ADIS homepage Sequencing reaction ordering and request tracking at MPIPZ
(for authorized users only!)
SeqOrderDB c2.6  

  1. How do I get access to the electronic sequence ordering system?

    Contact ADIS via the ADIS tasks interface with four pices of information:

    • your complete Name and your UNIX username,
    • your MPIPZ phone number,
    • the name of your group leader,
    • and the Kostenstelle(n) to be charged.

    Once this information has been processed by ADIS, you can use SeqOrderDB.

  2. Why do I need to fill all the fields in the order form?

    This is because the name of the resulting data file for each single reaction (which you finally will find in the ADIS folder within your UNIX account) is generated from the data YOU put in (code: GelLane-requestNo-username-template-primer.Seq). The program checks if all required data fields are filled, and it does not allow "shortcuts". Since UNIX file names do not allow special characters, you are not allowed to use those in the primer & template designations. Unfortunately, html does not (yet) support "autofill" or similar data input tools. You can only use the "tab" key and "cut & paste". However, since SeqOrderDB1.4 there are javascript-based functions which allow to fill the some fields semi-automatically.

  3. What is the current version of SeqOrderDB? or Why do my bookmarks do'nt work any more?

    Updates (and connected to that new links) are required from time to time to adopt the system to new needs or to incorporate improvements. If you bookmark the "entry-page" (http://adis.mpipz.mpg.de/SeqOrderDB/), there should be no trouble. Other links may change!

  4. What is the version history of SeqOrderDB?
    • Topics which have been adressed in SeqOrder Version 2.4 (since 17.05.2004):
      • Automatic base calling based on Phred has been implemented. The script that directs the required steps has been written by Thomas Rosleff Soerensen. The Phred20 values in the DB are now generated automatically, and the quality scores and DNA sequences generated are stored directly in the database. A Perl Module written by Martin Werber has been implemented that creates pdf files directly from the tracefile (designated "abi2pdf"). All files generated, as well as request-based bundles of files, are available for download via request tracking.
    • Topics which have been adressed in SeqOrder Version 2.1 (since 04.02.2004):
      • The order sheet is provided as a pdf form for printout.
    • Topics which have been adressed in SeqOrder Version 2.0
      • ... to be completed
    • Topics which have been adressed in SeqOrder Version 1.7 (since 30.07.2002):
      • Linking of newly ordered oligos which are used as primers to sequencing reactions has been implemented.
    • Topics which have been adressed in SeqOrder Version 1.6 (since 05.12.2001):
      • the whole AdisDB system has been moved to a separate, hardware-redundant computer (citrusXL)
      • UserDB has been reworked completly to accomodate working groups, buildings and departments in a correct way. The respective changes are incorporated into SeqOrderDB.
      • many minor improvements,
      • special tools to handle GABI-Kat requests have been implemented.
        - Linking of primers from the primer list to sequencing reactions is possible.
    • Topics which have been adressed in SeqOrder Version 1.5 (since 15.05.2001):
      • this update is a "maintenance update" which maily affects the programming structure. The access control has been improved, and the cgi's have been cleaned up to be uniform within OligoOrderDB, SeqOrderDB, and UserDB.
      • also, the request tracking system has been modified to present information on the read quality. Phred20-scores are presented. These indicate the quality of the sequence read.
    • Topics which have been adressed in SeqOrder Version 1.4 (since 18.01.2001):
      • the standard primer list is now part of the database, and if a request uses only one primer, the redundant work to type in the primer has been reduced.
      • a comment can be added to each reaction. This comment will end up in the trace file of the corresponding reaction. Very useful for automatted analysis of many samples (special software is required to extract the comment from the trace file!).
      • the system can now keep track of different prices for reactions from different requests. This will be used to offer "unchecked" (un-edited base calling) reactions at a reduced price, and edited reactions at a increased price. The default will be the cheaper "unchecked" reaction; you will need to activate the "check reaction" feature.
      • the handeling of the "status" of requests and reactions (that is: not activated / activated / in sequencing / done / charged) in the database has been compeltely rewritten.
      • the number of reactions in a given requests is now calculated in a status-dependent manner. You can now see in the "list of requests in queue" how many reactions in a request are still to be sequenced.
      • many small problems have been solved, and many smaller bugs have been removed.
    • Topics which have been adressed in SeqOrder Version 1.3:
      • since we were running out of request numbers, we needed to increase the number of digits in the request number. Up to version 1.2, SeqOrder did work with 4-digit request numbers. Starting with Version 1.3, it handles 6-digit request numbers. Since the file name length is restricted to 31 characters, the username needs to be shortened and will be represented by a "nickname" of 4 characters. The file names internally (within ADIS) contain only the "nickname" to replace the username. You (the users) do not really recognise that because this change is corrected by the UNIX scripts distributing the files. However, if you check the color printout of the reactions, you will find this nickname in the file designation.
      • a single request can not have more than 96 reactions (there is a special tool to generate requests in the 96-well microtiter plate format - ask us!)
    • Topics which have been adressed in SeqOrder Version 1.2:
      • A special form for large orders with related templates and identical primers has been implemented. This tool should help to create orders which contain "redundant" information. The templates in these requests are automatically named according to their position in a 96-well or 384-well plate.
      • Group leaders can send coworkers to activate orders placed by themselves.
      • Some bugs have been removed.
  5. How can I avoid long loading times of the pages? Why do I get error messages from my browser/System?

    • Due to the complex cgi- and Javascript programming you need recent software (operating system and/or browser, you need Navigator 4.X or higher) on your computer to avoid error messages or malfunction. Please read the error messages carefully since there are also messages telling about misconfigurations and other failures from the SeqOrder program itself.
    • The program NEEDS Javascript™ (version 1.2 or higher). If your browser does not support Javasript™, or if you disable Javascript in the preferences, SeqOrder will not work properly.
  6. Why am I not allowed to use the character ,.-;:_/\"!´`'#* and so on in my template and primer designations?

    Because many of these special characters are used by the different operating systems and programs which work with the data. It's obvious for the -. This is used to separate different pices of information in the name of the data file you get back from ADIS. If you put an additional - in the template or primer name, the respective information is no longer computer-readable.

    You are only allowed to use normal letters and numbers for naming template and primer. Javascript is used to reject wrong input and reports about the wrong characters used.

  7. Do I really need to get my order form signed?

    YES, you need the agreement of your group leader to spend money for sequencing. It can be a lot! It is really required that the person responsible for the Kostenstelle knows about the money spent.

    BUT - in a way similar to OligoOrderDB - you can become "authorised" for ordering sequences. Your GROUPLEADER needs to send a message to ADIS via the ADIS tasks interface with three pices of information:

    • the info that you are authorised for ordering sequencing reactions,
    • your complete Name and your UNIX username
    • and the Kostenstelle(n) to be charged.


    General information about the electronic sequence ordering & tracking system:

    • You need your MPIPZ UNIX user name and password to access the system
    • When prompted, please print the form and have it signed by your group leader.

    Last modified 2011-01-14 by ppriess
    In case of problems please contact us via the ADIS tasks interface. - Impressum.


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