Calendar:HD-2011/2011-7-27

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Proportal Project

1. For the microarray experiments Nitrogen Limitation and Light Sensing: Check if all of the genes have 0 in the mean(T) and mean(C) fields in each experiment. If they do, Alter the mean(T) and mean(C) fields to read "NA" or some other entry indicating that there is no data for these fields.

Solution:

c_mean in data_affydata table is allowed to be null, so just set 0 back to null,

   update data_affydata set c_mean = null where c_mean = 0;

t_mean is not allowed to be null in the table, first change its property to use null as default, then set 0 back to null,

   update data_affydata set t_mean = null where t_mean = 0;

To display a null value retrieved from DB, Django uses "None", which is to be changed to "NA". Modify ${OCEAN}/templates/expression/probeset.html as follows, from,

    e.t_mean
    e.c_mean

to,

    e.t_mean|default_if_none:"NA"
    e.c_mean|default_if_none:"NA"

2. Link each Genbank ID on the Genome page for each genome to it's Genbank web page so users can download the genome if they are interested.

Solution:

Modify the page: ${OCEAN}/templates/genome/genome.html

   GenBank ID: <a class="external" href="http://www.ncbi.nlm.nih.gov/nucleotide/Template:Genome.gb id">Template:Genome.gb id</a>

3. On the External Links page http://proportal.mit.edu/links/, add a link to

   VirMic website: http://www.cs.technion.ac.il/~itaish/VirMic/

Solution

   Modify ${OCEAN}/templates/basics/links.html

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