IMPORTANT POINTS for both the older version (5.03) and the new version (6.05)

Update 12/17/10: A new version of the Case It simulation is now available on the download page (v6.05). This version fixes several bugs in v6.04, two of which were significant. One bug in v6.04 occurred when bands were clicked so that the sequences could be added to the Export Field, e.g. for tree-building. The sequences were correct, but the names of the sequences that appeared in the Export Field were incorrect. This bug has been fixed. In addition, v6.04 did not allow for files with more than 990 DNA sequences to be loaded, but this is now possible (only the first 990 bands can be displayed on gels, however, even with the new version). In addition, an important new feature has been added to v6.05 – it is now possible to make the band widths narrower to more easily distinguish bands on a gel. Whenever a gel is loaded, two small buttons now appear above the gel to make them wider or narrower.

Update 12/21/10: Case It v6.05 works with either MEGA4 or MEGA5 bioinformatics software, available from the MEGA web site. After downloading from this site, place either MEGA4.exe or MEGA5.exe inside the ‘MEGA’ folder, located inside the ‘Case It v6′ folder. The Case It tutorial pages do not mention MEGA5.exe, but that version will work fine with Case It v6.05.

Do NOT download MEGA4.1 beta – it does not work properly with Case It v6.05. That executable has the name MEGA4x1.exe.

Note: Once MEGA is opened by Case It, the name of the MEGA executable in the ‘MEGA’ folder will be automatically changed to ‘MEGA4.exe’, regardless of which version was placed in the folder. This file name change is necessary for Case It to recognize MEGA, but does not affect functionality.

1. When saving photos of gels, blots, etc., make sure there is a ‘.jpg’ suffix at the end of filennames (e.g. ‘photo1.jpg’, ‘ELISAphoto.jpg’). If the suffix is deleted or does not appear automatically (see below), the resulting file will not save properly. Click here for an example.The default for the Windows operating system may be to hide filename extensions (suffixes), and if this is the setting for your computer the .jpg suffix will not appear automatically when you attempt to save photo images. If this is the case, you must manually append the .jpg suffix to the ends of filenames prior to saving. To avoid this, change the preferences (e.g. in Windows 7: My Computer -> Organize -> Folder and search options -> ‘View’ tab -> uncheck ‘hide extensions for known file types’),

Also, it is a good idea to always rename photos when you save them. If you do not and a file with the same name already exists, you will get a ‘file exists – do you want to replace it?’ message. If you answer ‘yes’, the file may not save properly, so to make sure rename it before saving to avoid any problems.

2. Case It Investigator is no longer being updated, so for access to all cases use the online Resource Manual instead.

3. There is a fundamental difference between PCR‘ and 96-well PCR. The former is used to generate PCR products for certain genetics disease cases, whereas the latter is used primarily to determine viral load for some of the protein-based cases such as HIV (it is also used in ‘Option B’ of the STD case).

4. By default, the ‘genomic smear’ option is ‘on’. This means that for DNA files ending with a .gen suffix (e.g. the Sickle Cell case), genomic smears appear automatically when a gel is run (the transparency of the smear can be adjusted by a slider). If you prefer, you can turn the genomic smear feature off - click here to for more information on the genomic smear.

5. Bug alert (v5.03 only)After taking a gel photo, use the ‘Go Back’ button on the Gel Photo Screen to return to where you were previously. Do not use the buttons on the navigation bar at the bottom of this screen to do this. Click here for an example.

6. If you experience jerky video playback of the HIV cases when using Investigator v2 (or the online videos via the ‘access cases’ link of the Case It home page), you will need to change the Quicktime settings of Windows XP. Click this link for more information, including a screen shot.