with classes for DNA and protein sequence analysis, alignment, database parsing, tools for structural biology, and other Bioinformatics. BioRuby is released under the GNU GPL version 2 or the Ruby license. BioRuby is one of a number of Bio* projects designed to reduce code duplication.. In 2011 the BioRuby project introduced the biogem software plugin system. Biogems are listed on biogems.info, with 2-3 new plugins being added every month.
The Taverna Workbench is an open source software tool for designing and executing workflows, created by the myGrid project and funded through the OMII-UK. Taverna allows users to integrate many different software components, including SOAP or REST Web services, such as those provided by the National Center for Biotechnology Information, the European Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab, BioMOBY and EMBOSS. The set of available services is not finite and users can import new service descriptions into the Taverna Workbench.
Taverna Workbench provides a desktop authoring environment and enactment engine for scientific workflows. The Taverna workflow enactment engine is also available separately, as a command line tool or as a server.
Taverna is used by users in many domains, such as bioinformatics, cheminformatics, medicine, astronomy, social science and music.
Some of the services for the use in Taverna workflows can be discovered through the BioCatalogue - a public, centralised and curated registry of Life Science Web services. Taverna workflows can also be shared with other people through the myExperiment social web site for scientists. BioCatalogue
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.
RDFScape is a project that brings Semantic Web "features" to the popular Systems Biology software Cytoscape. It allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape. A full list of features is reporte in Features.
Unlike other ontology-based features in Cytoscape, RDFScape doesn't consider ontologies as annotation, but as a knowledge-base that can be interpreted through standard inference processes and through custom inference rules. The result is that ontologies can be interpreted for specific analysis needs. For instance, a pathway ontology such as biopax can be easily abstracted to an interaction network. Or as a causal network, once of notion on causal effect is defined on the ontology.