MouSeek 1.0
by Caleb F. Davis
Jeff Noebels laboratory, Baylor College of Medicine
MouSeek is a relational database programmed using FileMaker
Pro* v4.1. It was designed to function as an intuitive interface through
which all information about a murine colony could be stored, searched,
and printed out in an efficient manner. MouSeek.zip (downloaded file) contains
all files both central and peripheral to usage of this program. This program
was designed at Baylor College of Medicine in Houston, TX by Caleb Davis,
that's me.
The specific needs of our lab dictated the form and function
of MouSeek, but, if necessary, its internal structure is flexible enough
to be useful in a wide variety of applications. FileMaker provides the
tools needed to tune MouSeek's performance to one's particular organizational
concerns. I have listed (see "Getting Started" below) a few sites that
have valuable information about relational databases in general, and FileMaker
in particular. Also there is a Word document in MouSeek.zip called "Revision
History" that I wrote while I was designing MouSeek. These sources of information
cover the basic vocabulary and skills necessary to use MouSeek and FMPro
effectively. Feel free to tinker with the program, and contact me if you
have any questions or suggestions. If there is enough interest then I may
release updates and/or user guides periodically.
Contents
System Requirements
What MouSeek can do for you
File Details
Getting Started
Using MouSeek
Troubleshooting
Contact Information
System Requirements
Miniumum
-
90MHz Intel* Pentium* processor or equivalent
-
FileMaker Pro v4.1 (download
a trial version)
-
16MB of RAM
-
65,000-color (High Color/16-bit) video display card (video)
-
Windows* 95 operating system
Recommended
-
120MHz Intel Pentium processor or better
-
FileMaker Pro v4.1 (download
a trial version)
-
32MB or more of RAM
-
65,000-color (High Color/16-bit) or better video display
card
-
Windows 95/98
-
Internet connection and web browser
*All brands and names are property of their respective
owners.
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What MouSeek can do for you
In our lab, we use MouSeek to maintain records for 5 inbred
mutant murine colonies. It allows us to keep track of birth dates for all
our litters, and it generates reports that tell us when to wean and number
progeny. Each mouse has its own record, and this makes it easy to know
which litter the mouse came from, its dam and sire, littermates, genotype,
phenotype, its exact cage location, other mice residing in that same cage,
any progeny it has produced, etc. For the mutant colonies that we are unable
to genotype by a more direct approach, MouSeek keeps records of the number
of litters and the number of affected offspring for each test-breeding
pair to assist with the identification of heterozygous mice.
MouSeek's features:
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Breeding cages: Tracks the number of litters, sex, genotype,
and phenotype of progeny.
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Weaning and Numbering: Generates dates to either wean or
number specific litters.
-
Non-breeding cages (holding cages): Keeps records of all
reserve male and female mice, along with their date of birth (DOB) and
which breeders they came from.
-
General record keeping: Keeps records of both living and
dead mice. Point and click to browse through many generations of mice.
-
Find/Sort: You can either find a specific mouse in the database,
or you can search for groups of mice that have the same criteria (i.e.
strain, DOB, littermates, etc.)
Other applications where MouSeek would be useful:
-
Toxicology studies: With a little manipulation, MouSeek can
be formatted to maintain details concerning which mice were given a specific
drug regimen, and then it can find and group mice according to which regimen
they received. If you are willing to get a little fancy, MouSeek can also
keep statistics according to treatment group, or records can be imported
into other databases for statistical analysis.
-
Developmental studies: MouSeek can also be manipulated to
keep track of plug date, and then generate lists as to which mice will
be at a specific gestation day on a specific date. When mice are sacrificed,
the phenotypes of the progeny can be recorded in the database and grouped
for statistical analysis.
Basically, MouSeek can be used to keep track of any animal
colony, and can be formatted to fit whatever applications you are using
with only a little creativity. Even if you have limited to no experience
with relational databases, I think you will find FileMaker and MouSeek
user-friendly enough to make the introduction easy to swallow, if not enjoyable.
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File Details
A relational database, if designed carefully, can be a powerful
information structure. MouSeek applies this power to the management of
a murine colony with five main files. (You will find many unfamiliar terms
defined in the first couple pages of the Revision History in the downloaded
zip file.)
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Options: From this file you can do pretty much everything:
search all the files for particular records, print reports, wean litters,
record births, create new cages (useful when first setting up the database),
transfer mice between cages, remove cages, record deaths of mice whether
they be in holding (non-breeding) cages, breeding cages, or unweaned litters.
This is the driver’s seat of the database.
-
Breeders: This file will contain information about
a breeding cage: why and when it was setup, if it is active or not, etc.
Information about the sire and dam(s) in the cage (tag number, genotype,
strain, DOB, and Litter ID) is shown in a portal. Another portal displays
information about each litter that the breeding cage generates: Litter
ID, DOB, # Pups, date of weaning (DOW), and # males and females. New litters
can be recorded for the breeder, or litters can be weaned from here also.
The Breeder ID is in the form BX where X is the number assigned to the
breeding pair.
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Litters: This file holds information on all of the
litters produced by our breeding cages. From Litters you can see information
about all the mice in the litter, assign genotypes to mice in the litter,
record deaths of unweaned pups, or go to the breeder record for the litter.
Nomenclature for the Litter ID is simple: BX-n is the nth litter from breeding
cage BX.
-
Mice: Every mouse in the entire mouse room has its
own record in this file. The strain, DOB, Litter ID, genotype, Cage ID,
and comments for each mouse are listed by tag #.
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Cages: This file stores records for every non-breeding
cage we have in the mouse room. Information about each cage includes the
sex, DOB, and DOW (if the mice in the cage came from the same litter),
strain, and general comments. In addition, a portal shows information about
each individual mouse in the cage like genotype, litter ID, etc. Nomenclature
for the Cage ID is really basic. Hn is the nth holding cage in the database.
The power of storing this information in a relational database
becomes evident when you think about collecting data from multiple generations
of mice: You can get to the record of a mouse’s litter and see all of its
littermates if the Litter ID field for the mouse is filled in with a valid
Litter ID (one matching a record in Litters). Furthermore, you can get
to the record of that litter’s breeder if the Breeder ID field (in the
Litters file) for the litter has a valid Breeder ID in it. If all of these
ID fields are entered correctly then you can jump from a mouse to its siblings,
to its parents, to its parents' siblings, etc. In this way it is a breeze
to browse (a little a"litter"ation) through many generations of mice for
data collecting purposes. (I’ve even begun a pedigree-drawer that will
do this graphically for you.) This is probably one of the most useful features
of the database, and I have made it foolproof because all ID numbers are
assigned automatically as new litter and mouse records are created through
births and weanings, respectively. Different nomenclature can be used in
the database, but extensive editing of the scripts that automate data entry
will be necessary if the user wishes to keep these relational links foolproof.
Every other file that the database uses (Transactions,
Litter Edits, and Mouse Edits) is a helper file. Deaths that occur in a
litter before a litter is weaned are stored in Litter Edits for easy access
through a portal in Litters. The Transactions file stores information about
when a mouse was moved from one cage to another. If we ever need to know
the state of a cage on a certain date, then we can search the Transactions
file for all records of mice moved into or out of that cage within a range
of dates. This has saved our you-know-whats a couple of times already when
we lost track of what males were breeding with what females. The Mouse
Edits file is one we haven’t been using very much, but we could store experiment
information in that file if we wanted to. Information can be entered through
a portal in Mice, so you should never really have to open this file directly,
but of course there is nothing stopping you from doing so.
That is pretty much it concerning the file structure.
Just about everything else in the database is tinkerable, meaning that
you can experiment with layouts and scripts and things, but these main
files and the relationships that link them together (Cage ID, Mouse ID,
Breeder ID, and Litter ID) should only be changed if you know what you're
doing.
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Getting Started
To install MouSeek after downloading the zip file, you need
to extract all of the zipped-up files to a single directory (name the directory
whatever you want) with an unzip program (WinZip
is a good one, though you must already have one if you're reading this!).
It will be convenient to keep all the zipped-up files in one directory,
but only the 8 files with .fp3 extensions are absolutely necessary. I also
recommend saving the downloaded zip file in the same directory so that
you can experiment with the database without worrying about losing the
original program. When you have done this, you must then make sure that
you have FileMaker installed on your computer (you can find a trial version
here).
When FileMaker is installed you can double click the file named "Options.fp3"
to launch the program. Have fun!
Learning the basic FMPro commands (creating records, scripts,
find requests, layouts, reports, etc.) will help you tailor MouSeek to
the needs of your lab. Here are some websites that I found useful when
I started learning about databases and FMPro:
Database
Design support from FileMaker
More
useful links
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Using MouSeek / Troubleshooting
CAUTION!!! Use of this program means you agree that neither
I nor Baylor College of Medicine can be held liable for any damage to your
data. Though I have done my best to eliminate bugs in the program, I strongly
advise using MouSeek as a backup to your current system until you are thoroughly
familiar with it. Also, it's a good idea to store the *.fp3 files in a
new zip file every time you update them. I say this because I don't want
someone to delete all their records on accident, not have a backup of their
data, and come to me to say that they weren't warned that this was possible.
MouSeek is the culmination of about 4 months of
coding and another 5 months of testing and revision. As is the case with
any software, bugs are sure to appear from time to time. Most of these
bugs have been exterminated as they pop up in our use of the program. However,
those who use the software differently than we do are sure to encounter
the "undesirables" that I didn't catch.
If you experience problems with MouSeek, please send email
to Caleb Davis.
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Contact Information
To the extent that I have free time I will try my best to
answer any questions that you might have. Thanks for using MouSeek and
be sure to let me know what you think about it.
Caleb Davis
Department of Neurology
Baylor College of Medicine
1 Baylor Plaza
Houston, TX 77030
cdavis@bcm.tmc.edu