Redmine@MIGALE

09/15/2017

10:32 AM Insyght, a conserved synteny - homolog browser Insyght_VM_standalone_user_guide_2-0-1.pdf

Thomas Lacroix

09/14/2017

03:41 PM Insyght, a conserved synteny - homolog browser Wiki edit: Release_notes_on_public_dataset (#6)

Thomas Lacroix

03:36 PM Insyght, a conserved synteny - homolog browser Public dataset: 2692 complete bacteria from Ensembl

Available here: http://genome.jouy.inra.fr/Insyght_2692_complete_bacteria/
For more details see the [[release no... Thomas Lacroix

09/06/2017

08:34 AM Insyght, a conserved synteny - homolog browser Wiki edit: How_To_Insyght_standalone_virtual_machine (#9)

Thomas Lacroix

08:33 AM Insyght, a conserved synteny - homolog browser Wiki edit: How_To_Insyght_standalone_virtual_machine (#8)

Thomas Lacroix

09/05/2017

02:49 PM Insyght, a conserved synteny - homolog browser Wiki edit: Requirements_for_Insyght's_standalone_virtual_machine (#4)

Thomas Lacroix

02:26 PM Insyght, a conserved synteny - homolog browser Wiki edit: Requirements_for_Insyght's_standalone_virtual_machine (#3)

Thomas Lacroix

08/28/2017

11:29 AM Insyght, a conserved synteny - homolog browser Web application rev 526

See the [[Release notes on web application]] Thomas Lacroix

11:22 AM Insyght, a conserved synteny - homolog browser Insyght's standalone virtual machine v2.0

A virtual machine (VM) allows for private analysis. Users can customize which genomes to compare, the blast parameter... Thomas Lacroix

11:10 AM Insyght, a conserved synteny - homolog browser Wiki edit: Guide_to_Insyght's_virtual_machine (#3)

Thomas Lacroix

11:09 AM Insyght, a conserved synteny - homolog browser Wiki edit: Release_notes_on_automated_install_recipes_VM (#1)

Thomas Lacroix

11:09 AM Insyght, a conserved synteny - homolog browser Wiki edit: Release_notes_on_database_schema (#1)

Thomas Lacroix

11:08 AM Insyght, a conserved synteny - homolog browser Wiki edit: Release_notes (#7)

Thomas Lacroix

11:06 AM Insyght, a conserved synteny - homolog browser Wiki edit: Release_notes_on_standalone_virtual_machine (#5)

Thomas Lacroix

11:06 AM Insyght, a conserved synteny - homolog browser Wiki edit: Release_notes_on_pipeline (#4)

Thomas Lacroix

11:00 AM Insyght, a conserved synteny - homolog browser Wiki edit: Release_notes_on_web_application (#10)

Thomas Lacroix

10:55 AM Insyght, a conserved synteny - homolog browser Wiki edit: Release_notes_on_web_application (#9)

Thomas Lacroix

10:33 AM Insyght, a conserved synteny - homolog browser Feature #8720 (In Progress): Pipeline rev 471 ; avoid non essential redondant data, decrease total database size by around 2 fold

Thomas Lacroix

08/25/2017

12:09 PM Insyght, a conserved synteny - homolog browser Amélioration #8732 (Closed): Pipeline rev 471 ; improve the accessibility of the VM by simplifying the pipeline into 1 master script (keeping error handling proper)

Thomas Lacroix

12:08 PM Insyght, a conserved synteny - homolog browser Bug #8731 (Closed): Pipeline rev 471 ; check_for_element_types_and_reorganize_elements_into_organisms.pl want to update already updated element type from previous run

Thomas Lacroix

12:07 PM Insyght, a conserved synteny - homolog browser Bug #8730 (Closed): Pipeline rev 471 ; ObjectElement.pm -> setaccession -> deal with multiple digit in accnum name, do not file prefix and postfix

Thomas Lacroix

12:07 PM Insyght, a conserved synteny - homolog browser Amélioration #8729 (Closed): Pipeline rev 471 ; check_db_consistency.pl : test that element lenght = sequence lenght

Thomas Lacroix

12:06 PM Insyght, a conserved synteny - homolog browser Amélioration #8728 (Closed): Pipeline rev 471 ; check_db_consistency.pl : test that genes.residues = micado.prot.feat.residues

Thomas Lacroix

12:05 PM Insyght, a conserved synteny - homolog browser Amélioration #8727 (Closed): Pipeline rev 471 ; script download_from_ncbi.pl : add the option -restrict_to_list_taxon_id_and_subnodes

Thomas Lacroix

12:00 PM Insyght, a conserved synteny - homolog browser Feature #8725: adapt to database schema rev 2: additional links and info from ncbi, add columns for convenience when querying the database (avoid cross tables querying)

-> additional info in table organisms: NCBI_assemblyaccession_IT, NCBI_assemblyname_IT, NCBI_lastupdatedate_IT, NCBI... Thomas Lacroix

11:53 AM Insyght, a conserved synteny - homolog browser Feature #8725 (Closed): 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

11:54 AM Insyght, a conserved synteny - homolog browser Feature #8726 (Closed): Pipeline rev 471 ; organize molecules into living organisms using assembly info

Thomas Lacroix

11:47 AM Insyght, a conserved synteny - homolog browser Amélioration #8724 (Closed): Pipeline rev 471 ; Task_add_entry (insert of primary data) : Make the script more resilient to errors and re-run, faster (generator and integrator)

Thomas Lacroix

11:46 AM Insyght, a conserved synteny - homolog browser Amélioration #8723 (Closed): Pipeline rev 471 ; fill_gene_entry.pl : generate data for table gene directly instead of after schema micado is filled w/ data

Thomas Lacroix

11:45 AM Insyght, a conserved synteny - homolog browser Amélioration #8722 (Closed): Pipeline rev 471 ; fill_gene_entry.pl : infer correct type directly here instead of subsequent script

Thomas Lacroix

11:44 AM Insyght, a conserved synteny - homolog browser Feature #8721 (Closed): Pipeline rev 471 ; add bdlink info on ncbi assembly id and accession, etc... for the table organisms (trough element accnum)

Thomas Lacroix

11:43 AM Insyght, a conserved synteny - homolog browser Feature #8720 (In Progress): Pipeline rev 471 ; avoid non essential redondant data, decrease total database size by around 2 fold

script TOOLS/remove_mirror_data.pl while waiting to change Align Thomas Lacroix

11:34 AM Insyght, a conserved synteny - homolog browser Amélioration #8719 (Closed): Pipeline rev 471 ; improved analyse_stats_db.pl

Thomas Lacroix

11:33 AM Insyght, a conserved synteny - homolog browser Feature #8718 (Closed): Pipeline rev 471 ; created script download_genome_files_from_ncbi.pl

helper script to download the genome file from ncbi ; the following options have been implemented : -NCBI_ASSEMBLY_SU... Thomas Lacroix

11:30 AM Insyght, a conserved synteny - homolog browser Amélioration #8717 (Closed): Pipeline rev 471 ; fill_gene_entry.pl : add Locus_tag directly in table genes

Thomas Lacroix

11:25 AM Insyght, a conserved synteny - homolog browser Amélioration #8716 (Closed): Pipeline rev 471 ; Task_add_entry : cleaner option -GENOME_FILES_FORMAT

Thomas Lacroix

11:23 AM Insyght, a conserved synteny - homolog browser Amélioration #8715 (Closed): Pipeline rev 471 ; Task_add_entry : added option -SKIP_NEIGHBOR_INFO as this info is not useful

Thomas Lacroix

10:58 AM Insyght, a conserved synteny - homolog browser Bug #8714 (Closed): Navigation jumps when moving with >> or << in ortholog table or genomic organisation

Thomas Lacroix

10:58 AM Insyght, a conserved synteny - homolog browser Bug #8713 (Closed): Compared organisms not sorted correctly for scope Whole organism

Thomas Lacroix

10:57 AM Insyght, a conserved synteny - homolog browser Bug #8712 (Closed): Synteny symbol not displaying correct number of pairs, it was missing gene mismatch and insertion

Thomas Lacroix

10:57 AM Insyght, a conserved synteny - homolog browser Bug #8711 (Closed): When transfering q genes from synteny to ortholog table view, s_insertion genes were transeferd as well

Thomas Lacroix

10:57 AM Insyght, a conserved synteny - homolog browser Bug #8710 (Closed): Error when the database was empty. Redirect user to use the guide to add data or check out http://genome.jouy.inra.fr/Insyght/ to test functionalities

Thomas Lacroix

10:56 AM Insyght, a conserved synteny - homolog browser Amélioration #8709 (Closed): Modified user interface to deal with database changes in schema: removal of elements.description (-> sequences.definition), elements.date_seq (-> sequences.date_seq), elements.version (-> sequences.version), genes.residue (-> prot_feat.proteine)

Thomas Lacroix

10:55 AM Insyght, a conserved synteny - homolog browser Bug #8708 (Closed): Fixed functionality to send email via smtp inra to report uncaught exception

Thomas Lacroix

10:55 AM Insyght, a conserved synteny - homolog browser Bug #8707 (Closed): Fixed examples taxon ids for release Archaea

Thomas Lacroix

10:55 AM Insyght, a conserved synteny - homolog browser Feature #8706 (Closed): Taxonomic browser, core / dispensable genome functionality : upon header selection, select all nodes in appropriate categories

Thomas Lacroix

10:37 AM Insyght, a conserved synteny - homolog browser Bug #8705 (Closed): Sometimes 2 references genomes are selected in the taxonomic browser (2 nodes in yellow) ; impossible to change the group for them...

Thomas Lacroix

10:36 AM Insyght, a conserved synteny - homolog browser Feature #8704 (Closed): Taxonomic browser, core / dispensable genome functionality : checkbox to select multiple genomes / nodes. Keyboard support.

asked by Pierre Renault Thomas Lacroix