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Insyght, a conserved synteny - homolog browser
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Insyght, a conserved synteny - homolog browser
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8726
Feature
Closed
Normal
Pipeline rev 471 ; organize molecules into living organisms using assembly info
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:01 PM
8725
Feature
Closed
Normal
adapt to database schema rev 2: additional links and info from ncbi, add columns for convenience when querying the database (avoid cross tables querying)
Thomas Lacroix
Thomas Lacroix
08/25/2017 12:00 PM
8721
Feature
Closed
Normal
Pipeline rev 471 ; add bdlink info on ncbi assembly id and accession, etc... for the table organisms (trough element accnum)
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:44 AM
8720
Feature
In Progress
Normal
Pipeline rev 471 ; avoid non essential redondant data, decrease total database size by around 2 fold
Thomas Lacroix
Thomas Lacroix
08/28/2017 10:33 AM
8718
Feature
Closed
Normal
Pipeline rev 471 ; created script download_genome_files_from_ncbi.pl
Thomas Lacroix
Thomas Lacroix
08/25/2017 11:33 AM
8706
Feature
Closed
Normal
Taxonomic browser, core / dispensable genome functionality : upon header selection, select all nodes in appropriate categories
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:55 AM
8704
Feature
Closed
Normal
Taxonomic browser, core / dispensable genome functionality : checkbox to select multiple genomes / nodes. Keyboard support.
Thomas Lacroix
Thomas Lacroix
08/25/2017 10:36 AM
6924
Feature
Closed
Normal
[Feature] PIPELINE: script integrate_taxo_data.pl : automatic management of the integration of the data for the tables micado.taxo and micado.taxo_names
Thomas Lacroix
Thomas Lacroix
09/07/2016 02:38 PM
6923
Feature
Closed
Normal
PIPELINE: script count_inserted_data.pl: utility to follow the data that have been inserted in the database
Thomas Lacroix
Thomas Lacroix
09/07/2016 02:38 PM
6922
Feature
Closed
Normal
PIPELINE: possibility to use Plast instead of Blast (Plast is ~5X faster than Blast)
Thomas Lacroix
Thomas Lacroix
09/07/2016 02:35 PM
6505
Feature
Closed
Normal
utilities to convert error report into stack trace with symbolMap file
Thomas Lacroix
Thomas Lacroix
06/03/2016 03:13 PM
6504
Feature
Closed
Normal
show info on PValue in ortholog table
Thomas Lacroix
Thomas Lacroix
06/03/2016 03:13 PM
6503
Feature
Closed
Normal
gene filter on PValue score if applicable
Thomas Lacroix
Thomas Lacroix
06/03/2016 03:13 PM
6502
Feature
Closed
Normal
over-representation (P-Value Fisher's Exact test) of orthologs whithin phenotype+ organisms in comparison to phenotype- organisms
Thomas Lacroix
Thomas Lacroix
06/03/2016 03:11 PM
6142
Feature
Closed
Normal
Better management of info panel: When we click on synteny info, we want to keep this disclosure panel open as we click on other synteny
Thomas Lacroix
Thomas Lacroix
04/06/2016 02:43 PM
6141
Feature
Closed
Normal
switch to no color for symbols q_gene_insertion or s_gene_insertion in genomic orga view when expanding a q or s insertion region
Thomas Lacroix
Thomas Lacroix
04/06/2016 02:43 PM
6136
Feature
Closed
Normal
direct link to GO, UniParc, PDB in the gene info panel (if available as annotation)
Thomas Lacroix
Thomas Lacroix
04/06/2016 02:41 PM
6134
Feature
Closed
Normal
different shade of grey to represent the alignment based on its %identity (>85% identity = black, between 50 to 85% = dark grey, etc.)
Thomas Lacroix
Thomas Lacroix
04/06/2016 02:40 PM
6133
Feature
Closed
Normal
Added support for url parameters: referenceSpecies, referenceStrain, referenceSubstrain, referenceAccnum, referenceGeneSetNames, referenceGeneSetLocusTag
Thomas Lacroix
Thomas Lacroix
04/06/2016 02:39 PM
6132
Feature
Closed
Normal
report 5 last history tocken in bug reporting tool
Thomas Lacroix
Thomas Lacroix
04/06/2016 02:30 PM
5832
Feature
Closed
Normal
PIPELINE: insertion of taxonomic data relevant to the dataset at hand only to save disk space.
Thomas Lacroix
Thomas Lacroix
02/09/2016 11:16 AM
5831
Feature
Closed
Normal
PIPELINE: support of .gbk files generated by prokka.
Thomas Lacroix
Thomas Lacroix
02/09/2016 11:15 AM
5830
Feature
Closed
Normal
PIPELINE: blast "organism vs all" instead of "element vs element" to be able to handle draft genomes with many contigs.
Thomas Lacroix
Thomas Lacroix
02/09/2016 11:15 AM
5829
Feature
Closed
Normal
PIPELINE: script to automatically correct elements types and group them into organisms.
Thomas Lacroix
Thomas Lacroix
02/09/2016 11:15 AM
5828
Feature
Closed
Normal
PIPELINE: option to recover from failure (computer shutdown, ...) without starting over for resources-consuming steps (blast and find synteny).
Thomas Lacroix
Thomas Lacroix
02/09/2016 11:14 AM
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