The redesign of the database and the web site
Dear Drosophila Community Colleagues:
As some of you may know, FlyBase has spent a good deal of effort to redesign our database and the web site. Our main goals were to bring the site up to generally accepted web standards and protocols, provide more intuitive entry to the site and afford easier access to the entire set of data held within the database. We at FlyBase are now confident enough in the functionality of the new site that we are replacing the existing site (http://flybase.org/) with release 2006_01. This is not to say that everything is perfect, known bugs are listed at end of this page. We welcome your comments on the site and are particularly interested in getting your feedback on the organization and usability of the report pages, the BLAST and GBrowse tools, the home page and the QueryBuilder search engine. An important benefit of the site is that it contains a major data update, including much new literature curation data and the up-to-date D. melanogaster genome assembly and annotation (Release_5.1). These data will only be accessible through the new web interface, and because of the integrated database that has been developed as part of our redesign; we believe the data are accessible in more powerful ways than had been possible previously.
For those familiar with the present site there is one feature that is utterly new and deserves special comment. This is our new "Matryoshka" format for report pages. The idea behind this design is that users coming to a page will have a condensed view of a given report that should fit on most screens including laptops. If more information is desired each subheading can be opened to reveal the contents, akin to the "doll within a doll" design of the Russian Matryoshka. Cookies are designed to store information on how a user interacts with the pages, so when another report page is opened it will appear with open segments according to the last page that the user had opened during their previous session. Buttons for opening and closing all sections are found at the top of the report pages. The new pages have been designed to have consistent look and feel throughout FlyBase. As noted the pages should fit on a wide variety of screens and the adoption of an elastic layout (not to be confused with the Matryoshka format) means users can enlarge or shrink the content to fit the available space and/or their visual acuity. To view the pages optimally the proportional font of your browser should be set as Times 16pt and the monospace font as Courier 13pt. (These are the standard defaults for browsers). The new site will work with most modern web browsers (Opera 8+, IE6, Firefox 1.5+ and Safari2). However, we chose not to support IE5.2 for Macintosh computers, or IE7, which fails to render some of the pages properly due to a change in page display technology.
Some Comments On The Home Page and Querying / Browsing Tools
HOME PAGE: The top part of the Home Page comprising the banner and the Navigation Bar will appear at the top of each page in the site. However, the text changes as one navigates from page to page. Home in the navigation bar provides a link back to the Home Page, or alternatively a mouse-over/click on the fly within the banner can be used to return to the Home Page. Within the Navigation Bar you will find a series of drop down menus that provide links that will take you to the indicated pages. The Navigation Bar also includes a box called "Jump to Gene" that allows users to move directly to specific Gene Report pages. This navigation aid will accept the full names of genes as well as valid gene symbols and synonyms, however at the moment its function is restricted to D. melanogaster. Below the Navigation Bar you will find a series of five imagelinks and a simple search interface called QuickSearch. The five imagelinks provide quick access to the major FlyBase functions/tools (these can also be found in the pull down menu under Tools). In addition to these access points there is a brief news section that will be used to highlight current issues and will not be allowed to expand beyond a certain size, so items should turn over fairly quickly. Older items will be available from the link under the News item in the navigation bar. Finally we have added a Commentary section that will present, on a rotating basis, items of interest to the fly community.
INTERROGATING FLYBASE: The two general query tools in FlyBase are QuickSearch and QueryBuilder. The advantage of QuickSearch is speed and simplicity; on the other hand, the advantage of QueryBuilder is recovering hit lists without false positives or false negatives. The home page's QuickSearch section provides users with similar search functions to those on the current home page. QuickSearch does not take advantage of the fact that FlyBase data are stored in many separate fields. For more powerful searching options, users should turn to QueryBuilder that can be found as one of the home page imagelinks as well as under the Tools and Help menus. QueryBuilder permits field-specific searching, taking advantage of the structure of the FlyBase database, and also allows queries to be refined and joined. On the QueryBuilder page we have included a tutorial for the use of this powerful search tool. Additionally, once the site has been indexed by Google, you will be able to use the Google search tool that can be found under the Tools and Help menus.
ACCESSING GENOMIC DATA: As is the case for the current version of FlyBase we also offer entry to genomic data and gene structure via BLAST and GBrowse. The BLAST page provides access to all of the Drosophila genomes sequenced to date as well as links from the BLAST hits directly to the relevant point in the GBrowse map of the annotated genomes of the various species. A grey vertical bar on the map indicates the position of the BLAST hit. Because of their interest to many FlyBase users, BLAST also includes other sequenced insect genomes. From within GBrowse one can also find genes or gene regions for D. melanogaster. We also provide the ability to search for orthologues of Dmel genes in the other species genomes. It is also possible to retrieve gene, transcript and protein sequences and to link to information on transposon insertions in genes from the gene reports. Again, note that the 2006_01 release includes new genomic data (D. melanogaster Release_5.1) and much new associated data aligned to the genome (such as new gene prediction sets for the dozen sequenced Drosophila species, P element transgenic insertions, locations of microarray features and RNAi features, etc.). Note that to see many of these features, you will need to select from the many "Track" options within GBrowse.
We sincerely hope that you enjoy using the new FlyBase interface. From time to time you may notice changes to the interface as we continue to improve the site. However, we would like to reassure you that the underlying data for release 2006_01 has been frozen, so you can safely use the release number as the basis for further work. We are depending upon your comments and feedback on the utility of the new site and encourage you to tell us what you find useful and what could be improved using the page:
Enjoy using FlyBase 2006_01 and we look forward to your input.
Your colleagues at FlyBase
For the latest list see the known problems page