PSF
•Clone Manager - cloning and protein expression LIMS•
Introduction
Clone Manager - the PSF cloning and protein expression system (LIMS) is based on an Oracle database (v. 8.1.6) and a frontend developed with Microsoft Access 97. In addition, some perl scripts and Java programs are used for batch data entry.
Manual
PSF Clone Manager Manual in PDF format
Contact
Please contact Konrad Büssow for questions/comments regarding this software.
Screenshots
Features
- Clone Manager stores objects like Primers, Clones, PCR reactions, proteins, DNA- and Protein gels and DNA- and Protein sequences alongside with specific biological properties of each object (e.g. a PCR has a template, two primers and specific reaction conditions)
- it contains a storage management which keeps track of plates and tubes containing any of these items
- A GUI is supplied which allows the user to create objects like PCRs, clones or primers etc and to assign them a storage place
- different kinds of experimental observations like PCR results (fragment size, abundancy) or results from expression experiments (protein sizes, abundancy, solubuility, success or failure of cleaning steps etc) can be entered interactively and are autmagically assigned to the objects they belong to. Results are always judged by the user – not by a »stupid« automatism – but the system supplies several support: prediction of DNA and protein sequences of tagged fusion constructs, calculated mol weights or already entered results of related, already done experiments.
- A batch clone management module allows creation, handling and evaluation of large numbers of cloning experiments simultaneously. For each cloning step, all necessary objects (PCR reactions to generate templates, plates to store them, gels to evaluate them... etc and last not least the newly made clones themselves) are created autmatically on mouseclick. Protocols are made in each step.
- Interface to »Zinsser Speedy« pipetting robots
- Integration. The system can be integrated in higher-level data management systems.
Limitations
Clone Manager is »work in progress« which is done to suit the needs of our project. Therefore some concepts used in this system are not of that general nature you might possibly expect. Some of these concepst are described here. PCRs are assumed to be performed using an already existing clone. Experimens starting with naturally occuring tissues are only supported somehow (It is possible to enter such experiments, however). Electrophoresis gels of PCRs and protein expression experiments can show several bands in reality. We always assume one (or no) band here.
Download and Installation
We make the database structure and the MS Access frontend available here. The system works well here but there is no experience yet of other people trying to install the software at their place. Therefore, problems during installation are likely be expected. If you are interested in using this system we recommend that you come in touch with us.
This is version 0.1.
To install the Oracle database objects, download the following SQL scripts and execute them using SQL-plus in the same order as they appear here:
CloneManager1Tables.SQL
CloneManager2Packages.SQL
CloneManager3Triggers.SQL
CloneManager4Views.SQL
CloneManager5Constraints.SQL
CloneManager6Data.SQL
The database user needs certain priviliges to run the scripts, e.g. "CREATE ANY PROCEDURE", etc. If the SQL scripts fail, this might be due to missing priviliges. Contact the database administrator.
Download the Microsoft Access 97 database file that is used as a frontend for the Oracle database:
PSFCloneManager.mdb (use Shift-LeftMouse to save)
If your using a later version of Access, you will have to convert the PSFCloneManager.mdb to your version. This should work rather automatically by opening the file, but we haven't tested this yet.
Install the Oracle Client Software on your local PC. This contains the Oracle ODBC driver.
The Access database contains links to our local database that have to
be changed to work in another local environment. You have to modify the
links to point to your local Oracle database. This is sometimes tricky.
First, create a ODBC Data Source for your Oracle database using
the Windows Control Panel. Make a File DSN with the name clonedb.
Don't enter a user yet, just the database SID in the first field!
The ODBC connection will appear as clonedb.dsn in the ODBC Data Source
Administrator.
Open PSFCloneManager.mdb and choose Database link refresh in the Administration menu. Click on one of the tables as a test and choose Refresh. If this works well, you may click on Refresh all. The software will delete the old database links and create new ones with your login details. You will see a prompt, Select unique database identifier, just press OK.
If Database link refresh does not work, try to delete/re-create the clonedb.dsn ODBC Data Source. Ultimately, you can also create the database links by hand, using get external data in the File menu.
Now you can go through the pull-down menus, open some forms and enter some data. We are yet to prepare a manual for the software, but part of it is self-explaining. The ORFer software can be used to enter GenBank sequence entries into your local Clone Manager database.
Good luck!
© 2003 by V. Sievert, Konrad Büssow last changed 12 Sep 2006