FAQs
Updating from version 4.1.1 to 4.1.2
Question:
What is different in version 4.1.2, and Why Mac users should update to 4.1.4?
Answer:
The 4.1.3 update corrects a bug that affected the display of the correct ID for the Stud in the mating form when the mating record was created using an "existing cage" option. It also corrects a bug in the "Current Matings" button. Importantly, this 4.1.3 update makes the program identical to the 4.1.2 download placed on the server on August 4th, 2011. Therefore, if you downloaded Mouse Colony (Runtime or Net versions) on or after 8/4/2011, you should not use this update. Additionally, the update only works if you have purchased Mouse Colony.
The version 4.1.4 for Mac is fully compatible with Lion. If you are running earlier versions of the Mac OS system, you do not need to upgrade now.
Question:
Who should install the update?
Answer:
Mac and PC owners running version 4.1.2 downloaded before 8/4/2011. Users running customized version MUST NOT install the update because they will lose the custom features. Please contact us if you have questions.
Question:
Windows Installation. Instructions for Mouse Colony and Mouse Colony Net.
Answer:
1) Make a Backup of the current Mouse Colony or Mouse Colony Net folder in a disk or flash drive.
2) Make sure that the Mouse Colony or Mouse Colony Net folder is in the Program Files Folder (Windows) . The Mouse Colony or Mouse Colony Net folder may be inside a folder labeled Simplified Data Tracking. This is OK, do not remove from there.
3) The Folder containing the stand alone application must be labeled Mouse Colony 4.1.1 or 4.1.2 and should contain a file labeled Mouse Colony with the extension USR (you will also see files for the Manual, Quick Start, etc.)
If you renamed the folder or the file, you must change them back to the original designation.
If you are using the Network version, the Folder containing the application should read Mouse Colony Net 4.1.1 or 4.1.2 and must contain a file also labeled Mouse Colony Net (you will also see files for the Manual, Quick Start, etc.)
If you renamed the folder or the file, you must change them back to the original designation.
4) Download and run the appropriate 4.1.3 Update installer (Mouse Colony 4.1.3 Update Installer for the stand alone version and
Mouse Colony Net 4.1.3 Update Installer for the network version).
5) Make sure that you are NOT running the previous version of Mouse Colony or Mouse Colony Net. If the program is open, close it.
6) The Updater will ask you to enter the account and password for the previous version several times (10-12 times). It is advisable that you set up an automatic login to avoid this.
7) Make sure that all your data are there.
If everything is OK, you can uninstall the older version or just leave it there.
Mac Installation. Instructions for Mouse Colony and Mouse Colony Net.
1) Make a Backup of the current Mouse Colony 4.1.1 or 4.1.2 folder in a disk or flash drive.
2) Make sure that the Mouse Colony 4.1.2 (or 4.1.1) or Mouse Colony Net 4.1.2 (or 4.1.1) folder is in the Applications Folder.
If you have an older version of the stand alone program that is labeled Mouse Colony, rename the folder containing the stand alone version: If you have an older version of the network version and the folder is labeled Mouse Colony Net, rename the folder:
3) Inside the Folder containing the stand alone application there must be a file labeled Mouse Colony.USR.
In the case of the Network version, the Mouse Colony Net 4.1.1 (or 4.1.2) folder must contain a file labeled Mouse Colony Net.fp7.
If you renamed the folder or the file, you must change them back to the original designation.
4) Download and run the Update Installer.
5) Make sure that you are NOT running the previous version of Mouse Colony or Mouse Colony Net. If it is open, quit the program.
6) The Updater will ask you to enter the account and password for the previous version several times (10-12 times). It is advisable that you set up an automatic login, by checking "add to key chain", to avoid this.
7) Make sure that all your data is there. If everything is OK, you can trash the older version or just leave it there.
Known Problems
Question:
Is it OK to use Mouse Colony in a Windows XP environment?
Answer:
Yes, Mouse Colony can be used with Windows XP: however, the graphics and fonts are not displayed as clearly and sharply as in Windows Vista or Windows 7. We strongly recommend the use of Mouse Colony with Vista or Windows 7.
Question:
What should I do if a dialog window asking for the Serial Number shows up after clicking on register in the registration form inside Mouse Colony? Have I finished the registration process if I do not see the registration form on the Mouse Colony website?
During the Registration process, in some Windows version (i.e. XP) you may not see the registration form on our website. In this case, after filling out the registration inside Mouse Colony and clicking "Register" you will only see a Mouse Colony Dialog asking for the Serial Number. You must activate the browser window by clicking on your browser on the bottom tool bar. The browser should display the registration form on the Mouse Colony website. See a detail description of the registration process below.
Instructions for downloading and Registering Mouse Colony:
1) Download the appropriate version of Mouse Colony.
2) Open the program and create the first login.
3) The program will offer to complete the registration: follow the on screen instructions.
4) After filling out the registration form within the program and clicking register, Mouse Colony will open your browser and the registration form on the website will appear pre-filled with the information previously entered. If you see a window asking for the registration code or serial number but you do not see the the registration form in the browser (Internet Explorer, Firefox or Safari), select your browser from the bottom tool bar. Some versions of Windows (i.e. XP) occasionally fail to display the browser window. You may also have to accept the Certificates for our site.
5) Make sure that all the information in the form is correct, an click "Register".
6) The website will email you a Serial Number or Code.
7) Enter the Serial Number in the open dialog window or the next time you use Mouse Colony. If it is correct, you will see a message indicating that the correct Serial Number was entered.
Installation and Using Mouse Colony the first time
Question:
What is the difference between Mouse Colony and Mouse Colony Net?
Mouse Colony is a stand-alone runtime application. It will run on your computer by itself, without requiring any other software. It can be used on only one computer and cannot be accessed via a network.
Mouse Colony Net is a version of Mouse Colony that requires FileMakerPro to function. It must be installed on a single computer; however, it can be accessed by up to 5 remote computers through a network. FileMakerPro must be installed in both the computer that hosts Mouse Colony Net and in the client computers that want to access it via a network connection.
Although this version of Mouse Colony may seem initially more expensive due to the requirement of the separate purchase of FileMakerPro, it is significantly cheaper than buying 5 copies of the runtime version of Mouse Colony. Additionally, this network version allows the centralization of the mouse lines that a lab has, simplifying backups and eliminating the duplication of data.
Question:
What system versions are supported by Mouse Colony?
Answer:
Mouse Colony functions with Mac 10.4 and later, and Vista and 7. Although Mouse Colony can be used with Windows XP, the graphics and fonts are not displayed with the quality observed in later version of the Windows operating system.
Question:
Can I place the different files/folders that are inside the Mouse Colony main folder in different location on my computer?
Answer:
NO. If you do this Mouse Colony may not perform at all. This is the difference between a Runtime Solution, like Mouse Colony, and a regular software application. Keep the Mouse Colony Folder without making any changes.
Question:
Can I make an alias or short cut for Mouse Colony?
Answer:
Yes, in the Mac use from the Finder>File>Make Alias or Command-L, on a PC, create a shortcut by right-clicking and select “create shortcut”.
Question:
Can I use the same copy of Mouse Colony in more than one computer?
Answer:
No, Mouse Colony should be installed and will work in only one computer. However, you should make daily back ups.
Question:
Where should I place Mouse Colony in my computer?
Answer:
It is recommended that you place Mouse Colony in the Application or Programs folder.
Question:
What should I do to open Mouse Colony the first time?
Answer:
After downloading the application, a) Make sure you are connected to the internet
b) Double click on the application with the mouse Icon
c) You will be required to create an account with a unique User ID and Password
d) You will be offered to register (recommended) and/or purchase Mouse Colony; however, you can start using it without registering or purchasing for 90 days.
Question:
Can I transfer Mouse Colony to another computer after I register my copy?
Answer:
No, not until you have purchased the Permanent Access Key. If you have the full version, you must deactivate Mouse Colony in the original computer (Menu>Resources>Deactivate Mouse Colony). To reinstall it in another computer, copy the Mouse Colony Folder to the new computer. When you first open Mouse Colony in the new computer, the application will contact Mouse Colony and we will send you the reactivation key. Remember, you have 36 hours to enter the key before it expires.
Question:
Do I have to create the first colony when I activate Mouse Colony?
Answer:
No, you can choose to close the application. Next time you open Mouse Colony will ask you to create a New Colony.
Question:
What do I need to create a new colony?
Answer:
The colony name, Principal Investigator (PI), and Gene 1 name are required. You can always change the PI name, Gene names, and other information in the colony report page.
Question:
How do I enter the first animal?
Answer:
To enter the first animals of a new colony, click on New Record (or select Menu>Records>New Record). Follow the on screen instructions. You will need an ID for the mice, unless you use Auto ID, cage number/ID, Date. Although the rest of the information can be entered later, it is advisable to include coat color, tag, and date of birth (DOB).
Question:
Do I need to save the records after making changes?
Answer:
No, Mouse Colony automatically saves the changes once you click outside the modified field, select a new window, or switch to another module.
Question:
Why can’t I use the upper left red button to close a window in the Mac?
Answer:
Unfortunately, this button does not work in Runtime Solutions.
Question:
What is the difference between Quit and Close buttons?
Answer:
Quit will exit the application while Close will close the active window. However, if the only active window is the current one, Close will exit the application. Mouse Colony will ask you to confirm that you want to Close the only open window.
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Mouse ID
Question:
What is the difference between using Auto ID, Active-Colony and Active-Database?
Answer:
Auto ID generates the next correlative higher number as a Mouse ID. Active-Colony will take into account the highest Mouse ID in the active colony, while Active-Database will take into account the highest ID in the entire Mouse Colony database.
Question:
Is there an advantage to using Auto ID Active-Database over Active-Colony?
Answer:
Yes, using Active-Database has the advantage that there will not be 2 animals with the same ID even in independent colonies. This will avoid any possible mix ups. However, Mouse colony is designed to detect animals with the same ID within a colony, and when animals are transferred from one colony to the other. In other words, there is little chance of having 2 animals with the same ID in the same colony.
Question:
Can I alternate between Auto ID active and inactive (manual entry)?
Answer:
Yes, you can switch back and forth in any way that suits your needs.
Question:
How do I enter a new mouse in the colony?
Answer:
If the animal comes from another lab or is purchased, use the New Record function. However, if the animal was generated by a mating between mice in the colony, use the mechanism in the Mating module that creates Mouse ID records for every pup. This is important for many of the analysis tools in Mouse Colony. Additionally, this method is extremely fast and accurate.
Question:
Can I restore a record after deleting it?
Answer:
No, this is because mouse Colony automatically saves the records. It is a minor price to pay for the security of not loosing data.
Question:
How can I delete a group of animals?
Answer:
The safest way is one by one. However, if you can make a search that retrieves the animals you want to delete, and only those you want to delete, you can use the “Delete Found Records” under Menu>Records.
Question:
What do the little green mice located by some fields mean?
Answer:
They indicate that there is a Tip that can be viewed by pointing the cursor at the adjacent field and waiting a couple of seconds.
Question:
Can I modify the pull-down fields?
Answer:
Most pull-downs, such as coat color, tag, strain, etc, are customizable. You should modify them to suit your needs.
Question:
How do I transfer an animal to another colony within Mouse Colony?
Answer:
Just click “Colony Transfer” in the right navigation panel (bottom). A window requesting the necessary information will open. You must select from a preexisting colony. If you need a new colony, cancel, create the new colony and then, start the transfer again. The new colony window also displays in a pull-down (bottom) all the colonies with the corresponding genes that have been altered. This is helpful if you have many colonies or colonies with different mutations of the same genes (KO, knock-in, transgenic). The transfer process will leave a copy of the Mouse ID record in the original colony and create a duplicate in the new colony. During the transfer, Mouse Colony will determine if there is an animal with the same ID in the target colony, and will request that you enter a new ID if there is such a duplicate.
Question:
What is the purpose of keeping information for previous cages that housed a mouse?
Answer:
This is done as a safety mechanism in case a mistake is made. In this way one can track where the mouse was before.
Question:
What is the function of “This Mouse Mating Record at a Glance”?
Answer:
This part of Mouse ID provides information about previous matings for the current mouse. It shows partners and if the last mating, in the case of a female, is active (the pups box turns dark gray for an active mating with no pups yet, and gray with the number of pups if the mating is active and pups have to be weaned).
Question:
What is the benefit of just displaying the animals that are currently alive in the colony?
Answer:
This is a matter of personal preference. Some would rather see only the live animals, particularly, in a very large colony, while other would rather see all the animals, both live and deceased. Regardless of your preference, both options are just a click away. The “Showing” status is displayed in red letters on top of the Mouse ID box.
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Mating
Question:
What is the function of the “Duplicate Record” button?
Answer:
This button was designed as a shortcut in case this is a continuous mating. Since Mouse Colony requires a fresh mating record for each litter, the “Duplicate” function can be used to set up the next mating after weaning. The only information that the user has to enter is the new Mating Date.
Question:
If I change the settings of Auto ID in the mating form would I affect the settings in the Mouse ID form?
Answer:
Yes, this action affects this function in the entire program.
Question:
How do I see or retrieve the Mouse ID record for a Pup?
Answer:
Click on the “Pup #” and the Mouse ID form will show up in a new window.
Question:
What happens if I change my mind when I am assigning IDs to the pups and want to use a different ID? Would this affect the Mouse ID?
Answer:
There is no Mouse ID record created until you actively click on “Create R’crd”. Therefore, you can do any changes to the Pup ID using the Clear (Clr) button and the Auto ID set to active or inactive. However, once you go through the process of creating a Mouse ID record, if you make changes in the Pup ID or Sex you will have to correct the Mouse ID record manually. Similarly, if you decide that you do not need the record, you have to delete it in the Mouse module.
Question:
What is the function of the Wean check box and Cause of Death for the pups?
Answer:
These fields are optional. A check in the Wean box just tells you that the pup was alive and weaned. We recommend using the empty Wean Box and Cause of Death in case you have a Pup that died before weaning and you decide not to create a Mouse ID record for it. In this way, you have an idea of what happened to it.
Question:
What is the difference between the Predicted Wean Date and Actual Wean Date?
Answer:
The Predicted Wean Date is automatically generated once you enter the delivery date. It will also show up in the Mating Status box in Cage Inventory and Scheduler as a reminder that pups have to be weaned. When you actually wean the pups, you should enter the Actual Wean Date, which will be also used as a source for the automatic entry of the Tail Snip Date in the Mouse ID module.
Question:
Why are MEF Date, E= and Approx Delivery empty?
Answer:
These are calculated dates that will only show up if you enter the Plug Date. This information will also show up in the Mating Status box in the Cage Inventory and Scheduler.
Question:
What is the Mating Check Box (upper right) used for?
Answer:
This is a piece of information that Mouse Colony uses to determine that the mating is active. This is important to obtain a list of Current Matings and for the information to be displayed in the Mating Status box. Although the user can check and uncheck this box at will, Mouse Colony takes care of it most of the time. For example, it includes the check when the mating is created and erases it when Pups are weaned or the mating is terminated. However, most of this “updating” is done when Mouse Colony is launched. Therefore, if you have kept Mouse Colony opened for several days the information may not be up to date.
Question:
Can I correct the Stud or Dam information?
Answer:
Yes, but be careful because this cannot be undone. Mouse Colony will warn you when you are changing this information.
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Phenotype
Question:
How do the Phenotype pull-downs work?
Answer:
The pull-downs on the left have been assigned to cover some common phenotypes, yet, they can be customized to your needs. To customize, go to the “Edit” option at the bottom of the list and select it. A window with a list will show up. Make all the changes you want and then, click OK. Now you can then select from your new options.
The pull-downs on the right side are completely customizable. You can select the Field Description by clicking on it and selecting “Edit” or “Other” (“Other” does not include the new selection permanently in the list).
Question:
How do the Pathology and Lab reports work?
Answer:
There are 2 ways you can utilize these fields to store information:
a: you can copy and paste any information in the box.
b: You can use the Insert and Remove options. When you click on “Insert” a window opens requesting that you localize in your hard disk the document to be inserted (make sure that the “Store only a reference to the file” box is checked). In reality, you are establishing a link to the file, which will not be stored in Mouse Colony. After selecting “Open”, you will see the title of the document in the first available box in Path/Lab report. If you double click it, the document will open. Importantly, Mouse Colony will remember where the document is, but it will not find it if you change its location after the link was established. For this reason, the Mouse Colony folder contains a Report folder where you can place all the documents of this type and not worry about losing the link.
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Experimental Data
Question:
What is the “Include in analysis” area for?
Answer:
This function allows you to select those animals you want to include in reports for data held on this page. There are 2 options: you can select the current animal using the check box, or several by clicking on the appropriate button. This will open a window with a list of all the animals that have records in the Experimental Data module. You can now select all the animals you want to include in the analysis. Keep in mind that the fact that all the animals with Exp. Data records are displayed does not mean that they all have data in the same parameters analyzed. For example, some animals were used for experiments that assess parameters 1 and 2, while others hold data for experiments that assessed parameter 3. Nevertheless, if an Experimental Data record does not contain data for the parameter selected for analysis, it will be ignored.
Question:
How do the parameters, units, and Age/Other work?
Answer:
For each individual colony you can store numerical data for up to 6 separate parameters of your choice. These parameters are global for the colony. In other words, if you select as parameter 1, glucose in blood, and as parameter 2, albumin in urine, all the Experimental Data records will show blood glucose and albumin in urine as parameters 1 and 2, regardless of whether you assess them in all the animals or not. The same is valid for the Units and the Age or time interval at which the parameter was evaluated. For example, it is likely that you will have a scenario in which parameter 1 and 2 hold data for animal IDs 32, 34, 35, 54, and 56; while parameter 3 and 4 hold data for animals 61, 62, 63, and 66. At the present time, Mouse Colony can only carry 6 parameters. However, if your needs exceed this capacity please let us know so future versions will address this issue.
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Experimental Design
Question:
How do I include an animal in an experiment?
Answer:
Just type the Mouse ID in the empty box and hit tab, return or enter. The information in the other fields will be populated automatically. If the Mouse ID does not exist, the Age(m)/Dead will display 0.0 and the other fields will be empty. To delete an animal, use the appropriate delete button.
Question:
Can I sort the list?
Answer:
Yes, the list can be sorted by Mouse ID and Genotype, by clicking on those titles.
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General Questions
Question:
Why can’t I access some fields to change the data?
Answer:
Some information is not held in the module where it is currently displayed, and the ability to access it has been blocked to avoid involuntary mistakes. For example, if you are in the Phenotype, Mating or other modules and want to edit the genotype or age for an animal, the fields are blocked, because this information is coming from the Mouse ID record. Thus, the genotype should be corrected there. In the case of the Age, the information is held in the Mouse ID record too and additionally, is the product of a calculation that includes the DOB. Therefore, to change the Age you must correct the DOB in the Mouse ID module.
This also applies to several other fields whose data are generated by a calculation, or whose information is protected.
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