CERF Plugins Descriptions

ABI Trace Viewer

The ABI Trace Viewer plugin will render any .ab1 sequence trace file as a pherogram, which users can scroll through directly on the notebook page to see the specific peaks for each residue in the sequence.

Clustal Alignment Viewer

The Clustal Alignment Viewer plugin will render any .aln sequence alignment file as an inline alignment, which users can scroll through directly on the notebook page to see the alignment for each position in the sequence.
(Please note: the .aln plugin is currently not working with the new version of CERF 3.5 please let us know if it's of interest to get this fixed.)

JMol Molecular Structure Viewer

The JMol Molecular Structure Viewer plugin will render a variety of molecular structure file types (including .mol and .pdb) as inline 3-D views which the user can interact with by clicking and dragging to rotate the display.

Plain Text Viewer

The Plain Text viewer will display any simple text file (.txt or .rtf) inline, so that rather than seeing a file icon for this type of file the user will see the actual contents of the file directly inline.

Genbank Sequence Viewer

The Genbank Sequence Viewer plugin will parse any Genbank sequence file (.gb or .gbk) and display it as a visual sequence map. Various elements and tracks will be parsed out and displayed, and the user can zoom in and out, with the ultimate resolution at the level of displaying the actual sequence data.

Please contact help-eln@bmi.cchmc.org if you there are other file types that you would like to see visualized directly in CERF.

Need Help?

For technical assistance with other research software, email software@bmi.cchmc.org. For basic desktop support or assistance with clinical information systems, call the Cincinnati Children's Service Desk, 513-636-4100, or visit the Information Services CenterLink site. UC employees should call the UCit Help Desk, 513-556-HELP.

A note about UCit software

UC researchers are served with desktop software by UCIT. In many cases this software is licensed specifically to UC employees only (i.e., people who receive paychecks from UC) or must be run on UC-owned or controlled equipment, making it inaccessible to Cincinnati Children's personnel. Please make sure you read the license agreement carefully before you use UC software.

Faculty and students of UC are eligible to purchase software from UC. However, when purchasing from UC, the license agreement states that the software can be installed only on your personally owned or UC-owned computer and not on machines owned by other institutions. Since Children’s Hospital is a separate entity from UC, installing software purchased from UC on CCHMC owned computers is a violation of that license agreement. There is a difference in the price of software purchased from Biomedical Informatics at Children’s Hospital versus from the UC Bookstore. This difference is because UC qualifies for the educational discount whereas Children’s Hospital does not. Although Cincinnati Children’s Hospital is affiliated with UC, we are not a degree granting institution. We are a hospital, therefore we only qualify for the healthcare/non-profit discount.