EAWAG-BBD Frequently Asked Questions

EAWAG-BBD Frequently Asked Questions

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  1. How is information in the EAWAG-BBD verified or validated?

  2. Why is the first letter of a compound name capitalized?

  3. Why don't you add a pathway for xxxx?
    How can I contribute a pathway?

  4. How is the work funded?
    How long will it continue to be free?

  5. Can you send me more information about xxxx?

  6. Why can't I connect to the database?

  7. Why can't I connect to some database web pages?

  8. How can I get more information on database plans and progress?
    I signed up for the e-mail list a month ago; why have I never received a progress report?

  9. What is the difference between aerobic, anaerobic, and an/aerobic?


How is the information in the EAWAG-BBD verified or validated?

Compound information is taken from the scientific literature or Internet resources, and whereever possible is verified using redundant sources. Reaction information, wherever possible, is also based on the scientific literature, and the literature reference is given on each reaction page, along with a link to a search of a subset of the Medline database for additional relevant articles. The EAWAG-BBD Medline searches are meant to introduce the literature, not necessarily provide a complete bibliography. Indeed, if a search returns "too many" citations, it may be restricted to only search titles, or restricted to include the words "microbial" or "bacterial." Reactions whose searches return larger numbers of citations spanning longer periods of time are better validated.

Contributions from workers in the field are also accepted; for example, the Dibenzothiophene Desulfurization Pathway. If these have not been published, the citation given is the name of the contributor, year of contribution and the phrase "personal communication." Each personally communicated pathway is reviewed by one or more members of our Scientific Advisory Board before the pathway is installed on our database.

Responsibility for the accuracy of the information in the sites we link to rests with their developers and maintainers, but we carefully review their content before deciding to link. Our users assist us in this important task by bringing to our attention errors in our site or in the material to which we link at another site.

Why is the first letter of a compound name capitalized?

If you look at EAWAG-BBD pathway maps, such as the Atrazine Pathway, it may be hard to separate the name of a compound (such as Atrazine) from the name of the enzymes which use it as a substrate (such as atrazine chlorohydrolase). For this reason, we decided to capitalize the first letter of compound names, while keeping enzyme names in all lower case.

Why don't you add a pathway for xxxx? How can I contribute a pathway?

With over 8 million organic compounds currently available, and more being synthesized every day, the EAWAG-BBD will never contain a microbial biodegradation pathway for EVERY compound. We began with pathways for a few compounds chosen in part because their metabolism was familiar to our Co-Directors. To these are added pathways for compounds selected in part because they interest available volunteers. 42 pathways were started by students in Fall, 1995 as a class assignment. These, and others, are being completed by volunteers as time permits.

Our present goal is to include degradation pathways for approximately 100 compounds, representing all major organic functional groups, classes of compound, and types of microbial metabolism. With appropriate structure and substructure search capabilities, this should allow one to predict the biodegradability of compounds that are not yet in the database. If you are interested in adding a pathway for a particular compound yourself, or working with a student to complete one, let us know. Volunteers can obtain academic credit.

How is the work funded? How long will it continue to be free?

Most work on the project, including time of the Co-Directors and the Scientific Advisory Board, is volunteered. Volunteers are listed on our Contributors page. The database has been supported in part by several sources, listed on our Acknowledgements page. We have no plans to charge for the information we provide, and only link to other information sources that are similarly free-of-charge.

Can you send me more information about xxxx?

We try to put as much information into our web pages as possible so we do not have any more information on the subject that we can give you. The maintainers of the pages are not the people who did the original lab work, so we do not have any insight into the pathway that cannot be obtained from the papers and we don't have a lot of knowledge of technical details either. However, if you take a close look at the information on the xxxx pages and follow the links provided, this should be a good start.

Other places where you can go to get more information:

PubMed Medline search:
http://www.ncbi.nlm.nih.gov/PubMed/
This is a good place to find recent references on most topics. You may have to go to the library to get the original articles. A college-level science librarian might also help.

The ChemFinder webserver:
http://www.chemfinder.com
This is a comprehensive source of web-based chemical information. All EAWAG-BBD compounds are indexed there and it has much more information.

The Bioremediation discussion group:
http://www.bioremediationgroup.org/
Look through their archives; your question might have already been asked and answered. If you want, you can join the discussion group (it's free). This could be a good forum to ask your questions.

Why can't I connect to the database?

The database is becoming increasingly popular. Our
hourly and daily use statistics indicate that the busiest times are between mid-morning and mid-afternoon (Central Time, -5 GMT) on weekdays. If you have difficulty accessing the database during those times, please try earlier or later in the day or on weekends. If your difficulty persists, please let us know.

Why can't I connect to some database web pages?

If you can connect to the main page of the database and other static pages, but have problems viewing a compound page or other dynamic pages, the problem may be related to the port used to view the dynamic pages. They use port 8015, not the usual port 80 used by default for web pages. You must ask your computer system administrator to open port 8015 for web access. Alternatively, you can use the EAWAG-BBD SRS mirror, which does not have that problem.

How can I get more information on database plans and progress? I signed up for the e-mail list a month ago; why have I never received a progress report?

Once or twice a month, we send e-mail progress reports to members of our e-mail users list. Join the list if you want. You will receive an e-mail acknowledgement when you sign up. If you don't get this message, you have NOT been added to the mailing list. A progress report is sent each time we update the EAWAG-BBD What's New page, containing much of the same material. If you read things there dated after you signed up for the e-mail list, but that you have not seen on an e-mail progress report, you also are not on the list. About 5 percent of the people who sign up for our email list enter a faulty e-mail address, and cannot be added to the list. If you think you signed up, but do not get an acknowledgement, this may have happened to you. Please sign up again, typing your e-mail address very carefully. Also, since this list is maintained by volunteers, if your access to e-mail is interrupted, so that a progress report is returned to us, you are removed from the list. If your e-mail access improves, please sign up again.

What is the difference between aerobic, anaerobic, and an/aerobic?

All pathways in the EAWAG-BBD are considered "aerobic", that is, to occur in the presence of oxygen, unless specified otherwise, by the use of the term "anaerobic" or "an/aerobic". A EAWAG-BBD pathway designated "anaerobic", such as the Benzoate Pathway (Anaerobic), only occurs when oxygen is absent. A EAWAG-BBD pathway designated "an/aerobic", such as the Organosilicon Pathway (An/aerobic), contains both aerobic and anaerobic reactions. The pathway narrative describes which is which.


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Page Author(s): Lynda Ellis

July 11, 2017 Contact Us

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