Organisms on Teaching server

[jvanheld]

The Teaching Web server only displays a handful of organisms even though several thousands of genomes are available on the command line.

This was a choice done earlier for didactic purposes. However it does not allow to use the phylogenetic tools.

We should revise this policy and decide whether we want or not to support phylogenetic tools on the Teaching server. If yes, we need to enable either all the organisms, or to display an extended list of organisms.

[jvanheld]

The selection of organisms displayed on the Web server is defined in rsat-code/perl-scripts/lib/RSAT/OrganismManager.pm.

Here is the relevant chunk of code.

    } elsif ($group_specificity eq "Plants") {
      push @specific_taxa, "Viridiplantae";

    } elsif ($group_specificity eq "Teaching") {

      ## Define a list of model organisms                                                                                                                                                           
      my @model_organisms = qw(                                                                                                                                                                     
                             Arabidopsis_thaliana.TAIR10.29                                                                                                                                         
                             Bacillus_subtilis_168_uid57675                                                                                                                                         
                             Drosophila_melanogaster                                                                                                                                                
                             Escherichia_coli_GCF_000005845.2_ASM584v2                                                                                                                              
                             Homo_sapiens_GRCh37                                                                                                                                                    
                             Homo_sapiens_GRCh38                                                                                                                                                    
                             Mus_musculus_GRCm38                                                                                                                                                    
                             Saccharomyces_cerevisiae                                                                                                                                               
                            );

      ## Check that each organism is properly instaled.                                                                                                                                             
      foreach my $org (@model_organisms) {
        if ($main::supported_organism{$org}) {
          push @selected_organisms, $org
        }
      }
    } elsif ($group_specificity eq "None") {
      @selected_organisms = &get_supported_organisms();

[morganeTC]

Hi @jvanheld,

I think your analysis is wise : because the phylogenetic tools add a lot of organisms to the server, it makes the interest of having the teaching server less, and this does not help the novice user.

If @amedina-liigh agrees, we could remove the phylogenetic tools from the Teaching server, and keep just the minimal organisms, which I think is OK is the chunk of code posted by @jvanheld

[jvanheld]

Hi @morganeTC

An alternative (that I would favour) would be to support phylogenetic analyses on the Teaching server, but with a carefully selected subset of species

• for Bacteria
• for Fungi (with a separate demo)

I think that it would be important to support the teaching of phylogenetic methods, which are quite original. I recognise that they are probably not as popular as peak-motifs or matrix-clustering (for example), but they represent an originality of RSAT compared to other software suites for the analysis of cis-regulatory sequences, so it would be worth improving their visibility.

But if this introduces too much complexity we can also hide these tools on the server.

Cheers

Jacques

[morganeTC]

Hi @jvanheld,

My thinking is that these tools add a lot of organisms in the list to choose from, and the whole point of the teaching server is to provide less organisms for naive users.

Maybe a way to meet would be to link the menu to either the Prokaryote or the Fungi server. It would be transparent for the user, would simplify the genomes maintenance (no need to maintain all these genomes on the teaching server), and limit the number of visible genomes for the novice users.

What do you think ?

[amedina-liigh]

Hi

Currently, the display shows only the set of model organisms, but behind organisms related to the bacteria in this set exist so the orthologous genes can be retrieved, from what I remember this works fine.

Takes space but does not give the users many more options, which I think is ok for the move user as Morgane said.

Cheers

Ale

---

Alejandra Medina Rivera, PhD Laboratorio Internacional de Investigación sobre el Genoma Humano Universidad Nacional Autónoma de México, Campus Juriquilla Blvd. Juriquilla 3001, Juriquilla, 76230 Santiago de Querétaro, QRO. Mexico @.***

On 22 Feb 2022, at 9:58, Morgane Thomas-Chollier @.***> wrote:

Hi @jvanheld https://github.com/jvanheld,

My thinking is that these tools add a lot of organisms in the list to choose from, and the whole point of the teaching server is to provide less organisms for naive users.

Maybe a way to meet would be to link the menu to either the Prokaryote or the Fungi server. It would be transparent for the user, would simplify the genomes maintenance (no need to maintain all these genomes on the teaching server), and limit the number of visible genomes for the novice users.

What do you think ?

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[morganeTC]

Ha OK ! i did not realise this is the way it works (sorry). Then we can keep it like it used to be.

[jvanheld]

OK, I close this issue