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  • Scripts for file dumping and conversion
    /home/acedb/ranjana/citace_upload/go_curation/protein2go_migration/split_into_curators. /home/acedb/ranjana/citace_upload/go_curation/protein2go_migration/
    539 bytes (84 words) - 19:05, 25 January 2013
  • Data mining
    #[[AceDB classes|AceDB classes]] - ''A comprehensive list of AceDB classes'' #[[AceDB classes tutorial|AceDB classes tutorial]] -''Examples and descriptions of commonly accessed classe
    2 KB (264 words) - 01:36, 1 April 2022
  • New Model Implementation Checklist
    **Status: file created, not yet checked in ACeDB **Status: file created, not yet checked in ACeDB
    1 KB (199 words) - 19:08, 10 February 2014
  • Quick response cheatsheet
    - use top command to check if sgiface is at 100%, if so restart ACeDB ==Restart AceDB==
    784 bytes (128 words) - 21:31, 5 November 2015
  • UserGuide:Display Tools
    The Tree Display shows the data relationships according to each ACeDB data model. Shown in the diagram: red color shows tags, blue color indicate ACeDB Schema
    2 KB (266 words) - 18:26, 17 August 2010
  • Xapian and wormbase
    cd /usr/local/wormbase/acedb/bin acedb> @dump_ace_for_search.script
    658 bytes (108 words) - 16:11, 5 October 2011
  • Orthology, Homology and Paralog data in WormBase
    it is in the ACeDB database on the genes as ortholog/paralog, but we also dump it since a whil ...files, as well as here: ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/acedb /Non_C_elegans_BLAST
    2 KB (336 words) - 14:08, 27 August 2015
  • Importing Protein Structure Data
    brie3:/usr/local/acedb/datasets/structure_data/ cshace: brie3:/usr/local/acedb/dumpdb/
    3 KB (408 words) - 23:36, 13 August 2010
  • Updating WormMart
    WormMart is built every 5 releases of AceDB. Currently, the machine ls2.res.oicr.on.ca is used to build WormMart, then === Get AceDB ===
    2 KB (289 words) - 18:24, 17 August 2010
  • Update Matrix Template
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    3 KB (489 words) - 18:14, 17 August 2010
  • ModENCODE TilingArray
    == Tiling Array Related ACeDB Models ==
    2 KB (220 words) - 00:19, 21 January 2011
  • General specifications
    ''Arabidopsis'': /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles/ ''Arabidopsis'': /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles
    2 KB (204 words) - 19:18, 17 November 2011
  • Update Matrix WS205
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    3 KB (530 words) - 18:14, 17 August 2010
  • Data mining:WQL tutorial
    [http://grain.jouy.inra.fr/ggpages/ggpages/aboutacedbquery.html About ACEDB Queries (not worm-specific)]
    296 bytes (41 words) - 15:12, 16 June 2011
  • Update Matrix WS209
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (717 words) - 18:20, 17 August 2010
  • Update Matrix WS214
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (719 words) - 18:21, 17 August 2010
  • Update Matrix WS208
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (738 words) - 18:20, 17 August 2010
  • WBConfCall 2021.12.16-Agenda and Minutes
    It's a acedb availability issue; Todd will investigate.
    295 bytes (40 words) - 16:40, 16 December 2021
  • Update Matrix WS211
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (723 words) - 18:21, 17 August 2010
  • Update Matrix WS212
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (723 words) - 18:21, 17 August 2010
  • Update Matrix WS210
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (725 words) - 18:20, 17 August 2010
  • C.remanei
    == ACeDB == The default code is used to show the ACeDB data and there is a GBrowse version available to show the GFF annotation. I
    2 KB (324 words) - 19:34, 11 August 2010
  • WebDev 2009.09.23-Agenda and Minutes
    == 5. Discuss AceDB -> PF (Xiaoqi; 10 minutes) ==
    2 KB (252 words) - 09:25, 28 September 2009
  • Update Matrix WS213
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (725 words) - 18:21, 17 August 2010
  • Update Matrix WS206
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (610 words) - 18:20, 17 August 2010
  • Update Matrix WS215
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (735 words) - 18:22, 17 August 2010
  • Update Matrix WS217
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (735 words) - 18:22, 17 August 2010
  • Phenote .ace citace upload
    /home/acedb/karen/WS_upload_scripts/phenotype/use_package.pl*<br> /home/acedb/karen/WS_upload_scripts/paper_object/get_paper_object.pl*
    5 KB (749 words) - 19:47, 17 May 2018
  • Update Matrix WS207
    |Has a wormbase_RELEASE directory been created in /u/l/w/acedb? |Mirror and Unpack AceDB files
    4 KB (762 words) - 18:20, 17 August 2010
  • Website:WormMine Builds
    ===== AceDB Dump ===== Did not specify AceDB dir in $ACEDB. Searching for tace...
    9 KB (947 words) - 18:27, 12 August 2014
  • AceDB class-Y2H
    [[Category:AceDB]]
    274 bytes (40 words) - 21:51, 11 August 2010
  • WormBase Model:Map error
    AceDB internal class
    169 bytes (19 words) - 14:38, 4 October 2010
  • WormBase Model:ManyMap
    Looks like an acedb internal as the xace code looks for it.
    206 bytes (28 words) - 14:34, 4 October 2010
  • WBConfCall 2023.10.05–Agenda and Minutes
    Example of how Strain curated in NS looks in ACeDB:
    339 bytes (48 words) - 22:45, 4 October 2023
  • UserGuide:Genetic Map
    ...forward genetic mapping. The WormBase Genetic Map inherited its look from ACeDB, however because of internet interface, many features have been changed. ACEDB MAP IMAGE SUBMENU
    4 KB (720 words) - 18:28, 17 August 2010
  • Website:WormBase::API
    The following AceDB model elements are handled generically in the reimplementation. This maxim * you should specify the name of the AceDB model element in lowercase in the configuration file
    2 KB (271 words) - 14:09, 19 June 2014
  • WS186
    The reason for that is that AceDB begins to struggle when one object is linked to 3. Obtain and install a suitable acedb binary for your system
    6 KB (683 words) - 05:51, 3 April 2008
  • WebDev 2016.02.23-Agenda and Minutes
    #*ACeDB to Datomic #**Took reorganized the folder structure when I took away the non ACeDB to Datomic from this repo .
    3 KB (478 words) - 15:41, 23 February 2016
  • WBConfCall 2020.08.20-Agenda and Minutes
    ** Want/need to synchronize Postgres with Hinxton and ACEDB * Chris G wanted to dump pathogenic species, find out how they align with acedb species. How do they get into Hinxton.
    3 KB (440 words) - 08:42, 3 September 2020
  • WBConfCall 2016.12.01-Agenda and Minutes
    Can we replace ACEDB Tree Display with Datatomic? We should continue to provide Tree Display. Ho
    450 bytes (62 words) - 16:44, 1 December 2016
  • WS185
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (680 words) - 07:37, 11 January 2008
  • InterMine Strategy Meeting: May 14, 2013
    * Create versioned folders of XML representing various acedb releases. Build mine off of these. Can be used to resurrect old mines. * Find out how to extract version of data in acedb
    2 KB (241 words) - 15:32, 15 May 2013
  • WBConfCall 2024.01.04-Agenda and Minutes
    ** WBVar02157532 - tur003 Variation page is not generated but exists in ACeDB and JBrowse #9376
    618 bytes (81 words) - 21:36, 2 January 2024
  • WormBaseComparativeGenomicsTools
    ...ailable from the Gene pages (link is called syntenic alignment). Or in the ACeDB database as Homol_data on the C.elegans and C.briggsae chromosomes. * ACeDB contains WABA homol_data on the chromosomes
    5 KB (727 words) - 17:31, 27 June 2009
  • WBConfCall 2021.03.04-Agenda and Minutes
    ...f aCeDB, an object database where modeling is easy for curators to do, and acedb handles XREFs and connecting data automatically. ** Caltech curators were writing .ace text files to load into acedb, and early forms were UIs for templates for .ace text files.
    4 KB (743 words) - 12:22, 5 March 2021
  • WBConfCall 2022.04.07-Agenda and Minutes
    ...take a look. Tree display + schema viewer + genetic map stop working when acedb goes down.
    2 KB (279 words) - 16:01, 7 July 2022
  • WS183
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (800 words) - 10:01, 8 November 2007
  • Linking To WormBase
    == Linking to Acedb Format == ...cal ACeDB database, create a link to <code>http://www.wormbase.org/db/misc/acedb?name=X;class=Y</code>, where X and Y are again replaced with the object nam
    6 KB (1,087 words) - 15:07, 19 June 2014
  • Relations Ontology
    **/home/acedb/kimberly/citace_upload/ro/ontology2ace/ro_obo_to_ro_ace.pl #In the /home/acedb/kimberly/citace_upload/ro/ontology2ace directory on tazendra, use the wget
    3 KB (453 words) - 18:27, 20 September 2023
  • Design Specs: Database Connectivity
    *do "reconnect" if dbh is not set, undef or time-out(AceDB) *http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/API/Service/acedb.pm
    6 KB (980 words) - 18:48, 11 August 2010
  • AceOjbect Redesign Page
    |No API necessary; AceDB internals. |No API necessary; AceDB internals.
    12 KB (1,559 words) - 18:14, 15 June 2011
  • WS230 Models.wrm
    ...models to supplement the new gff3 dumping functionality being added to the acedb code. Ace2SO class: gives a mapping from Acedb objects to their SO terms.
    3 KB (368 words) - 10:15, 1 February 2012
  • WS184
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (831 words) - 07:36, 11 January 2008
  • WormBase-Caltech Weekly Calls February 2016
    === Postgres data not in ACEDB === * Should we this data get into ACEDB to be converted to Datomic (via the existing pipeline)? Maybe, but only tem
    4 KB (571 words) - 16:48, 3 March 2016
  • Specifications for data submission to the Alliance
    |+Mapping of acedb tags to objects in JSON ! !!Acedb Tags in Annotation <br/> (From ?Disease_model_annotation class)!!Primary Ob
    2 KB (318 words) - 17:43, 26 October 2023
  • Building Frozen Releases
    acedb/ == AceDB ==
    8 KB (1,087 words) - 17:35, 19 June 2014
  • Dumping Script
    The papers cronjob is on the acedb account : ...le names in postgres (pap_nnnnn) and the tag names in the ?Paper model for ACeDB. At the top of the script, there is a list that maps postgres paper table
    2 KB (329 words) - 15:21, 7 August 2014
  • WBConfCall 2023.02.02-Agenda and Minutes
    ...63926 has no title in ACeDB. The paper title exists in postgres but not in ACeDB. In WS287, there are 8 papers from MEDLINE that have no title.
    2 KB (348 words) - 17:52, 2 February 2023
  • Alliance - migrating WormBase papers to Alliance ABC
    ...tech postgres not in acedb, and I thought that anything user-facing was in acedb, but it turns out corresponding author flags are not. It'd be mildly helpf ** The lag between data being updated at Caltech -> Built into acedb -> released into Alliance.
    3 KB (492 words) - 18:48, 17 March 2021
  • Physical Interactions
    ACeDB data models [http://wiki.wormbase.org/index.php/Gene_Interaction#Interactio
    559 bytes (71 words) - 20:41, 13 June 2011
  • WormBase Model:Transcript
    Start_not_found #acedb magic tag End_not_found #acedb magic tag
    4 KB (350 words) - 09:32, 17 June 2013
  • WBConfCall 2018.11.15-Agenda and Minutes
    * For now, we model in ACeDB and convert at Hinxton to Datomic. Curators don’t need to be too concerne ...to think about: what’s the advantage in modelling Datomic vs Modelling in ACeDB?
    2 KB (323 words) - 18:24, 15 November 2018
  • WS211
    The Non-elegans blastx data is no longer loaded into the full acedb database release. install acedb as usual from
    6 KB (766 words) - 16:38, 21 December 2011
  • WormBase-Caltech Weekly Calls March 2021
    === Spreadsheet for Data not in ACEDB === ...alena/Hinxton would like to know how much data at Caltech doesn't get into ACEDB
    5 KB (777 words) - 13:18, 1 April 2021
  • WormBase-Caltech Weekly Calls November 2020
    ...9 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new === Curating to human genes in ACEDB ===
    4 KB (695 words) - 14:44, 3 December 2020
  • WBConfCall 2018.09.06-Agenda and Minutes
    Due to ACeDB (which does not support unicode due to it's ancientness), not currently pos
    896 bytes (138 words) - 16:10, 6 September 2018
  • WBConfCall 2020.04.16-Agenda and Minutes
    As we winnow down the number of items at WormBase.org that directly depend on ACEDB (and there are very few left), # Hosting data at AceDB and automatic update from AGR update
    2 KB (303 words) - 18:23, 16 April 2020
  • WormMine
    | Orthology || ACeDB gene class (Ortholog and Ortholog_other tags) and there is also a OICR crea | Interaction || AceDB interaction class
    15 KB (2,088 words) - 16:16, 15 October 2020
  • WormBase Model:Multi counts
    Unused class in wormbase and it appears that the acedb source code doesn't look for this specific class.
    816 bytes (100 words) - 15:47, 4 October 2010
  • Data mining:AQL tutorial
    '''Documentation at AceDB web site''' [http://www.acedb.org/Software/whelp/AQL/ [2]]
    834 bytes (137 words) - 15:09, 16 June 2011
  • WebDev 2010.02.17-Agenda and Minutes
    * connection to AceDB and GBrowse -- persistent
    907 bytes (113 words) - 14:27, 19 February 2010
  • WBConfCall 2021.07.01-Agenda and Minutes
    ...in WormBase::Web::Controller::Tools->tools "Could not connect to database acedb _WS280, host: 7e85f19c6634" User wants to: This WBG article says, "Map data have been deposited in ACeDB." I would like to know the flanking markers used to map ccIs4251 and the ob
    2 KB (347 words) - 14:07, 2 July 2021
  • Software Life Cycle: 4. Updating The Production Servers
    Remove build WSXXX -- including acedb, mysql, and support DBs -- from the staging cluster: Remove build WSXXX -- including acedb, mysql, and support DBs -- from the production cluster:
    8 KB (1,229 words) - 16:17, 30 December 2013
  • WBConfCall 2014.08.07-Agenda and Minutes
    *Example data already accessible in the acedb database * the data is hidden in ACeDB and quite inaccessible
    3 KB (450 words) - 16:07, 7 August 2014
  • WBConfCall 2020.05.06-Agenda and Minutes
    22nd June-17th July - ACeDB production 8th June-3rd July - ACeDB production <!!!!!!EBI Farm move 22nd June - 3rd July!!!!!!!>
    2 KB (378 words) - 17:04, 11 May 2020
  • WBConfCall 2020.05.07-Agenda and Minutes
    22nd June-17th July - ACeDB production 8th June-3rd July - ACeDB production <!!!!!!EBI Farm move 22nd June - 3rd July!!!!!!!>
    2 KB (376 words) - 17:03, 11 May 2020
  • Building WormMart
    In simple terms, WormMart is built by transforming WormBase's AceDB database into a BioMart schema MySQL database. Standard BioMart tools are t 1a. Install the ACeDB Software
    6 KB (786 words) - 19:13, 18 June 2014
  • WS207
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (675 words) - 16:42, 21 December 2011
  • WS208
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    5 KB (581 words) - 16:50, 21 December 2011
  • WS212
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    5 KB (582 words) - 11:16, 21 December 2011
  • AceDB classes
    This is a list of the most prominent classes in use in the AceDB database employed by WormBase. [[Category:AceDB]]
    4 KB (568 words) - 11:06, 23 May 2011
  • WormBase-Caltech Weekly Calls April 2013
    **ACEDB software problem ***Possible but difficult to upgrade ACEDB software
    4 KB (651 words) - 16:11, 2 May 2013
  • WormBase gene association file/archive
    In the acedb user account on Tazendra at:/home/acedb/ranjana/GO: #copy the right go.go.<date> file from /home/acedb/ranjana/citace_upload/go_curation/go_dumper_files/ to this directory,change
    4 KB (629 words) - 18:27, 23 November 2020
  • WBConfCall 2021.04.01-Agenda and Minutes
    ...ags data that doesn't make it into acedb). We loose foreign characters in acedb, so we'll be able to keep those in postgres and pass them on to Alliance.<b Raymond: One postgres, two data streams one to acedb and a second to alliance<br>
    4 KB (709 words) - 13:27, 5 April 2021
  • AceDB class-Interaction
    [[Category:AceDB]]
    1 KB (143 words) - 21:51, 11 August 2010
  • WBConfCall 2013.10.17-Agenda and Minutes
    **acedb + website flat file **website flat file only with only database name and description stored in acedb
    2 KB (361 words) - 16:32, 17 October 2013
  • WBConfCall 2013.02.07-Agenda and Minutes
    ****Needs testing as may have implications for acedb. *Data will be kept in acedb for purposes of Cytoscape?
    2 KB (383 words) - 11:59, 15 February 2013
  • WBConfCall 2016.10.06-Agenda and Minutes
    *** Orthology data in WormMine seems *not* to come from WormBase / AceDB ...in WormMine came directly from Pather (via InterMine loader), rather than AceDB
    2 KB (369 words) - 16:38, 6 October 2016
  • InterMine Strategy Meeting: May 21, 2013
    * Find out how to extract version of data in acedb
    1 KB (169 words) - 16:51, 28 May 2013
  • WS196
    ...he GFF files and so visible in the genome browser but not via querying the acedb database. 3. Obtain and install a suitable acedb binary for your system
    6 KB (748 words) - 16:41, 21 December 2011
  • WS204
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (648 words) - 16:16, 21 December 2011
  • Populating the OA and New Dumping Script
    Can likely borrow a lot from the gpad parsing script on tazendra /home/acedb/kimberly/citace_upload/go/go_gpad_parser.pl Currently, that file is on tazendra here: /home/acedb/kimberly/citace_upload/go/gp_annotation.ace
    3 KB (484 words) - 22:19, 21 February 2015
  • WS173
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (639 words) - 10:55, 21 December 2011
  • WormBase-Caltech Weekly Calls February 2017
    === ACEDB dependencies === * Raymond was asked to collect all CIT curator uses of ACEDB, e.g. programmatic access via ACE Perl
    7 KB (1,073 words) - 16:26, 2 March 2017
  • Developer notes
    A number of elements are repeated across the AceDB schema. To make the external model easier to maintain, fetching and parsing <tr><th>Expected AceDB model tag</th><th>Object.pm method</th><th>config field</th><th>template ma
    3 KB (485 words) - 15:37, 19 June 2014
  • WS187
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (647 words) - 16:43, 21 December 2011
  • WS199
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (661 words) - 16:51, 21 December 2011
  • WS171
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (652 words) - 10:55, 21 December 2011
  • Movie
    There were 513 movies in acedb, all pertaining the RNAi class. We are going to generate the movie OA and i /home/acedb/draciti/Movies
    5 KB (814 words) - 18:48, 17 September 2018
  • WS179
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (843 words) - 10:53, 21 December 2011
  • WS131
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (669 words) - 11:18, 21 December 2011
  • Suggested pre-release data checks
    ...se of the database from Sanger. Ideally, you should give a description, an acedb query and expected outcome. I've added the one Igor sent regarding the RNAi ...rm after GFF and comparing that to the number of objects returned from the acedb query after QUERY. Those with an EXPECT instead of QUERY are where I couldn
    7 KB (659 words) - 17:39, 17 August 2010
  • WS107
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (659 words) - 11:17, 21 December 2011
  • WBConfCall 2013.06.06-Agenda and Minutes
    ** Michael: AceDB GFF3 dumper (no firm ETA)
    1 KB (168 words) - 16:06, 6 June 2013
  • WS203
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (662 words) - 16:50, 21 December 2011
  • WBConfCall 2023.12.07-Agenda and Minutes
    .../9376 WBVar02157532 - tur003 Variation page is not generated but exists in ACeDB and JBrowse] - Paolo close?
    1 KB (159 words) - 18:22, 7 December 2023
  • WS194
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (936 words) - 16:48, 21 December 2011
  • WS163
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (645 words) - 10:57, 21 December 2011
  • Evidence Code Ontology
    ** /home/acedb/kimberly/citace_upload/eco/ontology2ace/eco_obo_to_eco_ace.pl * Latest parsing script: /home/acedb/kimberly/citace_upload/go/gpad2ace/2020_July
    6 KB (834 words) - 17:56, 15 June 2020
  • WS158
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (673 words) - 11:07, 21 December 2011
  • WS209
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (687 words) - 16:50, 21 December 2011
  • WS198
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (692 words) - 16:51, 21 December 2011
  • WS197
    3. Obtain and install a suitable acedb binary for your system (available from [http://www.acedb.org/ www.acedb.org]).
    6 KB (672 words) - 16:43, 21 December 2011
  • WS201
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (665 words) - 16:42, 21 December 2011
  • WS175
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (680 words) - 10:54, 21 December 2011
  • WS200
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (722 words) - 16:43, 21 December 2011
  • WS117
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (695 words) - 11:17, 21 December 2011
  • WS146
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (670 words) - 11:09, 21 December 2011
  • WebDev 2011.02.09-Agenda and Minutes
    * Analyzing options which will not search through acedb.
    941 bytes (117 words) - 22:00, 9 February 2011
  • UserGuide:Release Notes
    The "Class counts from old =&gt; new build" under "ACEDB databases" is very helpful. It is a straightforward list telling people the
    1 KB (215 words) - 18:31, 17 August 2010
  • WS135
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (689 words) - 11:19, 21 December 2011
  • WS160
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (706 words) - 10:50, 21 December 2011
  • WS214
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (709 words) - 16:49, 21 December 2011
  • WS122
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (721 words) - 11:18, 21 December 2011
  • WS205
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (711 words) - 16:31, 21 December 2011
  • WormCloud:Overview
    As everybody knows Datomic is the main database that we are moving to from AceDB. Datomic is a DataLog and DynomoDB is an AWS database. We are using these t This repository contains code for converting AceDB Dumps to Datomic logs / databases.
    5 KB (842 words) - 19:41, 17 February 2016
  • November 2012 - Weekly Pipeline Set-up
    /home/acedb/kimberly/ccc_dicty/dicty_ccc_datafiles
    1 KB (205 words) - 17:10, 8 November 2012
  • WS195
    ...command prompt.<br><br>5. See the acedb website for more information about acedb and<br>&nbsp;&nbsp;&nbsp; using xace.<br><br>____________&nbsp; END _______ available at: [[ftp://ftp.sanger.ac.uk/pub2/wormbase/WS195/acedb/patches/inparanoid_patch.ace.bz2 inparanoid_patch]]
    11 KB (1,614 words) - 16:52, 21 December 2011
  • Data Model
    ...WormMine is built by a combination of different data sources (GFF3, FASTA, AceDB dumps, etc.) that are loaded and organized in different tables. At the mome
    1 KB (209 words) - 03:18, 13 November 2018
  • WS229 Models.wrm
    Cosmetic change to allow ACeDB code to dump the data stored in this tag correctly.
    1 KB (178 words) - 09:49, 26 October 2011
  • WBGene information and status pipeline
    !AceDB tag # /home/acedb/cron/populate_gin_locus.pl - updates information from nameserver nightly du
    9 KB (1,464 words) - 14:10, 29 May 2015
  • WS210
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (721 words) - 16:46, 21 December 2011
  • WBConfCall 2011.11.17-Agenda and Minutes
    Gary W created a 100 genomes acedb. It worked, but was slow. It certainly simplies certain processes if all genomes are in acedb,
    7 KB (1,220 words) - 15:50, 25 November 2011
  • WS182
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (716 words) - 16:48, 21 December 2011
  • WS192
    3. Obtain and install a suitable acedb binary for your system (available from [http://www.acedb.org/ www.acedb.org]).
    6 KB (763 words) - 10:43, 21 December 2011
  • WS142
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (720 words) - 11:09, 21 December 2011
  • WS112
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (735 words) - 11:17, 21 December 2011
  • WS213
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (764 words) - 16:45, 21 December 2011
  • WS138
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (740 words) - 11:19, 21 December 2011
  • WBConfCall 2021.03.18-Agenda and Minutes
    Most - but not all - scientific data is held in AceDB ** Example In ACeDB
    3 KB (487 words) - 16:36, 18 March 2021
  • WS191
    3. Obtain and install a suitable acedb binary for your system (available from [http://www.acedb.org/ www.acedb.org]).
    6 KB (756 words) - 16:53, 21 December 2011
  • WBConfCall 2012.07.019-Agenda and Minutes
    *Database corruption (ACEDB) problem *?Tree and ?Tree_node classes in ACEDB; do people use them?
    4 KB (617 words) - 17:01, 19 July 2012
  • Disease and Drugs
    ==Acedb model changes for human disease data in WB==
    5 KB (782 words) - 20:56, 8 January 2020
  • WS188
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (769 words) - 11:01, 21 December 2011
  • WormBase-Caltech Weekly Calls August 2020
    === Species in Postgres and ACEDB/Datomic === * Want to be sure that what gets dumped aligns with species loaded into ACEDB
    5 KB (880 words) - 15:40, 3 September 2020
  • WS178
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (762 words) - 10:53, 21 December 2011
  • WS176
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (783 words) - 10:46, 21 December 2011
  • WS172
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (783 words) - 10:55, 21 December 2011
  • Updating Postgres with New WS Information
    ...copy all .ace files from spica:/home/citpub/wen/WSDump/ to tazendra:/home2/acedb/cron/dump_from_ws/files/ *In the home2/acedb/cron/dump_from_ws/files directory, there is a file, latestDate, that logs t
    18 KB (2,743 words) - 17:14, 16 March 2023
  • WBConfCall 2024.04.04-Agenda and Minutes
    *Do we need to change the Database name in AceDB? No **IDs are stored in AceDB without the prefix, but with the Database name OMIM
    3 KB (525 words) - 17:20, 4 April 2024
  • WS154
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (749 words) - 11:08, 21 December 2011
  • WebDev 2009.10.07-Agenda and Minutes
    ...tions re: Chado and WB. Chado DB populated for modEncode effort with some AceDB data.
    1 KB (205 words) - 16:53, 7 October 2009
  • WS216
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (818 words) - 11:10, 21 December 2011
  • WebDev 2009.11.11-Agenda and Minutes
    * AceDB work to produce GFF3 (with Ed Griffith)
    1 KB (227 words) - 18:00, 11 November 2009
  • WS206
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (796 words) - 16:46, 21 December 2011
  • WS202
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    6 KB (770 words) - 11:06, 21 December 2011
  • WBConfCall 2012.04.19-Agenda and Minutes
    a) Really need to Unify disconnect between the ACeDB or Not ACeDB species ?? Gene pages would require ACeDB integration ??
    7 KB (1,182 words) - 13:50, 20 April 2012
  • WS180
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (771 words) - 10:52, 21 December 2011
  • WormBase Model:Map
    Lots of unused tags, but acedb internal class.
    2 KB (208 words) - 14:36, 4 October 2010
  • Software for nematode research
    *[http://www.acedb.org ACeDB] - ''The database engine that drives WormBase''
    2 KB (284 words) - 22:43, 16 August 2010
  • WBConfCall 2022.11.17-Agenda and Minutes
    ...an update about the Waterson scRNASeq graphs. The pictures are already in ACeDB so just wait for the web display.
    1 KB (217 words) - 20:07, 17 November 2022
  • Entity classes and problems
    From acedb on spica '''Allele/SNP''' -> ''acedb on spica'' ; Variation Report page<br>
    10 KB (1,696 words) - 17:21, 25 July 2013
  • WS193
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (944 words) - 16:52, 21 December 2011
  • WS147
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (815 words) - 11:09, 21 December 2011
  • WS170
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (820 words) - 10:51, 21 December 2011
  • WS127
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    7 KB (872 words) - 11:18, 21 December 2011
  • WormBase-Caltech Weekly Calls March 2020
    === Latest ACEDB === * Getting latest ACEDB build from staging FTP (for descriptions, etc.)
    6 KB (903 words) - 15:28, 2 April 2020
  • WS177
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    9 KB (819 words) - 10:53, 21 December 2011
  • ALTERNATE PROTOCOL 1: INSTALLING AND RUNNING WormBase LOCALLY
    ...advantage of two hard drives is that WormBase uses two separate databases (ACeDB and MySQL) which work better if put on separate disks. If installing WormBase on a computer with two hard drives, place the ACeDB component of WormBase on one drive and the MySQL component on the other; th
    4 KB (623 words) - 20:00, 11 August 2010
  • NBC sign off documentation
    ...ected to diseases would reappear on the new site, but I don't know how, as acedb might be a bit slowish to search through the text (but maybe it is fast eno ...ws227). I don't know of it was one of our best ideas to put the urls into acedb, as it now takes two months to fix broken links.
    4 KB (583 words) - 20:22, 29 July 2011
  • Life Stage
    .ace file to modify located here: /home/acedb/draciti/Life_stage /home/acedb/draciti/Life_stage/parse.pl
    14 KB (2,213 words) - 19:26, 12 February 2019
  • WebDev 2013.06.14-Agenda and Minutes
    ** to run on new data in acedb (catch data problems??!)
    2 KB (244 words) - 15:52, 14 June 2013
  • Adding Papers not in PubMed
    To do this, you will need to login to tazendra using the acedb account and access postgres with psql testdb.
    2 KB (247 words) - 19:37, 19 November 2010
  • Virtual Machines
    --acedb/ Xace - ''the graphical interface to AceDB''
    11 KB (1,664 words) - 18:43, 17 August 2010
  • Adding new Phenotype2GO annotations to postgres
    ...o GAF files for generating the WS249 upload are on mangolassi here: /home/acedb/kimberly/citace_upload/go/phenotype2go/new_annotation_entries/WS249_upload ***Files are currently on mangolassi here: /home/acedb/kimberly/citace_upload/go/phenotype2go/new_annotation_entries/WS249_upload/
    6 KB (1,087 words) - 19:52, 27 July 2015
  • Updating ontology (.obo) files for the OA
    ...that contains these objects. It needs to be updated with every release of acedb. The obo file is created from AQL queries of the latest WS. ...hows up in the term info box when selected. Keeping the file updated from acedb and showing this information in the term info box helps during curation as
    10 KB (1,644 words) - 18:48, 13 August 2020
  • WebDev 2009.12.09-Agenda and Minutes
    * GFF and acedb steps mostly complete
    2 KB (370 words) - 17:47, 9 December 2009
  • WS181
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (885 words) - 16:47, 21 December 2011
  • WormBase-Caltech Weekly Calls September 2012
    Migration away from ACEDB? *Scalability - ACEDB does not scale to genome-scale studies
    7 KB (1,074 words) - 17:19, 4 October 2012
  • WS190
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (913 words) - 16:46, 21 December 2011
  • WS169
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (787 words) - 10:56, 21 December 2011
  • WS225
    acedb DIR - Everything needed to generate a local copy of the The x) database.WS225.*.tar.gz - compressed acedb database for new release
    16 KB (1,674 words) - 11:38, 20 April 2011
  • AceDB classes tutorial
    [[Category:AceDB]]
    2 KB (281 words) - 21:51, 11 August 2010
  • WebDev 2016.03.22-Agenda and Minutes
    ...h of the website because it is no longer pulling specific information from AceDB. We will need to remove no-longer-required tests and make new ones to test
    2 KB (242 words) - 15:25, 22 March 2016
  • WBConfCall 2018.06.21-Agenda and Minutes
    ...b? Take home: leave the XREF in datomic for now and do not add new them to acedb.
    4 KB (691 words) - 17:16, 21 June 2018
  • WBConfCall 2021.10.07-Agenda and Minutes
    ...prefer we deprecate/retire Tree Display and remove one more dependency on ACEDB * Todd: these are periodic, recurring issues about depending on ACEDB
    5 KB (855 words) - 08:58, 8 October 2021
  • Specifications for a DAF for gene-disease data
    ...ired(R)<br/>Optional(O)!!Cardinality!!Example!!Definition!!Old DAF column!!Acedb tag!!Required format/Restriction!! ...axon||R||1||taxon:6239||NCBI taxonomic identifier for the organism||13||No acedb tag|| taxon:####
    10 KB (1,599 words) - 18:53, 24 January 2019
  • Paper Pipeline Scripts
    papers cronjob is on the acedb account :
    2 KB (320 words) - 20:59, 12 May 2017
  • WS174
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (938 words) - 10:54, 21 December 2011
  • Hinxton 2015.08- Meeting minutes
    ** Cannot re-implement AceDB's partial case-insensitivity in Datomic. ** GW to try again on acedb.ebi.ac.uk using /nfs/acedb/vol1 (purportedly low-latency storage)
    5 KB (741 words) - 10:57, 21 August 2015
  • WebDev 2010.04.07-Agenda and Minutes
    * builds of late have been slowed by acedb slowdowns
    2 KB (313 words) - 16:52, 7 April 2010
  • WebDev 2010.10.20-Agenda and Minutes
    * AceDB version issue -- need 4.9.39, monthly release; AC uses external server; TH
    2 KB (251 words) - 20:35, 20 October 2010
  • OA forms, tables, scripts, etc
    ...ome/postgres/work/citace_upload/antibody/use_package.pl<br>sym link: /home/acedb/xiaodong/antibody/use_package.pl ||Paper<br>Gene<br>Laboratory<br> || ||Xia ...home/postgres/work/citace_upload/concise/use_package.pl<br>sym link: /home/acedb/kimberly/citace_upload/concise/wrapper.pl and /home/postgres/work/citace_
    20 KB (3,050 words) - 21:01, 19 April 2017
  • Software Life Cycle: 1. Updating The Development Server
    ACEDB : /usr/local/wormbase/acedb <td>Unpack ACeDB</td>
    25 KB (3,632 words) - 03:11, 28 October 2013
  • WS217
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    8 KB (915 words) - 11:10, 21 December 2011
  • WBConfCall 2017-11-16-Agenda and Minutes
    ** Raymond - Issue came from not understanding acedb modeling for datomic conversion.
    2 KB (277 words) - 16:10, 17 November 2017
  • How to build a WormBase Virtual Machine
    --acedb/ ../current_databases/acedb/20GB.vmdk
    5 KB (752 words) - 23:33, 13 August 2010
  • Curation status
    ...eated allele'''||extvariation||afp, cfp, tfp, jfp||variation NS||old: home/acedb/karen/cur_status_sources/vargene_ref.txt; current:?||for paper-allele conne ...sion by genetic or other treatment'''|| genereg ||afp, cfp||postgres||home/acedb/karen/cur_status_sources/regulation_ref.txt||
    6 KB (841 words) - 08:24, 24 October 2014
  • WBConfCall 2015.12.03-Agenda and Minutes
    * ACeDB will certainly be used for at least the next year. * It makes sense to have curation use ACeDB for the time being.
    4 KB (684 words) - 19:43, 5 December 2015
  • Acceptable use policy
    ...that drives WormBase. In addition, the underlying databases at aceserver (Acedb and the Mysql GFF databases) are available for programmatic access (see Min
    2 KB (301 words) - 02:21, 1 April 2012
  • WormBase Release Workflow
    ...machine at OICR. Staging includes mirroring files from Hinxton, unpacking acedb, building BLAST and GFF databases, and dumping annotations.
    2 KB (328 words) - 13:05, 2 June 2014
  • WS222
    acedb DIR - Everything needed to generate a local copy of the The x) database.WS222.*.tar.gz - compressed acedb database for new release
    15 KB (1,647 words) - 10:06, 22 December 2010
  • New GO Progress Report Script
    Input files (available on tazendra in home/acedb/ranjana/GO/Progress_Reports/Test):
    2 KB (322 words) - 18:52, 2 December 2014
  • Linking script pipeline
    * First, a lexicon of entities is formed using the WormBase acedb and postgres databases and author-submitted data. ...'''Transgene''', and '''Variation''' are all formed by querying the latest acedb WormBase release on tazendra, which is updated daily from the Sanger/Hinxto
    14 KB (2,324 words) - 19:51, 9 January 2015
  • Administration:Installing WormBase
    '''acedb group''' ...is the group that will have write privileges to the acedb directory tree. Acedb administrators should be added to this group.
    26 KB (3,522 words) - 19:10, 18 June 2014
  • WS224
    acedb DIR - Everything needed to generate a local copy of the The x) database.WS224.*.tar.gz - compressed acedb database for new release
    15 KB (1,583 words) - 11:13, 21 December 2011
  • Co-op Documentation
    ...bject section contains most of the information related to interacting with ACeDB objects. ===ACeDB===
    11 KB (1,786 words) - 14:31, 17 May 2016
  • WormBase-Caltech Weekly Calls November 2011
    *Lookup if genome in ACEDB; if not, look up gene models in GFF databases *Run AQL queries from a local ACEDB instance for better performance (and fewer time outs)
    4 KB (612 words) - 17:13, 1 December 2011
  • OA for disease term
    ! Order !! Name !! Type !! Required? !! Shows in OA as !! acedb tag !! Postgres table name /home/acedb/ranjana/human_disease/diseaseterm
    8 KB (1,088 words) - 22:59, 29 July 2016
  • Transgene curation pipeline
    0 4 * * * /home/acedb/karen/cronjobs/assign_transgene_IDs.pl 0 4 * * sun cd /home/acedb/karen/transgene; ./use_package.pl
    9 KB (1,321 words) - 21:59, 3 May 2020
  • WormBase Models
    ...r this to be a development area, more for visualisation and clarity of the acedb models. ...document was 1st produced and also some are classes that are necessary for acedb to function correctly.
    16 KB (2,207 words) - 23:06, 9 January 2014
  • WBConfCall 2017-07-20-Agenda and Minutes
    ***Datomic database is not available until after the official ACeDB release ...ek build cycle to accommodate having to build Datomic database, as well as ACeDB
    7 KB (1,077 words) - 16:26, 20 July 2017
  • OICR-Configuring the development machine
    acedb/ // The Acedb database (including bin directory) * acedb group
    28 KB (3,957 words) - 19:55, 5 May 2022
  • ModENCODE Analysis & metadata discussion
    ...d the nomenclature we should adopt for ?Analysis/?Condition objects in the AceDB database.
    2 KB (340 words) - 08:50, 24 September 2010
  • WS228
    acedb DIR - Everything needed to generate a local copy of the The - database.WS228.*.tar.gz - compressed acedb database for new release
    14 KB (1,572 words) - 10:37, 11 November 2011
  • WormBase database schema
    The majority of the data stored within WormBase is held in an ACeDb database.
    2 KB (379 words) - 22:06, 10 October 2013
  • WBConfCall 2023.09.21–Agenda and Minutes
    * Stavros - Is Caltech postgres a view of acedb schema * Stavros - acedb harder to maintain, related to WB crashes ?
    9 KB (1,570 words) - 16:36, 21 September 2023
  • WormBase Infrastructure
    * a pool of redundant database servers running AceDB and MySQL ! acedb?
    9 KB (1,103 words) - 19:14, 18 June 2014
  • WBConfCall 2015.08.20-Agenda and Minutes
    A warm welcome to Adam. As he has helped evaluate candidate replacements for AceDB.....he is not a complete stranger. ...l be working with the Hinxton and OICR teams continuing development on the AceDB -> Datomic project and will be continuing from where Thomas left off with t
    6 KB (850 words) - 01:12, 22 August 2015
  • UniProtKB gpad to WormBase .ace
    **/home/acedb/kimberly/citace_upload/go/gpad2ace **for example: /home/acedb/kimberly/citace_upload/go/gpad2ace/2015_February
    5 KB (811 words) - 18:52, 3 November 2015
  • WormBase-Caltech Weekly Calls August 2019
    * Add slim terms into ACEDB? One option * Decided not to store ribbon info (slim terms and term order) in ACEDB, but rather in web code
    5 KB (759 words) - 15:02, 11 September 2019
  • Model changes to capture and consolidate human disease data
    **Disease relevant gene (dis_wbgene), acedb tag: Gene_by_biology//Add for WS278 **Variation (dis_variation), acedb tag: Disease_model_variation
    32 KB (3,649 words) - 20:55, 21 May 2020
  • WBConfCall 2015.02.5-Agenda and Minutes
    ...able to be done through WormMine and still needs curator to pull it out of ACeDB.
    2 KB (321 words) - 16:55, 5 February 2015
  • WS227
    acedb DIR - Everything needed to generate a local copy of the The - database.WS227.*.tar.gz - compressed acedb database for new release
    15 KB (1,738 words) - 11:20, 21 December 2011
  • Using private development sites
    3. All sites use the same Acedb and GFF databases. *Please* contact me before tinkering with them as these
    2 KB (381 words) - 18:42, 17 August 2010
  • WormBase-Caltech Weekly Calls April 2017
    ...omic would take over from ACEDB completely, but it seems we will still use ACEDB for some time for e.g. FMap * Wen will generate numbers for WS254 (resurrect WS254 ACEDB)
    7 KB (1,010 words) - 17:08, 4 May 2017
  • WS223
    acedb DIR - Everything needed to generate a local copy of the The x) database.WS223.*.tar.gz - compressed acedb database for new release
    15 KB (1,610 words) - 11:20, 21 December 2011
  • WS234
    acedb DIR - Everything needed to generate a local copy of the The - database.WS234.*.tar.gz - compressed acedb database for new release
    15 KB (1,653 words) - 10:13, 18 January 2013
  • WS218
    acedb DIR - Everything needed to generate a local copy of the The x) database.WS218.*.tar.gz - compressed acedb database for new release
    15 KB (1,756 words) - 11:21, 21 December 2011
  • Feature Requests
    acedb account on tazendra and I'll mark those as ``yes'' (the papers the acedb account on tazendra, and let me know which postgres tables
    6 KB (1,024 words) - 23:02, 13 August 2010
  • INTRODUCTION
    ...e'' genomic sequences; detailed, user-customized searches with WormMart or AceDB Query Language; batch downloads of many sequences at once; identifying the
    2 KB (365 words) - 00:06, 1 December 2010
  • WS230
    acedb DIR - Everything needed to generate a local copy of the The - database.WS230.*.tar.gz - compressed acedb database for new release
    17 KB (1,950 words) - 09:37, 7 February 2012
  • 2010.05 OICR WebDev Meeting
    ** acedb
    2 KB (280 words) - 19:14, 10 August 2010
  • WS219
    acedb DIR - Everything needed to generate a local copy of the The x) database.WS219.*.tar.gz - compressed acedb database for new release
    15 KB (1,622 words) - 11:11, 21 December 2011
  • WormBase-Caltech Weekly Calls March 2011
    *We will try to generate an ACEDB patch every other month, starting with the Paper class data *Since we use ACEDB, we have to patch WS with .ACE file, or rebuild whole thing
    13 KB (2,097 words) - 22:48, 7 April 2011
  • WS232
    acedb DIR - Everything needed to generate a local copy of the The - database.WS232.*.tar.gz - compressed acedb database for new release
    15 KB (1,729 words) - 14:15, 13 September 2012
  • WormBase-Caltech Weekly Calls August 2013
    ** /home/acedb/cron/curation_stats/get_daily_curation_stats.pl ** /home/acedb/cron/curation_stats/files/
    5 KB (850 words) - 15:32, 5 September 2013
  • WBConfCall 2013.10.02-Agenda and Minutes
    ** pre-processed tables, since acedb is slow
    3 KB (427 words) - 18:31, 3 October 2013
  • WormBase-Caltech Weekly Calls December 2015
    * There are automated conversion systems being established to convert ACEDB data and models into Datomic * Should the email info come from ACEDB or local Caltech postgres database?
    5 KB (776 words) - 16:50, 7 January 2016
  • Populating dois
    *And you can probably run the script manually by logging on as acedb and pasting :
    3 KB (466 words) - 17:00, 22 July 2014
  • WormBase-Caltech Weekly Calls June 2016
    ...As that had the same initial import timestamp, Wen determined the original ACEDB timestamps for those objects, and Juancarlos is updating the OA entries (cu * Testing instance of citpub ACEDB, single instance to be shared (cannot be used by multiple users simultaneou
    8 KB (1,224 words) - 15:34, 21 July 2016
  • Processing NBP alleles
    * 20151013 /home/acedb/karen/mid_release_scripts/nbp_maryann/parse_maryann.pl has been updated to *Move and rename file onto tazendra to /home/acedb/karen/mid_release_scripts/nbp_maryann/NBP_latest
    6 KB (920 words) - 00:20, 14 October 2015
  • General administration
    === Acedb === Acedb produces two logs. These are both located in the "database" folder of the c
    16 KB (2,589 words) - 20:19, 29 March 2012
  • WS237 Models.wrm
    These were seen to be the only remaining primary attribute classes and acedb does have kernal code expecting some of these tags to be present in the mod
    3 KB (475 words) - 14:53, 19 February 2013
  • Acceptance to first-pass
    * New data goes to the appropriate data curator for acedb object creation.
    3 KB (471 words) - 19:53, 19 April 2012
  • WBConfCall 2017-08-03-Agenda and Minutes
    * Purpose is to remove ACEDB-dependency
    2 KB (378 words) - 16:32, 3 August 2017
  • WS220
    acedb DIR - Everything needed to generate a local copy of the The x) database.WS220.*.tar.gz - compressed acedb database for new release
    16 KB (1,762 words) - 11:10, 21 December 2011
  • WS235
    acedb DIR - Everything needed to generate a local copy of the The - database.WS235.*.tar.gz - compressed acedb database for new release
    15 KB (1,708 words) - 10:14, 18 January 2013
  • WS284
    acedb DIR - Everything needed to generate a local copy of the The - database.WS284.*.tar.gz - compressed acedb database for new release
    17 KB (1,841 words) - 21:54, 11 May 2023
  • WS231
    acedb DIR - Everything needed to generate a local copy of the The - database.WS231.*.tar.gz - compressed acedb database for new release
    16 KB (1,820 words) - 14:15, 13 September 2012
  • SOP for generating GO files for citace and GO consortium uploads
    ...rom Protein2GO gpad - this file gets dumped first, and a copy put in /home/acedb/kimberly/citace_upload/go so the next script can access the final annotatio ...from Noctua models - this file gets dumped second, and a copy put in /home/acedb/kimberly/citace_upload/go so the next script can access the final annotatio
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  • WS224 Models.wrm
    These additions/changes were take from the core ACeDB models.wrm as these are used by more modern binaries.
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  • Markup excerpts
    ...h in the paper. The expression “[ttx-3::GFP]” in the Summary of mgIs18 in acedb
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  • WBConfCall 2020.11.05-Agenda and Minutes
    30th Nov 2020 - Acedb production 4 weeks Plus 1 week Datomic migration 04th Jan 2021 - Acedb production 4 weeks Plus 1 week Datomic migration
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  • WS233
    acedb DIR - Everything needed to generate a local copy of the The - database.WS233.*.tar.gz - compressed acedb database for new release
    17 KB (2,002 words) - 14:17, 13 September 2012
  • WS229
    acedb DIR - Everything needed to generate a local copy of the The - database.WS229.*.tar.gz - compressed acedb database for new release
    17 KB (1,988 words) - 11:15, 21 December 2011
  • Old pipeline for disease data
    ===Mapping between OA fields and acedb tags=== Script at : /home/acedb/ranjana/human_disease/count_disease.pl
    14 KB (2,085 words) - 20:27, 7 July 2022
  • 2008.01-Toronto
    **convert several select CGIs/AceDB classes to Catalyst Model::*.pm
    3 KB (365 words) - 19:14, 10 August 2010
  • ModENCODE Integration status
    Not in ACeDB yet because the data will be held as Features and we don't want lots of Fea Not in ACeDB yet because the data will be held as Features and we don't want lots of Fea
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  • Cronjobs
    ...s of the databases (when restarting) from the status information stored in acedb.
    2 KB (351 words) - 17:30, 19 June 2014
  • WBConfCall 2016.11.17-Agenda and Minutes
    *Juancarlos: no, from ACeDB *Raymond: how do we deal with discrepancies between acedb and datomic
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  • WS226
    acedb DIR - Everything needed to generate a local copy of the The - database.WS226.*.tar.gz - compressed acedb database for new release
    21 KB (2,346 words) - 11:15, 21 December 2011
  • WormBase-Caltech Weekly Calls April 2014
    === HTML format for special characters in ACEDB === * ACEDB doesn't support special character display (in concise decriptions, for exam
    10 KB (1,474 words) - 15:54, 30 April 2014
  • International C. elegans Meetings - UCLA
    **For 2021 abstracts: /home/acedb/kimberly/meeting_abstracts/2021_iwm_meeting_abstracts/AbsFiles_2021/AbsFile
    3 KB (532 words) - 13:33, 31 March 2022
  • WormBase Model:Method
    // Used a lot by acedb code for displaying data (on the FMap) and dumping data (via GFF)
    5 KB (504 words) - 15:09, 1 November 2010
  • WormBase-Caltech Weekly Calls July 2019
    ...n property to dump into OBO so our scripts can recognize them and populate ACEDB/Datomic; will look into; may require model change
    3 KB (427 words) - 15:32, 1 August 2019
  • WBConfCall 2020.06.18-Agenda and Minutes
    We can have two tags in ACeDB: genes_mentioned and genes_studied. The first tag can be automated and comp
    3 KB (490 words) - 17:22, 18 June 2020
  • Administration:Installing WormMine
    == 1. Generate ACeDB XML files == On a machine that has Acedb installed (such as <code>dev.wormbase.org</code>), check out the [https://g
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  • Processing Gene and Protein Names for Searches and Curation
    ...hem. For example, in case of WormBase, we get all classes except Gene from acedb and Gene list comes from postgres. SGD and FlyBase provide us with files on
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  • WBConfCall 2020.04.02-Agenda and Minutes
    ...submission form. An emailed html table is parsed and fields mapped to the acedb schema making suration semi automatic. If not enough info is provided or ID
    3 KB (523 words) - 11:20, 3 April 2020
  • WormBase-Caltech Weekly Calls November 2013
    ...that are flagged as "Not Checked" or "Irrelevant" will not be dumped into ACEDB, but "Relevant" papers will be * Separate meeting? Discussion topic - ACEDB/Database issues, smaller attendance
    10 KB (1,664 words) - 17:02, 4 December 2013
  • WormBase-Caltech Weekly Calls January 2022
    *Wen now downloads several full ACeDB classes from the latest WS release in the form of .ace files so we can also
    4 KB (600 words) - 18:40, 2 February 2022
  • Hinxton 2015.07- Meeting minutes
    ** ACeDB database done (MP) ** Ideal: Anyone can take an ACeDB database and load into a datomic instance
    11 KB (1,714 words) - 11:04, 27 July 2015
  • WormBase-Caltech Weekly Calls January 2014
    *Juancarlos can now modify WormBase widgets, but would need to learn how ACEDB is handled, if required *WOBr is not working off of ACEDB
    10 KB (1,583 words) - 18:16, 5 February 2014
  • Website:Application overview
    ...r that rests on top of AcePerl/AceDB. It's structure resembles classes in AceDB; however, models often cross class boundaries when aggregating data.
    10 KB (1,357 words) - 14:03, 19 June 2014
  • WBConfCall 2015.05.07-Agenda and Minutes
    * Give webteam dump of Parasite data to index ? Sounds good, currently using acedb format. Try homologs as starting point. Will look at current xml structur
    3 KB (558 words) - 17:29, 7 May 2015
  • WBConfCall 2020.02.06-Agenda and Minutes
    * AceDB datomic? - what do we want to do.
    3 KB (561 words) - 18:39, 6 February 2020
  • WBConfCall 2012.08.02-Agenda and Minutes
    **[Lincoln] Underlying database, there is a concrete plan to move away from acedb
    3 KB (560 words) - 16:24, 2 August 2012
  • WBConfCall 2021.06.17-Agenda and Minutes
    ** HX will unify the acedb and gff IDs so that the web code will not need to be changed.
    4 KB (576 words) - 16:28, 17 June 2021
  • GO-CAM GPAD
    my $annotFile = '/home/acedb/kimberly/citace_upload/go/gp_annotation.ace'; See lines 217 - 228 in /home/acedb/kimberly/citace_upload/go/gpad2ace/2018_October/go_gpad_parser.pl
    11 KB (1,439 words) - 22:10, 5 November 2018
  • WBConfCall 2020.10.01-Agenda and Minutes
    * Michael Paulini found that some Transgene IDs were missing in acedb from db to db
    3 KB (534 words) - 17:29, 1 October 2020
  • Former How To Build A WormBase Mirror
    ...it requires both ACeDB and MySQL to be installed. The middleware layer for ACeDB is AcePerl, and the middleware layer for MySQL is the Bio::DB::GFF module, * [http://www.acedb.org AceDB], v4.9t or higher
    60 KB (9,496 words) - 23:06, 13 August 2010
  • WormBase-Caltech Weekly Calls March 2014
    * We still keep "Date_last_updated" and "Curator_confirmed" in ACEDB in the #Evidence hash * ACEDB timestamps have been proven useful
    8 KB (1,218 words) - 17:46, 2 April 2014
  • Specifications for WB gpi file
    ! Tag in AceDB model
    5 KB (720 words) - 20:46, 10 October 2016
  • WormBase-Caltech Weekly Calls April 2021
    * How will we best handle AceDB hash structures? likely use something like Mark QT demonstrated * An initial idea was to promote data in ACEDB that may be underutilized or many users may be unaware of
    11 KB (1,782 words) - 17:55, 13 May 2021
  • WBConfCall 2012.05.03-Agenda and Minutes
    ** no infrastructure for non-acedb species
    4 KB (599 words) - 00:25, 4 May 2012
  • WormBase-Caltech Weekly Calls March 2018
    * Data has gone into ACEDB, but no display is configured yet ...ogether? Go right into Datomic? Need to check, but will probably pull into ACEDB and do the conversion to Datomic at the same time?
    11 KB (1,703 words) - 15:27, 5 April 2018
  • Developer documentation
    * [[Building WormMart|Building WormMart]] - ''How to convert a WormBase AceDB database into WormMart'' * AceDB classes -> API progress matrix (index of classes; see [https://spreadsheets
    12 KB (1,638 words) - 18:25, 18 June 2014
  • WBConfCall 2015.07.16-Agenda and Minutes
    * It currently consists of a perl script that queries an acedb database for data from Gene, CDS, Transcript and Pseudogene classes to prod
    4 KB (708 words) - 16:41, 16 July 2015
  • Gene Interaction/archive
    *.ace dumper at /home/acedb/xiaodong/gene_gene_interaction/dump_ggi_ace.pl # cd to directory on tazendra: /home/acedb/xiaodong/textpresso_ggi
    50 KB (5,228 words) - 15:10, 21 July 2017
  • OA and scripts for disease data
    The gene-disease OA (connected in AceDB models to ?Gene class) and the newer Disease_model_annotation data are now #All disease related files at: home/acedb/ranjana/human_disease
    36 KB (4,595 words) - 18:10, 15 March 2023
  • Gene Interaction
    * on tazendra: /home/acedb/xiaodong/oa_interactions_dumper ** /home/acedb/xiaodong/oa_interactions_dumper/Interaction_OA_Dumper_Output_Archive -- C
    53 KB (6,521 words) - 20:51, 7 March 2019
  • Updating WormBase
    ~ftp/pub/wormbase/acedb /usr/local/acedb/elegans_WSXXX
    34 KB (5,450 words) - 18:24, 17 August 2010
  • WBConfCall 2011.11.03-Agenda and Minutes
    *Can ACEDB handle the Tiers system?
    4 KB (609 words) - 20:57, 3 November 2011
  • WormBase-Caltech Weekly Calls October 2013
    * Issue is with denormalization of ACEDB to flat file ...objects in ?Construct objects? In Postgres, ACEDB, or both? Denormalize in ACEDB?
    13 KB (1,983 words) - 16:40, 7 November 2013
  • 2013 Advisory Board Meeting
    * Plans for retirement of the Acedb (Kevin/Todd; 15 mins)
    4 KB (462 words) - 08:54, 8 October 2014
  • WormBase-Caltech Weekly Calls June 2020
    * Will load into ACEDB soon * Person and Laboratory addresses in ACEDB have a different format, so looking to reconcile
    8 KB (1,228 words) - 20:57, 14 July 2020
  • WBConfCall 2013.08.15-Agenda and Minutes
    Does it handle acedb hashes? If it can be reached through xpath, it can be handled.
    4 KB (689 words) - 11:13, 29 August 2013
  • Topic pages
    **process pages will link summaries of processed with the most recent acedb data ...eric.cgi to tazendra -- J''' DONE, the next time you run it with wget from acedb account commandline on tazendra it will update, or the next time the cronjo
    20 KB (3,088 words) - 19:17, 13 August 2020
  • WormBase-Caltech Weekly Calls August 2011
    ACEDB vs Web Display
    4 KB (650 words) - 17:08, 1 September 2011
  • WormBase-Caltech Weekly Calls July 2020
    * Spreadsheet to map ACEDB/XML attributes to ACEDB attributes: https://docs.google.com/spreadsheets/d/1-fpzVU3rblN3Rp38wQjd312
    9 KB (1,369 words) - 22:47, 5 August 2020
  • Entering WBG Articles
    ...onvert them to standard characters before reading into the database, since ACeDB doesn't allow special characters.
    5 KB (761 words) - 21:04, 10 February 2012
  • Phenote+ Phenotype Curation
    ...ripted for readout into Phenote. The files are stored on tazendra in /home/acedb/karen/populate_gin_variation.
    5 KB (782 words) - 20:35, 24 September 2010
  • Antibody
    ***/home/acedb/xiaodong/antibody/use_package.pl <strike>[is located in tazendra:( /home/acedb/wen/phenote-antibody/dump_antibody_ace.pl)</strike>
    21 KB (2,888 words) - 19:58, 9 April 2021
  • Downloads
    AceDB, the database that drives WormBase http://www.acedb.org
    8 KB (1,219 words) - 22:33, 24 October 2011
  • WBConfCall 2012.12.06-Agenda and Minutes
    ...e exploring alternatives to CouchDB to store highly connected graphs (form ACeDB)
    5 KB (752 words) - 18:55, 6 December 2012
  • WBConfCall 2012.02.16-Agenda and Minutes
    === ACeDB WS231 models sign-off ===
    5 KB (800 words) - 10:09, 17 February 2012
  • WS221
    acedb DIR - Everything needed to generate a local copy of the The x) database.WS221.*.tar.gz - compressed acedb database for new release
    17 KB (1,758 words) - 16:47, 21 December 2011
  • WS289
    acedb DIR - Everything needed to generate a local copy of the The - database.WS288.*.tar.gz - compressed acedb database for new release
    16 KB (1,733 words) - 21:55, 11 May 2023
  • Model changes
    Sample ACeDB format of data using nemametrix tech note from here: http://nemametrix.com/
    7 KB (934 words) - 19:56, 27 September 2016
  • Documentation for workflow and scripts
    **acedb_port.txt is the location of the port of the acedb server. **acedb_host.txt is the IP address/hostname of the acedb server.
    15 KB (2,321 words) - 17:36, 18 August 2017
  • GPAD to .ace file
    Located here: /home/acedb/ranjana/citace_upload/go_curation/ptgo_to_ace
    6 KB (894 words) - 18:00, 11 November 2013
  • OA-phenotype
    tazendra /home/acedb/work/allele_phenotype/use_package.pl ...a and mangolassi at /home/acedb/work/allele_phenotype '''This file ? /home/acedb/work/allele_phenotype/legacy_information.txt There are no entries with "[
    23 KB (3,334 words) - 19:01, 31 October 2017
  • WormBase-Caltech Weekly Calls May 2021
    ...tly to the web team for display, rather than load all the data into Citace/ACEDB (introducing heavy load to system) and have it pass through the whole build
    5 KB (670 words) - 15:31, 3 June 2021
  • WBConfCall 2013.11.21-Agenda and Minutes
    ...e conferences in Dec. and Jan. to brainstorm possible databases to replace ACeDB and then do tests for these ideas.
    6 KB (909 words) - 21:56, 21 November 2013
  • WormBase-Caltech Weekly Calls June 2011
    *Querying ACeDB
    5 KB (752 words) - 17:07, 7 July 2011
  • WS215
    3. Obtain and install a suitable acedb binary for your system (available from www.acedb.org).
    19 KB (1,735 words) - 11:07, 21 December 2011
  • WormBase-Caltech Weekly Calls January 2021
    * Corresponding authors not tracked in ACEDB, because authors are just text names not IDs
    5 KB (873 words) - 14:41, 4 February 2021
  • WormBase-Caltech Weekly Calls January 2012
    *Indexed ACEDB data used for searches; create table from indexed data?
    5 KB (847 words) - 17:49, 1 March 2012
  • Source and maintenance of non-WBGene info
    !AceDB tag
    8 KB (1,375 words) - 05:12, 21 April 2020
  • WormBase-Caltech Weekly Calls October 2012
    *Proposal: read CSHace data into ACEDB and then read in CITace minus data (which would overwrite CSHace data with
    5 KB (843 words) - 17:26, 1 November 2012
  • WormBase-Caltech Weekly Calls November 2014
    * Old life stages in ACEDB as string name instead of life stage ID
    5 KB (843 words) - 16:32, 4 December 2014
  • Feature WishList
    ...ic way, we could actually move much meta information on objects OUT of the acedb database into a more amenable database/interface structure.
    6 KB (842 words) - 17:01, 21 October 2011
  • WormBase Staff Resources
    #* Describe where this data is - acedb tag? other data source?
    7 KB (1,036 words) - 14:30, 14 January 2016
  • N-Browse Installation & Interaction Data
    .... After it is installed, Wormbase interaction data needs to be dumped from AceDB and loaded to MySQL. Finally, the data in the MySQL database needs to be pr
    7 KB (1,133 words) - 17:52, 16 August 2010
  • WormBase-Caltech Weekly Calls October 2020
    * The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated g
    6 KB (861 words) - 19:23, 5 November 2020
  • Overview
    ...hows up in the term info box when selected. Keeping the file updated from acedb and showing this information in the term info box helps during curation as
    7 KB (1,148 words) - 23:02, 23 October 2014
  • Gene Expression micropublications
    /home/acedb/public_html/draciti/Micropublication/ /home2/acedb/public_html/draciti/Micropublication/uploads/
    21 KB (3,194 words) - 02:08, 17 May 2018
  • Genetics Markup by Textpresso and First Pass
    * New data goes to the appropriate data curator for acedb object creation.
    7 KB (1,133 words) - 20:36, 23 July 2013
  • WormBase-Caltech Weekly Calls October 2019
    ...isted of only whitespace, some of which were causing errors upon upload to ACEDB ** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putativ
    13 KB (2,025 words) - 16:28, 7 November 2019
  • WBConfCall 2012.02.02-Agenda and Minutes
    === ACeDB models ===
    8 KB (879 words) - 09:32, 3 February 2012
  • Gene Regulation
    '''I've dumped .ace file for WS232 on tazendra: /home/acedb/xiaodong/gene_regulation/gene_regulation.ace.20120419''' -X 04/19/2012 ...pg.err (there's a few check them out, need to fix the source file at /home/acedb/xiaodong/gene_regulation/GR_OA.ace ) DONE on tazendra, live on 2010 11 08
    59 KB (8,367 words) - 22:00, 14 December 2018
  • Postgres queries
    Corresponding acedb queries:
    10 KB (1,650 words) - 18:12, 29 January 2024
  • Administration:WormBase Production Environment
    acedb ...with the exception of GBrowse -- almost entirely independent, with its own AceDB and MySQL databases.
    32 KB (4,370 words) - 20:48, 18 June 2014
  • WormBase-Caltech Weekly Calls July 2012
    *What if Postgres (as opposed to ACEDB) became main repository of person info?
    6 KB (944 words) - 16:25, 1 November 2012
  • WormBase-Caltech Weekly Calls August 2014
    * Will compare performance of Datomic vs. Postgres and ACEDB, etc.
    6 KB (974 words) - 17:28, 3 September 2014
  • RNAi/archive
    ...ge" field must be filled in with an official life stage name, as stored in ACeDB/WormBase. For an official list of Life Stage names in WormBase, see: ...free of errors, you may wish to test both *.ace files by reading them into ACEDB and ensuring that they read into the database with no errors.
    47 KB (7,989 words) - 23:40, 1 September 2015
  • WormBase-Caltech Weekly Calls December 2011
    *Suppress entire objects from loading to ACEDB if has dead genes? No, still dump, but add cautionary remark?
    6 KB (903 words) - 16:37, 5 January 2012
  • WormBase Model:Sequence
    // if RNA tag, acedb outputs U in place of T in sequence output
    12 KB (1,258 words) - 09:29, 5 October 2010
  • COMMENTARY
    ...some searches allow uploading large files for queries. Searches using the ACeDB Query Language (AQL) are also feasible. Information about how to use WormBa ...omplished in 1998 with AcePerl (Stein and Thierry-Mieg, 1998). AcePerl and ACeDB became the core of WormBase at its founding in 2000 (Chen et al., 2005), al
    30 KB (4,765 words) - 20:03, 11 August 2010
  • Tasks in Progress
    **Updating API and interface to account for changes to the ACeDB Schema/Model ...r CHROMOSOME pages due to loading issues (sequence is too large and blocks acedb for a while)
    29 KB (4,254 words) - 20:25, 27 April 2012
  • WormBase-Caltech Weekly Calls September 2015
    * Thomas wrote an ACEDB-to-Datomic converter; Juancarlos testing with a subset of data
    6 KB (906 words) - 21:38, 30 September 2015
  • WormBase-Caltech Weekly Calls May 2018
    ...ved mostly by Datomic now, but we (Caltech curators) are still modeling in ACEDB only ...completely move everything into Datomic (become completely independent of ACEDB)?
    14 KB (2,226 words) - 15:31, 7 June 2018
  • Annotation of Disease scripts
    ...{ # if there is disease relevance, dis_diseaserelevance, convert '-->" for acedb,
    10 KB (1,461 words) - 23:06, 27 February 2017
  • WormBase-Caltech Weekly Calls March 2013
    **Whereas AQL and WQL will be obsolete when we leave ACeDB, AcePerl will still be useful (even if the details need updating)
    7 KB (1,047 words) - 15:34, 4 April 2013
  • RNAi
    0 3 * * sun /home/acedb/gary/phn_suggested/phn_suggested_oa.pl ..._homol" and "Uniquely_mapped" will be omitted from the OA and populated in ACEDB after probe mapping to the genome at the EBI during the build process.
    29 KB (4,152 words) - 20:29, 30 July 2019
  • WormBase-Caltech Weekly Calls February 2012
    *Old objects updated OK and read into ACEDB without problems
    7 KB (1,070 words) - 17:47, 1 March 2012
  • WormBase-Caltech Weekly Calls July 2013
    ACEDB, Citace Minus
    7 KB (1,059 words) - 15:37, 1 August 2013
  • WormBase-Caltech Weekly Calls June 2017
    * There are several ?RNAi objects in ACEDB that refer to multiple phenotypes, each with their own remark and penetranc
    8 KB (1,213 words) - 15:29, 6 July 2017
  • WormBase-Caltech Weekly Calls 2023
    *They will then copy the files to the dockerized system - acedb@caltech-curation.textpressolab.com <br/> **scp: scp -P 2022 <file> acedb@caltech-curation.textpressolab.com:/path/to/file/(-p is to specify port wit
    36 KB (4,994 words) - 17:27, 14 February 2024
  • Micropub Pipeline
    * if authors submit through the form the images are stored here: /home2/acedb/public_html/draciti/Micropublication/uploads/
    9 KB (1,391 words) - 19:47, 19 April 2023
  • FAQs
    ...ented database, ACeDB, which is the "master" database containing all data. ACeDB can be accessed both remotely and locally, through both commandline and web ...g genomics sequence, ESTs, OSTs, SNPs, genes, RNAs etc) are extracted from ACeDB and are deposited in a "slave" MySQL database, to support some key features
    67 KB (10,954 words) - 09:22, 19 February 2013
  • WormBase-Caltech Weekly Calls March 2015
    * Issues came up with layered hash references in ACEDB when converting to Datomic
    7 KB (1,058 words) - 15:32, 2 April 2015
  • WormBase-Caltech Weekly Calls April 2012
    *This is because ACEDB only handles names, not IDs
    7 KB (1,158 words) - 17:20, 3 May 2012
  • WormBase-Caltech Weekly Calls April 2020
    * ?ECO_term to replace ?GO_code in ACEDB models
    7 KB (1,020 words) - 15:33, 7 May 2020
  • Migration
    -rwxrwxr-x 1 todd wormbase 840 Jul 6 14:06 acedb
    16 KB (1,576 words) - 17:44, 16 August 2010
  • WormBase-Caltech Weekly Calls October 2016
    * Disease data dumped from ACEDB, based on Disease Ontology; not comprehensive for OMIM disease list
    8 KB (1,289 words) - 18:11, 10 November 2016
  • WormBase-Caltech Weekly Calls June 2019
    *Is 'WBDisease_annotation:00000004' too long for acedb?
    8 KB (1,121 words) - 14:01, 15 July 2019
  • Concise Descriptions
    /home/acedb/ts/wspec/ ...a symlink to make the most recent downloaded models file the file used by acedb on tazendra:
    47 KB (6,852 words) - 04:27, 8 December 2020
  • WormBase-Caltech Weekly Calls May 2017
    * ACEDB to Datomic? AGR dependent activities? May need to consider both
    8 KB (1,229 words) - 15:31, 1 June 2017
  • Pictures
    ...re_source- to tazendra scp picture_source acedb@tazendra.caltech.edu:/home/acedb/draciti/picture_source/ /home/acedb/draciti/picture_source/populate_obo_data_pic_picturesource.pl
    120 KB (19,719 words) - 16:44, 20 October 2023
  • WormBase-Caltech Weekly Calls May 2014
    * Wen can install relevant versions of ACEDB (WS238 - WS243?) to pull annotation numbers
    8 KB (1,234 words) - 12:36, 4 June 2014
  • Contacting the Community
    /home/acedb/ranjana/concise_emailing/generate_list_papers_concise_email.pl http://tazendra.caltech.edu/~acedb/ranjana/concise_list_to_email.html
    13 KB (2,062 words) - 14:01, 4 August 2017
  • WormBase
    /home/acedb/kimberly/ccc/ccc_source/worm
    11 KB (1,666 words) - 17:53, 19 June 2014
  • Paper Tables in Postgres
    ...ds the information on editors of paper objects, mostly books. The current ACeDB ?Paper model dumps Editors as ?Text, but there is not a separate ?Editor cl For the ACeDB dumping script, the month is converted to a number.
    25 KB (3,238 words) - 16:42, 8 November 2019
  • WormBase-Caltech Weekly Calls April 2018
    * Difficult to query this out of ACEDB
    8 KB (1,262 words) - 15:34, 3 May 2018
  • TAIR CCC
    '''Note that the source files have been moved to /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles/ and stored on tazendra at: /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles
    24 KB (3,814 words) - 18:31, 8 August 2011
  • WormBase-Caltech Weekly Calls September 2016
    * Data will be pulled from ACEDB and used to generate display
    9 KB (1,490 words) - 15:35, 6 October 2016
  • WormBase-Caltech Weekly Calls December 2012
    *DO terms going to citace/ACEDB for upload
    9 KB (1,339 words) - 19:02, 31 January 2013
  • WormBase-Caltech Weekly Calls August 2015
    * Juancarlos working with Kevin and Thomas on integrating/migrating ACEDB data (priority GeneAce) to Datomic
    8 KB (1,220 words) - 16:26, 3 September 2015
  • WormBase-Caltech Weekly Calls 2022
    ...re information. If hidden it stays in Caltech postgres, and doesn't go to acedb.
    10 KB (1,547 words) - 21:31, 2 January 2024
  • WormBase-Caltech Weekly Calls October 2017
    * GO CAM models do not go into ACEDB, yet
    10 KB (1,586 words) - 15:30, 2 November 2017
  • Generation of automated descriptions
    /home/acedb/ranjana/concise_testing/populate_automated_concise_descriptions.pl Both populating and dumping scripts at:/home/acedb/ranjana/concise_testing
    65 KB (9,380 words) - 22:39, 5 July 2018
  • All OA tables
    ...Transgene/Rearrangement Phenotype Curation<br> dumper on tazendra at /home/acedb/work/allele_phenotype/use_package.pl ''' <br> note: this dumper makes both ...es tables for the Expression Pattern class<br> dumper on tazendra at /home/acedb/draciti/oa_expr_ace_dumper/use_package.pl '''
    37 KB (5,333 words) - 19:07, 27 June 2019
  • Unused Attributes
    ! ACeDB Model ! ACeDB Tag
    35 KB (4,174 words) - 10:52, 2 February 2015
  • Phenote Fields
    ...it. Text temp scale (C) is accepted, displayed in the .ace and migrated to acedb. We will need to request that these symbols are displayed on the website.
    12 KB (1,991 words) - 23:45, 14 February 2011
  • Updating go.ace file
    **Script on tazendra: /home/acedb/kimberly/citace_upload/go/ontology2ace/go_obo2ace/go_obo_to_go_ace.pl
    15 KB (1,936 words) - 16:29, 29 June 2018
  • WormBase-Caltech Weekly Calls January 2013
    *Relational DB vs ACEDB
    10 KB (1,553 words) - 18:04, 7 February 2013
  • WormBase-Caltech Weekly Calls January 2015
    * ACEDB, Kris Gunsalus' server at NYU (defunct), Nikhil Bhatla's connectivity brows http://tazendra.caltech.edu/~acedb/daniel/00046176_Wei14_temp.pdf
    10 KB (1,453 words) - 18:52, 4 February 2015
  • Missing PMIDs
    ...to the pap_identifier tables in postgres. File located on Tazendra: /home/acedb/draciti/DOI/doi_automatic_retrieval. dr
    14 KB (2,344 words) - 23:02, 14 December 2011
  • Transgenes
    /home/acedb/wen/phenote_transgene/ObsoleteTg.txt ...nslate the transgene trp postgres data into .ace format for uploading into AcEDB.
    29 KB (4,575 words) - 16:23, 3 March 2022
  • WormBase-Caltech Weekly Calls August 2012
    *Dependency on ACEDB?
    12 KB (1,878 words) - 15:55, 6 September 2012
  • WormBase-Caltech Weekly Calls April 2019
    * Make modification to ACEDB model?
    11 KB (1,676 words) - 15:28, 2 May 2019
  • Expression Pattern
    this lists are kept updated with what is in acedb daily using the following cronjob: this lists are kept updated with what is in acedb daily using the following cronjob:
    104 KB (15,303 words) - 19:39, 11 May 2023
  • Pipeline for identifying papers with disease or disease gene ortholog
    On Tazendra: /home/acedb/ranjana/human_disease
    15 KB (2,102 words) - 05:17, 25 September 2014
  • Person
    * /home/acedb/cecilia/citace_upload/get_pap_person_ace.pl * /home/acedb/cecilia/citace_upload/errors_in_pap_person.ace (vim this and get two# with
    119 KB (18,888 words) - 00:05, 2 May 2014
  • VariationConciseDescriptions
    **Variation Affects Gene + gene exists with cns_summary table entry; acedb model Gene->Gene_info->Concise_description */home/acedb/ranjana/concise_testing/populate_automated_concise_descriptions.pl -> /hom
    36 KB (5,076 words) - 01:38, 2 March 2016
  • Searching WormBase for Information About C. elegans (Wiley)
    ...sae genomic sequences; detailed, user-customized searches with WormMart or AceDB Query Language; batch downloads of many sequences at once; identifying the ...advantage of two hard drives is that WormBase uses two separate databases (ACeDB and MySQL) which work better if put on separate disks.
    103 KB (16,375 words) - 23:39, 30 November 2010
  • FP curator comments for St.Louis and Sanger structure correction data type
    | 4567||(gene names not yet in acedb) GLR-4 (AF318608) ~ C06A8.9 NMR-2 (AF318614) ~ T01C3.10 ||2/2/02 21:01 ...||alternative transcripts CeTM I through IV from figure 2 are not shown in acedb ||2/2/02 21:01
    40 KB (4,083 words) - 23:02, 13 August 2010
  • CCC Form 2.0 Specifications
    #Test files for C. elegans are on mangolassi here: /home/acedb/kimberly/ccc_2_testing/20130426_WB_test_files
    30 KB (4,868 words) - 14:50, 11 June 2013
  • Molecule
    /home/acedb/karen/molecule/chebi_missing/find_missing_chebi_in_other_oa.pl *Dumper - Molecule.ace made from /home/acedb/karen/WS_upload_scripts/Molecule/dump_molecule_ace.pl
    50 KB (6,966 words) - 19:15, 13 August 2020
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