What's New in the UM-BBD?

December 9, 2011
Pathways for permethrin, (US), (CH), or (UK), and cypermethrin, (US), (CH), or (UK), insecticides of the pyrethroid family, have been added. These pathways were contributed by students from Manchester College, Indiana, under direction of their instructor, Jeffery P. Osborne. The Remove Product feature in the UM-PPS is now available in the ETHZ UM-PPS. More information is available in about PPS. In the Links page, a link for Microbial Informatics and Experimentation was added, and the link for GREP: Generator of Reaction Equations and Pathways at Trinity College Dublin, Ireland was updated.

November 15, 2011
A pathway for ibuprofen, (US), (CH), or (UK), a common non-steroidal anti-inflammatory drug, has been added. This pathway was contributed by a student from Manchester College, Indiana, under direction of her instructor, Jeffery P. Osborne. As requested by a UM-PPS user, a feature was added to the UM-PPS to permit users to remove products, and the reactions and compounds that lead from them, from predictions. For more information, see About the UM-PPS. This feature is presently not available at the ETHZ UM-PPS. The UM-BBD Microorganism page, and the related Microorganism Search on the Microoganism page and the Search page, have been updated, including removing or updating non-working links and fixing bugs. In the Links page, the link for Search Bacterial Nomenclature Up-To-Date was deleted.

October 12, 2011
A pathway for phenylacetate, an intermediate in biodegradation of many aromatic pollutants, (US), (CH), or (UK), has been added, and the styrene pathway, (US), (CH), or (UK), has been updated. In the Links page, the link for the Plasmid Genome Database was deleted.

September 14, 2011
A pathway for methamidophos, an organophosphorous insecticide, (US), (CH), or (UK), has been added. On text pathway map pages and the list of all microorganisms, the links to World Data Centre for Microorganisms (WDCM) microorganism database have been removed. Lists of all pathways and all microorganisms are available. The Swiss mirror of the UM-BBD now includes the "Display a Pathway" link at the bottom of each reaction page, and the Swiss UM-PPS has been updated to version 2.0. Now there is better redundancy for all UM-BBD and UM-PPS resources. In the Links page, a link for the CACTUS online SMILES translator from the National Cancer Institute was added, and the link for the Google Directory of Biotechnology was deleted.

August 10, 2011
The pathways for bisphenol A, (US), (CH), or (UK), and morpholine, (US), (CH), or (UK), have been updated. On enzyme and reaction pages, the links to enzyme entries in the ExPASy enzyme database have been updated. Lists of all enzyme and all reaction pages are available. The UM-BBD now contains information on over 200 pathways, 1400 reactions, 900 enzymes, and 1300 compounds. Congratulations to all present and past UM-BBD developers and users who have helped us achieve these milestones. In the Links page, a link for the European Food Safety Authority (EFSA) Journal was added, the link for the ExPASy Enzyme Database was updated, and the link for Boehringer Mannheim Biochemical Pathways from ExPASy was deleted.

July 6, 2011
A pathway for isocarbophos, an organophosphorous insecticide and acaricide, (US), (CH), or (UK), has been added, and the pathway for dibenzothiophene, (US), (CH), or (UK), has been updated. Our academic license for the ChemAxon MarvinView and MarvinSketch applets has changed. Only the applet tools for Molecular Weight and Naming are fully functional. All other tools will either not run or will only run in Evaluation Mode. More information on Marvin applets is available. In the Links page, links for OxDBase: a database of biodegradative oxygenases, at the Institute of Microbial Technology, India, and the Pesticide Properties Database, at the University of Hertfordshire, UK, have been added, and the link for the World Federation for Culture Collections has been updated.

June 1, 2011
A pathway for ketoprofen, a non-steroidal anti-inflammatory drug, (US), (CH), or (UK), has been added. In the Pathway Prediction System, when a predicted pathway is too complex for display, the prediction is rerun with a decreased number of levels and a message is displayed under the last compound row. This is documented in About the PPS. A new publication is available: Gao J, Ellis LB, Wackett LP. (2011) "The University of Minnesota Pathway Prediction System: multi-level prediction and visualization." Nucleic Acids Research 2011. April 12. This citation and a link to the full text of the article is found on the Publications page.

April 15, 2011
A pathway for 5-nitroanthranilate, a natural product used as a starting material for other nitroaromatic compounds and dyes, has been added, (US), (CH), or (UK), and the pathway for the phthalate family has been updated, (US), (CH), or (UK). In the Links page, the link for the Environmental Fate Database from SRC has been updated.

March 17, 2011
A pathway for malathion, an aliphatic organothiophosphate pesticide, has been added, (US), (CH), or (UK), and the pathway for nicotine, (US), (CH), or (UK), has been updated. In the Pathway Prediction System, a new option for printing and viewing results is available. Users can now use the [PDF] button to download a .pdf version of the results web page. This is is the best format for archival purposes, and is documented in About the PPS and the Resize pages. The Resize page links to example .pdf files. Also in the Pathway Prediction System, aromatic ring dioxygenation and monooxygenation rules have been restricted from acting on rings with long aliphatic side chains. This improves the accuracy of predictions for these rings. For example, see the prediction for 2-(4-oxido-4-oxobutyl)benzoate, C1=CC=C(C(=C1)CCCC(=O)[O-])C(=O)[O-]. In the Biochemical Periodic Tables, all links to TOXFaq articles, such as the one in the Arsenic page, were updated. A new publication is available: Helbling DE, Hollender J, Kohler HP, Singer H, Fenner K. (2010) "High-throughput identification of microbial transformation products of organic micropollutants." Environ Sci Technol. 2010 Sep 1;44(17):6621-7. This citation is found on the Publications page. The What's New page restarts; 2010 activities have been archived.

January 12, 2011
A pathway for alachlor, a chloroacetanilide herbicide, (US), (CH), or (UK), was added, and the pathway for naphthalene, (US), (CH), or (UK), was updated. On the Links page, links were updated for the journals Bioinformatics, Nucleic Acids Research, and Journal of Biochemistry.

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