FORUMCategory: BioinformaticsNo command line experience
dmorais Staff asked 3 years ago



Is it possible to do Bioinformatics analysis without command line experience?
What are the options offered by Compute Canada?

2 Answers
Best Answer
jflucier Staff answered 3 years ago



Although most the software used in bioinformatics are command line based there are several platforms that tries to create a graphical interface to these software.

One of most well known platform is called Galaxy (https://usegalaxy.org/). This platform was developed  by the PennState University team and has been adopted by many bioinformaticians. Galaxy creates a web interface around all main tools used in bioinformatics and allows the users to create complex workflow by dragging, dropping and connecting boxes in its graphical interface. Users are not required to know any command line to create the workflows.

Compute Canada supports and hosts a platform called GenAP (https://www.genap.ca/) which offers web based graphical tools. One of such tools is Galaxy. The Galaxy on GenAP is connected to Compute Canada clusters and the jobs run transparently on those supercomputer without the need of any intervention from the user.
Anyone with a Compute Canada account can use GenAP.

jstafford answered 3 years ago



Yes and no.

There are platforms like Galaxy and GenAP (an improved, secure version of Galaxy that runs on Compute Canada systems) available that make it possible to point-and-click your way through an entire analysis without ever having to use the command line.
However, I personally find it easier to use the command line (tools like Galaxy throw all the options for bioinformatics tools at you at once, which can make it intimidating to get started), and it’s much easier to see what’s actually “going on” behind the scenes. If you’re curious about how to get started, the Software Carpentry organization has a great set of tutorials you can use to teach yourself in an hour or three: http://swcarpentry.github.io/shell-novice/

jrosner Staff replied 3 years ago

There are also many in-person software carpentry workshops offered across the country, some of which are presented by Compute Canada. You can find information on these at https://software-carpentry.org/workshops/
Also check our own News and Events page for training sessions