Transition to the New BioCyc, EcoCyc, and MetaCyc Web Sites

In February 2009 SRI released Phase II of our redesign of the Web sites for BioCyc, EcoCyc, MetaCyc, and HumanCyc. Our goals in this redesign were to make the sites more pleasant to the eye, to make existing functionality easier to use, to introduce new search capabilities, and to lay the groundwork for later expansions of the Web site capabilities.

Two key resources to assist you in this transition are the Search Help page and the webinar Transitioning to the Updated BioCyc Web Site.

Here are a few key points to keep in mind as you use the new site.

• The new Web site does not work well with Internet Explorer version 6. Please upgrade to version 7.

• Due to a bug in Firefox, the Firefox Web browser is significantly slower in conjunction with our Web site than is other Web browsers such as Safari, Internet Explorer, and Google Chrome. If you are finding Firefox to be too slow we suggest switching to another Web browser. We have reported the bug to the Firefox developers but we do not know when they will fix it.

• The old BioCyc query page, formerly at URL http://biocyc.org/server.html, is obsolete. Its functionality has been replaced by the Search and Tools menus within the new toolbar that appears on all pages.

• Be sure to select the organism you want to search using the new organism selector [explain how]. If you usually query a database other than EcoCyc, you can establish it as your default by creating a BioCyc account and setting the default organism within your preferences [create account].

• Notice that sometimes new items will appear in the toolbar. For example, when you are viewing a pathway page, a Pathway menu will appear with operations specific to pathways.

• Please try out our new search tools, which we hope you will find to be more powerful and easier to use [help for search tools]. They are:
  • Search Menu → Genes/Proteins/RNAs

  • Search Menu → Compounds

  • Search Menu → Reactions

  • Search Menu → Pathways

  • Search Menu → Search Full-text Articles -- (EcoCyc only) Search against an Escherichia coli corpus of 24,000 full-text articles and 6,000 abstracts.

We'd appreciate hearing your feedback or suggestions on the new site [provide feedback].