Visualize clustalW alignment on public galaxy

Question: Visualize clustalW alignment on public galaxy

2.8 years ago by

Philipp.rathert • 30

Germany

Philipp.rathert • 30 wrote:

Dear all,

I would like to demonstrate galaxy to my bachlor students in a basic biochemistry course I am teaching.

The first and easiest exercise should be a basic clustalW alignment of a couple of sequences using clustalW.

Unfortunately I haven't found a good way to present these alignments on the server. I saw that there are some Java visualizations possible (e.g.BioJS) to implement but it seems these are not present on the public galaxyproject.org server. We have alocal instance where I could try to install these, but the students are not integrated into our network.

Maybe somebody knows about an open server where biojs is installed or has another way of presenting a clustalW alignment in a more graphical way so students like it...

Thanks a lot,

Philipp

visualization clustal • 733 views

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modified 2.8 years ago • written 2.8 years ago by Philipp.rathert • 30

2.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It sounds as if you plan to do more than demonstrate the tool (which could be done from your server without the students directly accessing it with their own accounts).

One good option is to use a Cloudman Galaxy for teaching purposes. AWS offers grants for education and this is the choice most instructors use, including the Galaxy Training Network. More details:
https://wiki.galaxyproject.org/BigPicture/Choices
https://wiki.galaxyproject.org/Teach

Using the public Main Galaxy instance at http://usegalaxy.org is not recommended for teaching purposes. If there is a large surge in exact activities from a single location, this can impact the entire server for everyone else using it around the world. This will lead to the jobs and accounts undergoing immediate suspension to protect the normal flow of work.

Hopefully the cloud works out for you, Jen, Galaxy team

ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

2.8 years ago by

Philipp.rathert • 30

Germany

Philipp.rathert • 30 wrote:

Hi Jennifer,

I didn't think about this, but you are totally right. Maybe i find a way to give the students access to my local instance, where I have more control.

Otherwise i go for the cloud option... Thanks a lot.

However, this does not solve the visualization question.

Anybody having a good tool for that in mind?

ADD COMMENT • link modified 2.8 years ago • written 2.8 years ago by Philipp.rathert • 30

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