User Information

The original Biology Workbench was the first such utility, but there are now many interesting workbench ventures. While we are partial to ours, each of the others offers an alternative vision of what a workbench might be. Here are some examples. If yours (or your favorite) isn't here, send the link along to us here and we'll add it to the list.

  • BioExtract is an integrated data-and-tools workbench, with a bent towards plant biology. It makes use of a combination of web services, local data warehousing, and direct SQL to provide users with access to a variety of data resources; it allows users to add tools locally and via web services.
  • The Biology Student Workbench. This is the original Biology Workbench, but with an interface designed to make entry easier for students. There are also many additional features for teachers, such as opportunities to access and share curricula.
  • The Mobyle project has now replaced the Pasteur Institute PISE server. This group now offers data storage and user accounts.
  • BioExtract is a community focused, highly configurable workbench environment that relies on web services for analysis, and gives the user a lot of freedom in configuring their work environment.
  • The Galaxy project is designed for both Developers and Biologists, it provides EMBOSS and Hyphy, as well as other tools, and permits the contribution of XML interfaces by outside developers.
  • MorphoBank is a collaboration environment for the extracting information from images that can be used in the inference of phylogeny. This site makes use of the Adobe FLEX platform to enable lightweight analysis of images.
  • Anabench. This is a Workbench that provides access to a number of tools using CORBA and Java.
  • BIRCH integrates systematics tools in a Linux environment that can be accessed remotely (via Virtual Network Computing); it is used locally or remotely by individuals with accounts on the host Unix machine.
  • Geneious is a proprietary program for download by individual users; users install, maintain, and administrate the hardware resources required. Geneious has free and fee based versions.
  • The RENCI Bioportal is an implementation of the PISE software in a Java environment for Grid Computing at the University of North Carolina.
  • MiGenAS (Microbial Genome Analysis System) This is a nicely architected research tool developed at the Max Planck to help with genome annotation on a large scale. It provides some interesting workflow possibilities. It is built on JBoss/EJB, and accesses tools through Web Services and CORBA.
  • The ARB is a community-driven effort that integrates multiple tools for phylogenetic analysis and local data storage that can be downloaded and installed on user resources.
  • wEMBOSS A portal to the EMBOSS suite provided by Martin Sarachu of the Argentinian EMBnet Node and Marc Colet from the Belgian EMBnet node. The architecture provides a plone front end, and provides user workspaces, ability to save work, keyword search.
  • GenePattern is an downloadable software package that combines scientific workflow with more than 90 genomic analysis tools.
  • The Systems Biology Workbench A downloadable framework (Linux and OSX) that permits interoperability between several systems biology tools.