November 25, 1996
A new pathway for beta-hexachlorocyclohexane was added. The beginning of this is the first anaerobic pathway in the UM-BBD. Peter Middledorp and Ryan McLeish were added to our Contributor's Page. On our Useful Internet Resources page, we updated the link to Entrez, and are changing all our Entrez links to their new server as time permits. A new Awards page was added, linked to on the UM-BBD Home Page. The three awards we have received already, and any we receive in the future, are based on our development due in part to the comments and suggestions for improvement we receive from our users, and we thank you for these.
November 8, 1996
A new pathway for 2,4-dichlorobenzoate was added. This is the first pathway arbitrarily chosen to be a "trunk pathway" linking other UM-BBD pathways to intermediary metabolism. Reactions and compounds were transferred to it from the toluene pathway, and it continues one branch of the 4-chlorobiphenyl pathway.
On our Useful Internet Resources page, we updated links to Bioremediation Research Abstracts at the Hazardous Substances Research Centers and to Bioremediation Links at Maxygen, Inc., and replaced the link to PUMA with a link to its successor, WIT. We added links to the Bioremediation Discussion Group, the Database for Environmental Fate of Chemicals, and the National Academy Press Environmental Reading Room. We added on-page links to page subsections.
Intermediary metabolism links were changed from PUMA to KEGG: Kyoto Encyclopedia of Genes and Genomes. Hugh McTavish has taken over maintenance of the Conference page. A link to the UM-BBD Developers Photo Gallery was added on our Contributors page. There you can see 1995 and 1996 end-of-summer local developer group images. Other contributors are encouraged to send us photographs or gif or jpeg image files, or give us image URLs. We would be happy to add them to this page. E-mail links at the bottom of all pathway, compound, and reaction pages, were changed to send mail to: BBDMaster@email.labmed.umn.edu instead of individual page authors. Please use this e-mail address if you have questions on individual pathway, compound or reaction pages, and your message will be directed to the person best able to answer it. The information in About the UM-BBD was updated to reflect this change. Chemical formulas on compound and reaction pages were completely changed to use subscripting and superscripting. All future pathways will use this.
September 30, 1996
A search on EC codes has been added to the Search page, and a link to a browsable index of these codes in numeric order has been added to the Index page. BBD users expressed a need for a search of reaction type in our user survey. This search meets part of that need. The information on compound pages has been updated in the About the UM-BBD page. Links to the National Toxicology Program and the University of Akron's Hazardous Compound Database have been updated, and new links to Worksafe Australia's Hazardous Substances and Exposure Standards Databases and the Bioremediation Resources on the Internet from the Canadian National Water Research Institute have been added, on the Useful Internet Resources page. A new Graduate Research Assistant, Dong Jun Oh, has been added to the Contributors page. An award from NSF has been added to the Acknowledgments page. The e-mail links at the bottom of pathway, compound, and reaction pages are changing, to send mail to: BBDMaster@email.labmed.umn.edu instead of individual page authors. Please use this e-mail address if you have questions on individual pathway, compound or reaction pages, and your message will be directed to the person best able to answer it. This change has been implemented in the naphthalene, dichloroethane, and pentachlorophenol pathways, and will be carried out in other pathways as time permits.
August 9, 1996
We have added two new pathways: The Tyrosine Pathway and the 4-Chlorobiphenyl Pathway, a model for the aerobic biodegradation of polychlorinated biphenyls (PCBs). Both contain client-side imaged clickable pathway maps. Chemical formulae on compound pages in these pathways are the first to be written using subscripting. Compound pages will be changed to use this as time permits. We added a page for Software Tools that are helpful in the development or use of the UM-BBD. It is linked to at the bottom of the UM-BBD home page. We added the USDA's Agricultural Research Service Pesticide Properties Database to our Useful Internet Resources page. We added two new contributors: John Haddock from Southern Illinois University at Carbondale, and Michelle Wagner from the University of Minnesota. Background color for the UM-BBD home page and associated pages was changed to white.
July 24-25, 1996
We added the Trichloroethylene Biodegradation Pathway. This pathway makes two firsts: the first reaction (catalysed by soluble methane monooxygenase) to have a graphic of the reaction mechanism, and the first clickable graphic pathway map to use client-side imaging. If your browser has problems with this map, please let us know. Most compounds in the atrazine pathway have been added to the Klotho Biochemical Compounds Declarative Database, joining those in the glyphosate and dichloroethane pathways. A search for CAS Registry Numbers has been added to our Search page. We have CAS numbers for most of our compounds, and will add the remainder as time permits. We have added statements on the significance of the biodegradation pathways for atrazine, 1,2-dichloroethane, naphthalene, toluene, and 2,4,5-T. Now all pathways in the database have significance statements, and they will be a standard feature of all new pathways. Most of our compounds are now indexed in the ChemFinder WebServer. Their entries for compounds we contain link back to our pages, so one can use their more sophisticated structure and other searches, and easily see if the compounds returned are in the UM-BBD. A link to the page for MicE/BioC 5-309, Biocatalysis and Biodegradation, has been added to the UM-BBD home page. We added the Organic Chemical Database at Colby College, Maine, to our Useful Internet Resources page. We added a new UM-BBD student contributor, Colin Sweeney, from the University of Minnesota, Morris.
June 17, 1996
The glyphosate and 2,4,5-T pathways have clickable, graphical pathway maps. The compounds in the glyphosate and 1,2-dichloroethane pathways have been added to the Klotho Biochemical Compounds Declarative Database. These pathways' compound pages link to the corresponding Klotho pages, which provide 3-D images, SMILES representations, tertiary coordinate files in PDB format and other information. These Klotho pages link back to the UM-BBD. The About the BBD page has been updated, and now contains much more information, including annotations to pathway, reaction and compound pages. Read it! You may learn something new, even if you think you already know it all. Frequently Asked Questions about the UM-BBD (and their answers!) are now available, through links on the UM-BBD home page and the About the BBD page. The Publications page has links to two new UM-BBD abstracts. The directors of the UM-BBD, Lynda Ellis and Larry Wackett, are developing a graduate-level course, Biocatalysis and Biodegradation (MicE 5-309), based on the UM-BBD. MicE 5-309 will be offered completely over the Internet starting in Fall, 1996. Students will learn microbial catabolic metabolism, Internet information resources for biotechnology, how to author Web pages, and will develop UM-BBD pathways for the biodegradation of environmental pollutants. For further information on the course, e-mail firstname.lastname@example.org
May 15, 1996
The 1,2-dichloroethane pathway has a clickable, graphical pathway map, and its compound pages have links to National Toxicology Program Chemical Health & Safety Data. All dibenzothiophene desulfurization pathway compound pages include CAS numbers. The Useful Internet Resources page has links to OSHA Computerized Information Service (OCIS), including links to browse (Web) or search (Gopher) OCIS Chemical Sampling Information. The link to the Ligand Chemical Database has changed, and Ligand links to enzymes on reaction pages have been updated. We added a new student contributor: Trung Bui.
May 1, 1996
We have changed all our EXTOXNET and Entrez document and search links on relevant compound and reaction pages. We added a link to NTP Chemical Structures on the Useful Internet Resources Page. The first survey of the UM-BBD e-mail users list has been analyzed. Response rate was 57/224 (25%) and we thank all who responded. Results and our comments on them are linked to from our use statistics page.
April 12, 1996
The Glyphosate Biodegradation Pathway has been added. A clickable graphical pathway map and statement of its significance has been added to the PCP Pathway. Three new sites were added and one site link was changed on our Useful Internet Resources page. The Hazardous Chemical Database at the University of Akron, the National Toxicology Program and its Short-Term Toxicity Study Reports and Chemical Health & Safety Data and information on Biotechnology in Waste Management from the Australian Biotechnology Association, Ltd. were added, and the link to the EXTOXNET home page was changed. EXTOXNET and Entrez document and search links are being changed on relevant compound and reaction pages. A link was added on our Publications page to an outside review of the UM-BBD which appeared in the American Society for Microbiology (ASM) News.
March 21, 1996
The 2,4-D pathway has been updated to add the reaction which produces the antibiotic protoanemonin, two clickable graphical pathway maps, the significance of the pathway, and a link to an external animation of the first two steps in the pathway. A search for molecular formula has been added to the search page. The Publication link on the home page and associated pages has been changed to Publications and now list several publications related to the UM-BBD. Two new links have been added to the Useful Internet Resources page: one to the Toxic Waste Site in the Microbe Zoo at Michigan State University, and one to the journal Nucleic Acids Research Online. All compound pages in the atrazine and dichloroethane pathways now include CAS numbers.
March 8, 1996
GenoBase now links back to the UM-BBD. To test this, follow the GenoBase link for any enzyme for which we have a 4-digit EC code, such as naphthalene dioxygenase (EC 22.214.171.124). We added two new links to our Useful Internet Resources page, one to an EPA Bioremediation Resource Guide, and one to the DOE Environmental Sciences Division. We added a new student contributor: Michael Burns.
February 16, 1996
We added the orcinol pathway, the first of the 42 pathways begun by students in Fall, 1995 to be completed. It is also the first pathway to have a clickable graphical pathway map. We added a clickable graphical pathway map for the naphthalene degradation and dibenzothiophene desulphurization pathways. The conference page returns (access through the home page and its associated pages).
February 2, 1996
We added the dibenzothiophene desulfurization pathway. This pathway marks three firsts: It is the first pathway contributed to the UM-BBD by scientists working outside the University of Minnesota: Margie Romine of Pacific Northwest National Labortory first submitted the pathway, and it was updated by Kevin Gray of Energy BioSystems Corp. It is the first pathway to have a graphical, as well as a text, pathway map, as recommended by a person on our e-mail user's list. And it is the first pathway to purposely NOT continue to intermediary metabolism. The rationale for that is on the text pathway map. We were awarded a 4-star rating (their highest) by McKinley Review on January 21, 1996. Their award logo is now on our home page and it links to their home page. To find the UM-BBD review there, search on "biodegradation." Comments from our users assist us in making this an award-winning resource, and we thank you. We archived the 1995 What's New page. We added several new links to our Useful Internet Resources page: three compound information resources and three sites for general biodegradation information, including a site listing conferences and seminars on environmental topics.
January 10, 1996
The compound pages in the Atrazine, 2,4-Dichlorophenoxyacetic Acid, Naphthalene, Pentachlorophenol, Toluene, and 2,4,5-Trichlorophenoxyacetic Acid Pathways have a new format, including chemical formula, molecular weight and, where available, CAS number for each compound. The reactions in the Atrazine Pathway have been further updated. The Guestbook has been revised to include a e-mail acknowledgment sent to every guestbook signer. We have added two new members to our Scientific Advisory Board, which now includes: Peter Chapman, EPA Florida; Irwin C. Gunsalus, EPA Florida; Thomas Leisinger, ETH Zurich; Andreas Kiener, Lonza AG; and Jack Trevors, U Guelph. We have added two new student contributors: Eva Young and Dong Jun Oh.
January 27, 1997 Lynda Ellis
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