Online teaching with CodonCode Aligner

[Peter Richterich]

The COVID-19 pandemic has prompted many universities to switch to online teaching. CodonCode Aligner is widely used in teaching; this post explains options for using CodonCode Aligner for online classes.

Option 1: Trial and demo licenses
Everyone who installs and uses CodonCode Aligner for the first time automatically gets a 30-day fully functional trial. The trial allows the use of all functions in CodonCode Aligner, including saving, export, and printing. For online classes where CodonCode Aligner is used for less than 30 days, for example in just one of several modules, letting student use the trial version can be a viable options. We suggest to add instructions for students to delay installing and using CodonCode Aligner until the relevant part of the online class starts.

For classes that need to use CodonCode Aligner for longer periods, or where students have used CodonCode Aligner in the past, an alternative option is to use the demo mode in CodonCode Aligner. After the initial 30-day trial period, CodonCode Aligner automatically reverts to demo mode. Most functions in CodonCode Aligner are still available in demo mode, but saving and exporting functions are disabled. For classes where students need to deliver proof that work has been done, we suggest to accept screen shots rather than exported files. When CodonCode Aligner is used as one of multiple programs in a multi-step bioinformatics process, the input files for subsequent steps can be made available to students separately, for example on a web or ftp server.

Using trial and demo licenses has significant advantages. Courses can be set up without any need to contact CodonCode about licenses for the course; no License Server needs to be set up for the class; and potential technical problems with access to the License Server are avoided.

Option 2: License Server Access through VPN
For on-campus classes where CodonCode Aligner is used in a lab setting, a typical approach is to set up a License Server for the class. This approach can also be used for online classes, but only if the university already has a system setup to access the internal university network through VPN or a similar system (if in doubt, please check with your computer support experts). This setup requires to install the Aligner License Server on a computer that students can access through the university VPN, and to request a temporary license for the Aligner License Server for the duration of the class. With this setup, some students may experience problems in accessing the License Server due to anti-virus software, firewalls, or similar issues.