November 17, 1995
3-D structures are available. Entrez now links to a structure database, and where a structure exists for one of the enzymes in the UM-BBD, we have changed the Medline reference to make viewing that structure possible. For example, from the protocatechuate 2,3-dioxygenase reaction page, follow the "Medline reference with structure" link. At the Entrez document report page, select "Structure" from the top list of choices. Entrez provides instructions on how to obtain the structure coordinates and view the structures from links in their Structure Summary pages. Go back to the Entrez document report, and choose "UM-BBD" to return to the UM-BBD. The 2,4-D Pathway has been changed, reformatting reaction pages and updating them and the pathway map to reflect increases in reaction knowledge and to include more and improved Medline and Genbank searches. Each 2,4-D reaction page now has a 2-, 3-, or 4-digit EC code. Links to intermediary metabolism have been changed to the PUMA database, at Argonne National Laboratories. Our link to Access Counts (on the UM-BBD Main Menu) has been replaced by more complete Use Statistics.
November 3, 1995
Our e-mail users list now has 152 members. Our newest pathway, the 1,2-Dichloroethane Pathway has been contributed and programmed by Renhao Li. An e-mail list member recommended that we include pathways for the biodegradation of aliphatic hydrocarbons; this is a first step in that direction. The Naphthalene Pathway Map has been simplified by removing enzyme-bound intermediates. Naphthalene and pentachlorophenol pathway reactions, such as the one for naphthalene dioxygenase, have been reformatted. This includes replacing the single gene link with a GenBank search, even when only one gene is found, allowing users to obtain new sequences whenever they are added to GenBank. Also, when a Medline search returns over 20 citations in these pathways, it has been restricted to titles, to return a smaller number of more relevant citations. And links to these pathways' reaction graphics now include their size. Reactions in other pathways are being reformatted to incorporate these changes.
September 25, 1995
The 2,4-dichlorophenoxyacetic acid pathway reactions now allow Medline searches for their enzymes. Where appropriate, all reaction pages now allow GenBank searches for their enzymes. Entrez MEDLINE and GenBank now link to the UM-BBD. To test this, go to the Entrez MEDLINE Lee, et al. (1995) citation, and select the UM-BBD button at the top of that page to go to the UM-B BD naphthalene 1,2-dioxygenase reaction page. UM-BBD MEDLINE and GenBank links are being updated where needed to make use of this feature.
September 6, 1995
The pathway menu pages have been removed, and all information unique to them has been added to the pathway maps. These, for example, the Toluene Pathway Map, now become the main entry points for information on each pathway. Where there are multiple GenBank entries for naphthalene pathway enzymes, these reaction pages now allow GenBank searches.
August 28, 1995
The home page and its associated pages have been revised to add links to a recent publication and a Related Conferences, Workshops and Seminars page. Associated pages now also have links to other such pages at both their top and bottom.
August 21, 1995
Most 2,4-dichlorophenoxyacetic acid and toluene pathway reactions now have references. Most pentachlorophenol, most toluene, and some 2,4,5-trichlorophenacetic acid pathway reactions now allow Medline searches for their enzymes. All reaction pages have been reformatted where necessary for consistency.
July 28, 1995
All inline pathway compound images are now "clickable" for downloading. To test this, go to the revised atrazine compound page and click or otherwise select the compound image. All naphthalene, most pentachlorophenol (PCP), and all 2,4,5-trichlorophenoxyacetic acid pathway reactions now have references. Naphthalene reaction pages now allow Medline searches for their enzymes. On July 26, 1995, these returned between 2 and 51 citations, depending on the enzyme.
July 13-14, 1995
Added a separate page for all pathway links. Revised the home page to count accesses and to contain standard links to all its associated pages. Put these same links on each associated page. Revised the copyright wording on each page. Added links to the scientific literature to the Useful Internet Resources page.
June 30, 1995
Added another new pathway, 2,4-Dichlorophenoxyacetic Acid, contributed and programmed by Brian Hill, Dartmouth College. Revised the home page to add a link to a Guest Book.
June 20, 1995
Added our first new pathway, 2,4,5-Trichlorophenoxyacetic Acid, contributed and programmed by Brian Hill, Dartmouth College. Revised the home page to add a link to a Contributors page. Revised the What's New page to include links to most changes.
June 5-6, 1995
All toluene pathway reactions are now balanced. Graphics were added for all toluene pathway compounds and reactions. The atrazine -> hydroxyatrazine reaction is now animated.
May 19, 1995
All naphthalene pathway reactions are now balanced. Added graphics for all naphthalene pathway compounds and reactions. Changed all compound graphics to inline images on compound pages. Revised home page to add a link to a Guided Tour page.
May 9, 1995
All pentachlorophenol (PCP) pathway reactions are now balanced wherever possible. Added graphics for all PCP pathway compounds and reactions. Revised home page with links to Useful Internet Resources and Acknowledgements pages.
April 24, 1995
All atrazine pathway reactions are now balanced. Added graphics for all atrazine pathway compounds and reactions.
April 5, 1995
Revised home page, with graphical banner, AboutBBD, and What's New links.
March 30, 1995
Split each pathway into separate pages; added name and date to each page.
February 25, 1995
The UM-BBD was first installed on a server, with initial information on four pathways, atrazine, naphthalene, pentacholorophenol, and toluene.
January 28, 1997 Lynda Ellis
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