xBio:D Wiki - User contributions [en]

Tyrannoscelio Server Management

2015-08-07T20:09:47Z

Jcora: /* Mount Remote Devices */

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'''Tyrannoscelio Server Management (tyrannoscelio.biosci.ohio-state.edu)'''

== General Locations ==
* Data Directory: ''/data/''

== Data Backup ==
=== Offsite Backup Job ===
Tyrannoscelio mediates transferring backup files from MegaRaid, the inside the rack NAS, to the ASC offsite shared share. Both of these devices are mounted as directories on the server.

See cron jobs: <code>sudo crontab -l</code>

=== Mount Remote Devices ===
The system-wide mounted devices are located in the fstab file and can be modified through the ''nano'' program: <code>sudo nano /etc/fstab</code>

The MegaRaid share is mounted with the line <code>//128.146.250.101/OSUC_Share /share/MegaRaid_Share cifs credentials=/home/jcora/.megaraid.cred,gid=osuc_backup,dir_mode=0770,file_mode=0770 0 0</code>, which will not need updated unless the ''jcora'' password changes.

The ASC share is mounted with the line <code>//research.asc.ohio-state.edu/units/EEOB/njohnson-backup /share/ASC_Share cifs credentials=/home/nfj/.asc_nas.cred,gid=osuc_backup,dir_mode=0770,file_mode=0770 0 0</code>. The OSU credentials file, ''/home/nfj/.asc_nas.cred'', will need updated every time the password for the Ohio State federated login of ''johnson.2'' changes.

[[Category:OSUC Private]]

XBio:D Data Management

2015-08-07T19:59:59Z

Jcora:

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'''xBio:D Data Management'''

This section provides instructions on performing common data management tasks on the xBio:D database that are not privy to general users. These tasks are not available through web applications and must either be performed by running a script or a database procedure.

== Change Occurrence (Specimen) Record CUID ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC updateSpmID(old_cuid, new_cuid);</code>. The procedure will only produce output when a problem occurred.

== Remove Occurrence (Specimen) Record ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC removeSpm(cuid);</code>. The procedure will only produce output when a problem occurred.

== Merged/Remove Locality Name ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC change_locality(obsolete_loc_name, valid_loc_name);</code>. The procedure removes the obsolete locality and places all of the occurrence records from the obsolete locality into the valid locality name. There is also an additional, optional parameter ''coll_date'', which accepts the format DD-MON-YYYY, that will change the functioning of this procedure to change only those occurrence records that were collected on that particular date. If all of the occurrences were collected on that day, the locality is removed. The procedure will only produce output when a problem occurred.

== Add Collection Records or Taxon Checklist as a Project to the xBio:D IPT ==
# Log into the database server (''osuc.biosci.ohio-state.edu'') via SSH and open DwC-A collection export script, ''export_dwca_collections.py''. This script is set to run every Sunday at 8PM.
## <code>ssh [username]@osuc.biosci.ohio-state.edu</code>
## <code>sudo nano /var/www/cgi-bin/export_dwca_collections.py</code>
# Go to the ''handleDwCAExport'' function and add the taxon or collection you would like to export.
## The ''exportDwCA'' function of the OJ_Exporter package takes the collection ''Storage_Regime_ID'' as the identifier.
## The ''exportTaxonDwCA'' function of the OJ_Exporter package takes the taxon ''tnuid'' as the identifier.
# Execute the ''export_dwca_collections.py'' script immediately or wait until after the weekly export execution
# Download the DwC-A file created for the new collection or checklist
## Collection records example: ''http://osuc.biosci.ohio-state.edu/data_exports/dwca_1.zip''
## Taxon checklist example: ''http://osuc.biosci.ohio-state.edu/data_exports/dwca_tax_195000.zip''
# Create project in xBio:D IPT for the data you will be disseminating.
## Log into IPT and go to ''Manage Resources''
## Scroll to the bottom to ''Create New Resource'', specify a short name and resource type, then upload the previously exported file and create resource
## Fill in the metadata section of the resource with the appropriate values for provider, owner, etc.
# Log into the hymfiles server (''osuc.biosci.ohio-state.edu'') via Remote Desktop and open IPT DwC-A import script, ''populate_ipt.py''. The Python script is located in ''C:\backup_scripts''.
# Go to the ''handlePopulateIPT'' function and add the taxon or collection you would like to export.
## The numeric identifiers are the same as defined in the ''export'' step above
## The second parameter for the populate script is the resource short name specified above.
# Register and publish the new project. The resource will now be available on GBIF and can be shared with other data aggregators like iDigBio, VertNet, etc.

== Specialized Scripts for DB processing Tasks ==
These scripts include DOI lookup for xBio:D publication, processing the gender of people, and uploading of PDFs into Zenodo. The scripts are located in ''/scripts'' on the Database server.

== Aggregation Update ==
Many DB queries use tables that are aggregated from many separate tables to speed up processing. These aggregation tasks are performed automatically every Saturday under the DB job named ''aggregation_update''. These tasks include the following:
* '''''processDescriberIDs''''' - Goes through each taxonomic concept that does not already have a describer specified within the ''Protonym'' table and attempts to infer from an original description or replacement name literature annotation the author of the taxon. If a match is found, then the individual describer or describer party is added to the ''Protonym'' table.
* '''''update_people_stats''''' - Builds the ''AGGR_Person_Stats'' table that contains the # of occurrences collected, # of papers published, # of determinations made, # of distinct events collected, and the total # of contributions for each person.
* '''''update_genera_stats''''' - Builds the ''AGGR_Genus_Stats'' table that contains the # of occurrences determined, # of papers published, # of images taken, # of collections deposited, and distinct events collected for each tnuid.
* '''''update_place_children''''' - Builds the ''AGGR_Place_Children'' table that contains a place along with each subordinate place at any lower position within the geopolitical hierarchy.
* '''''update_taxon_children''''' - Builds the ''AGGR_Taxon_Children'' table that contains a tnuid along with each subordinate tnuid at any lower position within the taxonomic hierarchy. Species-group taxa are excluded as parent taxa within this table.
* '''''update_fossil_taxa''''' - Builds the ''AGGR_Fossil_Taxa'' table that contains a tcid for each taxon concept that is a fossil. Fossil status is only applied to species-group taxa, so this procedure also added taxa in which all of its subordinate taxa are fossils.
* '''''update_recordings''''' - Builds the ''AGGR_Taxon_Recordings'' table that contains a tnuid and recording info id for any recording that is contained within the taxon.
* '''''update_images''''' - Builds the ''AGGR_Taxon_Images'' table that contains a tnuid and image id for any specimen or taxon image that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_habitats''''' - Builds the ''AGGR_Habitat'' table that contains a tnuid and habitat for any occurrence that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_taxon_contributors''''' - Builds the ''AGGR_Taxon_Contribs'' table that contains a tnuid, contributor, and contribution flags for every contribution from the contributor within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_inst_tcids''''' - Builds the ''AGGR_Inst_Tcids'' table that contains the tcids for every collection where an occurrence is present. Species-group taxa are excluded as parent taxa within this table.
* '''''update_associations''''' - Builds the ''AGGR_Taxon_Assocs'' table that contains a tnuid and associated tnuid for every taxon that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.

[[Category:OSUC Private]]

Collection (OSUC) Private Portal

2015-08-07T19:49:31Z

Jcora:

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'''Welcome to the OSUC Private Portal'''

This section of the wiki is private for users associated with the C.A. Triplehorn Insect Collection (OSUC). All subsequent pages, in order to be private, must be protected. Protect new pages by clicking the down arrow next to "View history" at the top, then select "Protect". When the protection setting page is loaded, choose "OSUC users group" from the "Edit" box to reject all users who are not part of the OSUC users group from editing or reading the page.

== General ==
* [[Miscellaneous Publications]]

== Infrastructure ==
* [[xBio:D Data Management]]
* [[xBio:D Applications]]
* [[xBio:D Database Server Management]]
* [[Collection Server Management]]
* [[Hymfiles Server Management]]
* [[Macroteleia Server Management]]
* [[Tyrannoscelio Server Management]]
* [[Initiate ASC Offsite Backup]]
* [[OBCP Cluster Management]]

== Bioinformatics ==
* [[Data Validation]]

[[Category:OSUC Private]]

Hymfiles Server Management

2015-08-07T19:48:58Z

Jcora: /* Data Backup */

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'''Hymfiles Server Management (hymfiles.biosci.ohio-state.edu)'''

== General Locations ==
* IIS Web Directory: ''C:\inetpub\wwwroot''
* xBio:D IPT Directory: ''C:\ipt_data''
* Redmine Home Directory: ''D:\redmine''
* Backup Scripts Directory: ''C:\backup_scripts''

== Applications / Services ==
* PDF storage - http://hymfiles.biosci.ohio-state.edu/pdfs-osuc/
* PDF storage (Antbase) - http://hymfiles.biosci.ohio-state.edu/pdfs-antbase/
* DB Manager taxon images - http://hymfiles.biosci.ohio-state.edu/taxon_images
* Bonobo Git Server - http://hymfiles.biosci.ohio-state.edu/Bonobo.Git.Server/
* Redmine Bug Tracker/Project Manager - http://hymfiles.biosci.ohio-state.edu/redmine/

== Data Backup ==
File backups of the web files and the python files are handled by the RealtimeSync program using Windows Task Scheduler.

[[Category:OSUC Private]]

Collection Server Management

2015-08-07T19:35:35Z

Jcora:

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'''Collection Server Management (delong.biosci.ohio-state.edu)'''

== General Locations ==
* IIS Web Directory: ''D:\wwwroot''
* DEA Home Directory: ''D:\python_projects\dea''
* Backup Scripts Directory: ''C:\backup_scripts''

== Applications / Services ==
* DEA - http://xbiod.osu.edu/dea/
* Specimage - http://specimage.osu.edu
* xBio:D Gateway (Redirects)
* Collection Web Site - http://bugs.osu.edu
* Collection Web Site (Wordpress) - http://osuc.osu.edu/osuc-wp/
* xBio:D Wiki - http://xbiod.osu.edu/wiki/
* NFJ Lab Web Site - http://wasps.osu.edu
* BLB mp3 storage - http://osuc.osu.edu/blbmp3s/

== Data Backup ==
=== DEA Database Backup ===
The database is backup up daily at 9PM via the mysql_backup.bat script. This script create a database dump and transfers saves this file to the ''dumpfiles'' directory of the web directory.

=== File Backup ===
File backups of the web files and the python files are handled by the SyncToy program using Windows Task Scheduler.

[[Category:OSUC Private]]

Collection Server Management

2015-08-07T19:34:53Z

Jcora:

----

'''Collection Server Management (delong.biosci.ohio-state.edu)'''

== General Locations ==
* IIS Web Directory: ''D:\wwwroot''
* DEA Home Directory: ''D:\python_projects\dea''
* Backup Scripts Directory: ''C:\backup_scripts''

== Applications / Services ==
* DEA - http://xbiod.osu.edu/dea/
* Specimage - http://specimage.osu.edu
* xBio:D Gateway (Redirects)
* Collection Web Site - http://bugs.osu.edu
* Collection Web Site (Wordpress) - http://osuc.osu.edu/osuc-wp/
* xBio:D Wiki - http://xbiod.osu.edu/wiki/
* NFJ Lab Web Site - http://wasps.osu.edu
* BLB mp3 storage - http://osuc.osu.edu/blbmp3s/

== Data Backup ==
=== DEA Database Backup= ==
The database is backup up daily at 9PM via the mysql_backup.bat script. This script create a database dump and transfers saves this file to the ''dumpfiles'' directory of the web directory.

=== File Backup ===
File backups of the web files and the python files are handled by the SyncToy program using Windows Task Scheduler.

[[Category:OSUC Private]]

VSysLab Application Information

2015-08-07T19:31:19Z

Jcora: Protected "VSysLab Application Information" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

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'''vSysLab Application Information (http://vsyslab.osu.edu)'''

== General Information ==
* Server: ''Database (osuc.biosci.ohio-state.edu)''
* Directory: ''/var/www/html/vSysLab''
* APIs: ''vSysLab, OJ_Break (v1 & v2)''
* Git URL: ''http://hymfiles.biosci.ohio-state.edu/Bonobo.Git.Server/vsyslab.git''

== Files ==
=== Site-Wide ===
* vSysLab-new.js
* vSysLab.css

=== Pages ===
* index.html - vSysLab_Index.js
* add_new_det.html - vSysLab_AddNewDet.js
* contributors.html - vSysLab_Contributors.js
* export_lif.html - vSysLab_ExportLIF.js
* export_nexus.html - vSysLab_ExportNexus.js
* export_pwt-xml.html - vSysLab_ExportPWT-XML.js
* export_sdd.html - vSysLab_ExportSDD.js
* export_taxpub.html - vSysLab_ExportTaxPub.js
* home_page.html - vSysLab_HomePage.js
* import_lucid.html - vSysLab_ImportLucid.js
* import_nexus.html - vSysLab_ImportNexus.js
* invalid.html - vSysLab_Invalid.js
* list_collections.html - vSysLab_ListCollections.js
* make_desc.html - vSysLab_MakeDesc.js
* manage_chars.html - vSysLab_ManageChars.js
* manage_details.html - vSysLab_ManageDetails.js
* manage_images.html - vSysLab_ManageImages.js
* manage_matex.html - vSysLab_ManageMatEx.js
* manage_measurements.html - vSysLab_ManageMeasurements.js
* manage_OTUs.html - vSysLab_ManageOTUs.js
* new_user.html - vSysLab_NewUser.js
* prepare_matex.html - vSysLab_PrepareMatEx.js
* prepare_species.html - vSysLab_PrepareSpecies.js
* project_page.html - vSysLab_ProjectPage.js
* project_settings.html - vSysLab_ProjectSettings.js
* reorder_char_groups.html - vSysLab_ReorderCharGroups.js
* reorder_chars.html - vSysLab_ReorderChars.js
* reorder_otus.html - vSysLab_ReorderOTUs.js
* score_otu_char.html - vSysLab_ScoreOtuChar.js
* show_matrix.html - vSysLab_ShowMatrix.js
* show_otu_char.html - vSysLab_ShowOtuChar.js

=== Helper Scripts ===
* http://hymfiles.biosci.ohio-state.edu/scripts/vSysLab.pl
* http://osuc.biosci.ohio-state.edu/cgi-bin/vSysLab-osuc.pl

[[Category:OSUC Private]]
[[Category:xBio:D Application Info]]

Specimage Application Information

2015-08-07T19:30:25Z

Jcora: Protected "Specimage Application Information" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

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'''Specimage Application Information (http://specimage.osu.edu)'''

== General Information ==
* Server: ''Collection (delong.biosci.ohio-state.edu)''
* Directory: ''D:\wwwroot\Specimage''
* APIs: ''Specimage, OJ_Break (v1 & v2), vSysLab''
* Git URL: ''http://hymfiles.biosci.ohio-state.edu/Bonobo.Git.Server/specimage.git''

== Files ==
=== Site-Wide ===
* Specimage.js
* Specimage.css

=== Pages ===
* index.html - Specimage_Index.js
* addBodyPart.html - Specimage_AddBodyPart.js
* addBodyPartComb.html - Specimage_AddBodyPartComb.js
* addSpmImage.html - Specimage_AddSpmImage.js
* editSpmImage.html - Specimage_EditSpmImage.js
* getImageInfo.html - Specimage_GetImageInfo.js
* listSpmImages.html - Specimage_ListSpmImages.js
* manageProject.html - Specimage_ManageProject.js
* rss.html - Specimage_RSS.js

=== Helper Scripts ===
* http://osuc.osuc.edu/scripts/Specimage.pl

[[Category:OSUC Private]]
[[Category:xBio:D Application Info]]

Specimage Application Information

2015-08-07T19:30:04Z

Jcora: Created page with "---- '''Specimage Application Information (http://specimage.osu.edu)''' == General Information == * Server: ''Collection (delong.biosci.ohio-state.edu)'' * Directory: ''D:..."

DEA Application Information

2015-08-07T19:23:45Z

Jcora: Protected "DEA Application Information" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

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'''DEA Application Information (http://xbiod.osu.edu/dea/)'''

== General Information ==
* Server: ''Collection (delong.biosci.ohio-state.edu)''
* Web Directory: ''D:\wwwroot\dea2''
* Django Directory: ''D:\python_projects\dea''
* APIs: ''DEA (Django), DEA (xBio:D), OJ_Break (v1)''
* Git URL: ''http://hymfiles.biosci.ohio-state.edu/Bonobo.Git.Server/dea.git''

== Accessing Django Admin ==
=== General ===
The Django administrative interface for DEA provides access to the underlying MySQL database that supports DEA. This interface can allow an admin to change the owner for a file, remove actions associated with a file, remove a zombie'd background processing job status, and more.

=== Logging Into Collection Server (Delong) ===
In Windows, open the Remove Desktop application and enter to ''osuc.osu.edu''. Log in using the Windows login credentials.

=== Access Django Admin Web Interface ===
Open Internet Explorer, and type in the URL ''http://localhost:8081/admin/dea_rest/''. Log in using the Django login credentials.

== Background Processing ==
DEA uses Celery to handle the queuing and running of background tasks that are specified within the ''tasks.py'' file within DEA Django. A RabbitMQ server brokers the messages to process these tasks with the operating system. Each time a background task is started, a record in the 'DEA_Action_Status" table is created that contains the current status of the background task. Once the task completes, the status of the record is changed to the returned status of the task. DEA will periodically poll the status until a change occurs, and when it does, DEA will handle the message and remove the record.

== Changing Ownership of a File ==
In the Django Admin interface, go to the ''Dea_Files' table. The search at the top will search for a particular filename in which the owner is desired to be changed and filters on the right can additional assist in this task. When the file is located, click on the record and adjust the ''owner'' field to the appropriate username for the new owner.

== Files ==
=== Site-Wide ===
* dea.js
* dea.css

=== Pages ===
* index.html - dea_index.js
* batchCheckTaxa.html - dea_batchCheckTaxa.js
* batchEnterLocalities.html - dea_batchEnterLocalities.js
* batchEnterSpecimens.html - dea_batchEnterSpecimens.js
* loadFile.html - dea_loadFile.js
* setCollectingMethods.html - dea_setCollectingMethods.js
* setCollectors.html - dea_setCollectors.js
* setDates.html - dea_setDates.js, Date_Interpreter.js
* setDeterminer.html - dea_setDeterminer.js
* setFieldCodes.html - dea_setFieldCodes.js
* setHabitats.html - dea_setHabitats.js
* setLocalities.html - dea_setLocalities.js
* stats.html - dea_stats.js

[[Category:OSUC Private]]
[[Category:xBio:D Application Info]]

DEA Application Information

2015-08-07T19:22:29Z

Jcora: Created page with "---- '''DEA Application Information (http://xbiod.osu.edu/dea/)''' == General Information == * Server: ''Collection (delong.biosci.ohio-state.edu)'' * Web Directory: ''D:\..."

VSysLab Application Information

2015-08-07T18:41:17Z

Jcora: Created page with "---- '''vSysLab Application Information (http://vsyslab.osu.edu)''' == General Information == * Server: ''Database (osuc.biosci.ohio-state.edu)'' * Directory: ''/var/www/h..."

Database Manager Application Information

2015-08-07T17:42:07Z

Jcora: Protected "Database Manager Application Information" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

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'''Database Manager Application Information (http://osuc-mgr.osu.edu)'''

== General Information ==
* Server: ''Database (osuc.biosci.ohio-state.edu)''
* Directory: ''/var/www/html/db_mgr''
* APIs: ''DBManager, OJ_Break (v1 & v2)''
* Git URL: ''http://hymfiles.biosci.ohio-state.edu/Bonobo.Git.Server/db_mgr.git''

== Files ==
=== Site-Wide ===
* db_mgr.js
* db_mgr.css

=== Pages ===
* index.html - db_mgr_index.js
* addAssocReference.html - db_mgr_addAssocReference.js
* addAssocType.html - db_mgr_addAssocType.js
* addBGSource.html - db_mgr_addBGSource.js
* addBLBLocality.html - db_mgr_addBLBLocality.js
* addCitedReference.html - db_mgr_addCitedReference.js
* addCollMethod.html - db_mgr_addCollMethod.js
* addInst.html - db_mgr_addInst.js
* addJournal.html - db_mgr_addJournal.js
* addLocality.html - db_mgr_addLocality.js
* addMicrophone.html - db_mgr_addMicrophone.js
* addOrg.html - db_mgr_addOrg.js
* addParty.html - db_mgr_addParty.js
* addPeriod.html - db_mgr_addPeriod.js
* addPerson.html - db_mgr_addPerson.js
* addPlace.html - db_mgr_addPlace.js
* addPub.html - db_mgr_addPub.js
* addRecorder.html - db_mgr_addRecorder.js
* addRecordingCut.html - db_mgr_addRecordingCut.js
* addTaxon.html - db_mgr_addTaxon.js
* addTaxonImage.html - db_mgr_addTaxonImage.js
* addUser.html - db_mgr_addUser.js
* addVocType.html - db_mgr_addVocType.js
* adminEditUserInfo.html - db_mgr_adminEditUserInfo.js
* annotate.html - db_mgr_annotate.js
* annotatePub.html - db_mgr_annotatePub.js
* editAnnotation.html - db_mgr_editAnnotation.js
* editLocality.html - db_mgr_editLocality.js
* editPerson.html - db_mgr_editPerson.js
* editPub.html - db_mgr_editPub.js
* editRecordingCut.html - db_mgr_editRecordingCut.js
* editSpecimen.html - db_mgr_editSpecimen.js
* editUserInfo.html - db_mgr_editUserInfo.js
* exportMetadata.html - db_mgr_exportMetadata.js
* extractSpecimens.html - db_mgr_extractSpecimens.js
* forgotUser.html - db_mgr_forgotUser.js
* linkPDF.html - db_mgr_linkPDF.js
* mailingList.html - db_mgr_mailingList.js
* manageAPI.html - db_mgr_manageAPI.js
* manageOHVisitors.html - db_mgr_manageOHVisitors.js
* manageTaxonConcept.html - db_mgr_manageTaxonConcept.js
* manageTaxonName.html - db_mgr_manageTaxonName.js
* paginatePDF.html - db_mgr_paginatePDF.js
* processBLBDigitalInfo.html - db_mgr_processBLBDigitalInfo.js
* synonymizePerson.html - db_mgr_synonymizePerson.js
* synonymizeTaxon.html - db_mgr_synonymizeTaxon.js
* uploadBLBmp3s.html - db_mgr_uploadBLBmp3s.js
* uploadPDF.html - db_mgr_uploadPDF.js

=== Helper Scripts ===
* http://osuc.biosci.ohio-state.edu/cgi-bin/db_mgr.pl
* http://hymfiles.biosci.ohio-state.edu/scripts/db_mgr-hymfiles.pl
* http://osuc.osuc.edu/scripts/db_mgr-delong.py
* http://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break.py
* http://osuc.biosci.ohio-state.edu/cgi-bin/vSysLab-osuc.pl

[[Category:OSUC Private]]
[[Category:xBio:D Application Info]]

Database Manager Application Information

2015-08-07T17:41:42Z

Jcora: Created page with "---- '''Database Manager Application Information (http://osuc-mgr.osu.edu)''' == General Information == * Server: ''Database (osuc.biosci.ohio-state.edu)'' * Directory: ''..."

XBio:D Applications

2015-08-07T16:11:57Z

Jcora:

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'''xBio:D Applications'''

This section provides basic information on the structure of xBio:D web applications and links to pages for each individual application. The application pages have information on which server the application is located, the file structure and interactions, and any niche maintenance feature that may be useful.

== Basic Structure ==
Each xBio:D web application is built upon a MVC (Model-View-Controller) concept. The model, which contains the data, is located in the xBio:D database and is accessed via xBio:D APIs. Each application tends to have its own API for entering and retrieving application-specific information into the database and uses the OJ_Break API to obtain general information. The view of the applications are the HTML pages and CSS styling that provide a look-and-feel and structure for the data handled by the controller. The controller part is mediated by JavaScript and uses the xBio:D APIs to populate information retrieved from the database into the structure from the HTML pages. Each HTML page has its own JavaScript page that is included on page load. Every application has its own JavaScript page as well that is also included on page load for each page.

== Applications ==
* [[HOL Application Information]]
* [[DEA Application Information]]
* [[Database Manager Application Information]]
* [[vSysLab Application Information]]
* [[Specimage Application Information]]

[[Category:OSUC Private]]
[[Category:xBio:D Application Info]]

Category:XBio:D Application Info

2015-08-07T16:10:24Z

Jcora: Redirected page to XBio:D Applications

#REDIRECT [[XBio:D Applications]]

HOL Application Information

2015-08-07T16:09:40Z

Jcora: Protected "HOL Application Information" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

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'''HOL Application Information (http://hol.osu.edu)'''

== General Information ==
* Server: ''Database (osuc.biosci.ohio-state.edu)''
* Directory: ''/var/www/html/HymOnline''
* APIs: ''OJ_Break (v1)''

== Files ==
=== Site-Wide ===
* HymOnline.js
* HymOnline.css

=== Pages ===
* index.html - HymOnline_Index.js
* agent-full.html - HymOnline_Agent-Full.js
* export.html - HymOnline_Export.js
* inst-full.html - HymOnline_Inst-Full.js
* ios.html - HymOnline_iOS.js
* journal-full.html - HymOnline_Journal-Full.js
* literature-viewer.html - HymOnline_Literature-Viewer.js
* map-full.html - HymOnline_Map-Full.js
* map-large.html - HymOnline_Map-Large.js
* place-full.html - HymOnline_Place-Full.js
* reference-full.html - HymOnline_Reference-Full.js
* rss.html - HymOnline_RSS.js
* updates.html - HymOnline_Updates.js

=== Helper Scripts ===
* http://hymfiles.biosci.ohio-state.edu/scripts/OJ_Break.pl
* http://hymfiles.biosci.ohio-state.edu/scripts/OJ_Break.py

[[Category:OSUC Private]]
[[Category:xBio:D Application Info]]

HOL Application Information

2015-08-07T16:09:20Z

Jcora:

HOL Application Information

2015-08-07T15:58:26Z

Jcora: Created page with "---- '''HOL Application Information (http://hol.osu.edu)''' == General Information == * Server: ''Database (osuc.biosci.ohio-state.edu)'' * Directory: ''/var/www/html/HymO..."

XBio:D Applications

2015-08-07T15:02:57Z

Jcora:

Tyrannoscelio Server Management

2015-08-07T14:31:03Z

Jcora: /* Mount Remote Devices */

----

'''Tyrannoscelio Server Management (tyrannoscelio.biosci.ohio-state.edu)'''

== General Locations ==
* Data Directory: ''/data/''

== Data Backup ==
=== Offsite Backup Job ===
Tyrannoscelio mediates transferring backup files from MegaRaid, the inside the rack NAS, to the ASC offsite shared share. Both of these devices are mounted as directories on the server.

See cron jobs: <code>sudo crontab -l</code>

=== Mount Remote Devices ===
The system-wide mounted devices are located in the fstab file and can be modified through the ''nano'' program: <code>sudo nano /etc/fstab</code>

The MegaRaid share is mounted with the line <code>//128.146.250.101/OSUC_Share /share/MegaRaid_Share cifs credentials=/home/jcora/.megaraid.cred,gid=osuc_backup,dir_mode=0770,file_mode=0770 0 0</code>, which will not need updated unless the ''jcora'' password changes.

The ASC share is mounted with the line <code>//research.asc.ohio-state.edu/units/EEOB/njohnson-backup /share/ASC_Share cifs credentials=/home/nfj/.asc_nas.cred,gid=osuc_backup,dir_mode=0770,file_mode=0770 0 0</code>, which will need updated every time the password for the Ohio State federated login of ''johnson.2'' changes.

[[Category:OSUC Private]]

Tyrannoscelio Server Management

2015-08-07T14:30:24Z

Jcora: /* General Locations */

----

'''Tyrannoscelio Server Management (tyrannoscelio.biosci.ohio-state.edu)'''

== General Locations ==
* Data Directory: ''/data/''

== Data Backup ==
=== Offsite Backup Job ===
Tyrannoscelio mediates transferring backup files from MegaRaid, the inside the rack NAS, to the ASC offsite shared share. Both of these devices are mounted as directories on the server.

See cron jobs: <code>sudo crontab -l</code>

=== Mount Remote Devices ===
The system-wide mounted devices are located in the fstab file and can be modified through the ''nano'' program: <code>sudo nano /etc/fstab</code>

The MegaRaid share is mounted with the line <code>//128.146.250.101/OSUC_Share /share/MegaRaid_Share cifs credentials=/home/jcora/.megaraid.cred,gid=osuc_backup,dir_mode=0770,file_mode=0770 0 0</code>, which will not need updated unless the ''jcora'' password changes.

The ASC share is mounted with the line <code>//research.asc.ohio-state.edu/units/EEOB/njohnson-backup /share/ASC_Share cifs credentials=/home/nfj/.asc_nas.cred,gid=osuc_backup,dir_mode=0770,file_mode=0770 0 0</code>, which will need updated every time the password for the Ohio State federated login of''johnson.2'' changes.

[[Category:OSUC Private]]

Tyrannoscelio Server Management

2015-08-06T21:08:46Z

Jcora: Created page with "---- '''Tyrannoscelio Server Management (tyrannoscelio.biosci.ohio-state.edu)''' == General Locations == == Data Backup == === Offsite Backup Job === Tyrannoscelio media..."

----

'''Tyrannoscelio Server Management (tyrannoscelio.biosci.ohio-state.edu)'''

== General Locations ==

== Data Backup ==
=== Offsite Backup Job ===
Tyrannoscelio mediates transferring backup files from MegaRaid, the inside the rack NAS, to the ASC offsite shared share. Both of these devices are mounted as directories on the server.

See cron jobs: <code>sudo crontab -l</code>

=== Mount Remote Devices ===
The system-wide mounted devices are located in the fstab file and can be modified through the ''nano'' program: <code>sudo nano /etc/fstab</code>

The MegaRaid share is mounted with the line <code>//128.146.250.101/OSUC_Share /share/MegaRaid_Share cifs credentials=/home/jcora/.megaraid.cred,gid=osuc_backup,dir_mode=0770,file_mode=0770 0 0</code>, which will not need updated unless the ''jcora'' password changes.

The ASC share is mounted with the line <code>//research.asc.ohio-state.edu/units/EEOB/njohnson-backup /share/ASC_Share cifs credentials=/home/nfj/.asc_nas.cred,gid=osuc_backup,dir_mode=0770,file_mode=0770 0 0</code>, which will need updated every time the password for the Ohio State federated login of''johnson.2'' changes.

[[Category:OSUC Private]]

Macroteleia Server Management

2015-08-06T15:35:38Z

Jcora: Protected "Macroteleia Server Management" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

----

'''Macroteleia Server Management (macroteleia.biosci.ohio-state.edu)'''

== General Locations ==
* Apache Web Directory: ''/var/www/''
* GBrowse Directory: ''/etc/gbrowse2/''
* Platygastroid Sequence Data Directory: ''/seqs/''
* Trissolcus basalis Assemblies and Reads Directory: ''/media/VolRaid1/''
* Windows Virtual Machine Directory: ''/vm_images/''

== Data Backup ==
See cron jobs: <code>sudo crontab -l</code>

[[Category:OSUC Private]]

Macroteleia Server Management

2015-08-06T15:35:07Z

Jcora: Created page with "---- '''Macroteleia Server Management (macroteleia.biosci.ohio-state.edu)''' == General Locations == * Apache Web Directory: ''/var/www/'' * GBrowse Directory: ''/etc/gbro..."

Biological Association Type Terms

2015-08-06T15:15:53Z

Jcora: /* Biological Association Type Terms */

'''Introduction'''

This section contains information on the available biological association terms that are currently available in the xBio:D system. Biological associations within xBio:D represents a two-way relationship between the first organism and the second, and the association type is separated by a slash (/). For example, if you want to show a parasitoid-host relationship in which the specimen record you have is for the parasitoid (A) and the unvouchered associate (B) is its host, the association type ''emerged from egg of / host egg of'' would be read ''parasitoid (A) emerged from host (B)'' and conversely ''host (B) is a host egg of parasitoid (A)''. If you would like another biological association term added into xBio:D, please contact [mailto:cora.1@osu.edu Joe Cora] and request the addition.

== Biological Association Type Terms ==
{|
!Association Type
!Description
|-
|adult of / pupa of
|
|-
|among pieces of fallen nest of / fallen nest pieces contained
|
|-
|at base of large / large with base containing
|
|-
|between leaves of / leaves containing
|
|-
|burrowing into / contains burrowing
|
|-
|buzz pollinating / buzz pollinated by
|
|-
|collected in / contains
|
|-
|collected in drilled / drilled collecting site of
|
|-
|collected near / living near
|
|-
|collected near eggs / eggs present near
|
|-
|collected near flowering / flowering living near
|
|-
|collected near gall / gall present near
|
|-
|collected near nymph of / nymph present near
|
|-
|collected near stand of / stand present near
|
|-
|collected on / collecting site of
|
|-
|collected under / collecting site above
|
|-
|collected with / used to collect
|
|-
|collected with dung of / dung used to collect
|
|-
|collected with pheromone of / pheromone used to collect
|
|-
|collected with rotting / rotting used to collect
|
|-
|collection site of / collected on
|
|-
|egg ectoparasite of / host egg of
|
|-
|egg parasite of / host egg of
|
|-
|egg predator of / prey egg of
|
|-
|emerged from / produced
|
|-
|emerged from cocoon of / host cocoon of
|
|-
|emerged from diapausing eggs of / diapausing host eggs of
|
|-
|emerged from egg of / host egg of
|
|-
|emerged from egg sac of / host egg sac of
|
|-
|emerged from freshly killed / freshly killed host of
|
|-
|emerged from gall of / host gall of
|
|-
|emerged from immature of / host immature of
|
|-
|emerged from larva of / host larva of
|
|-
|emerged from leaf of / host leaf of
|
|-
|emerged from mossy gall of / host mossy gall of
|
|-
|emerged from mummy of / host mummy of
|
|-
|emerged from nest of / host nest of
|
|-
|emerged from nymph of / host nymph of
|
|-
|emerged from ootheca of / host ootheca of
|
|-
|emerged from pod of / host pod of
|
|-
|emerged from pole of / host pole containing
|
|-
|emerged from pupa of / host pupa of
|
|-
|emerged from pupal chamber of / host pupal chamber of
|
|-
|emerged from puparium of / host puparium of
|
|-
|emerged from seed of / host seed of
|
|-
|emerged from sentinel egg mass of / host sentinel egg mass of
|
|-
|emerged from tunnel of / host tunnel of
|
|-
|emerged from twig of / host twig of
|
|-
|fed upon by / feeding on
|
|-
|feeding on / fed upon by
|
|-
|feeding on bark of / fed upon bark by
|
|-
|feeding on bud, shoot of / fed upon bud, shoot by
|
|-
|feeding on bulb of / fed upon bulb by
|
|-
|feeding on egg of / fed on egg by
|
|-
|feeding on flower of / fed on flower by
|
|-
|feeding on fruit, nut, seed of / fed on fruit, nut, seed by
|
|-
|feeding on gall of / fed on gall by
|
|-
|feeding on leaf gall of / fed upon leaf gall by
|
|-
|feeding on leaf of / fed upon leaf by
|
|-
|feeding on root of / fed upon root by
|
|-
|feeding on shoot of / fed upon shoot by
|
|-
|feeding on silk and end of ear of / fed upon silk and end of ear by
|
|-
|feeding on stem of / fed upon stem by
|
|-
|feeding on tree trunk of / fed upon tree trunk by
|
|-
|feeding on twig, branch of / fed upon twig, branch by
|
|-
|flying after / flying from
|
|-
|gregarious egg parasitoid of / host egg of
|
|-
|host egg of / emerged from egg of
|
|-
|host egg of / solitary egg parasitoid of
|
|-
|host larva of / larval parasitoid of
|
|-
|host of / parasite of
|
|-
|hyperparasite of / host of
|
|-
|in abandoned nest of / abandoned nest containing
|
|-
|in artificial colony of / artificial colony containing
|
|-
|in bark crack of / bark crack containing
|
|-
|in burrow of / burrow containing
|
|-
|in buttress of / buttress containing
|
|-
|in canopy of / canopy containing
|
|-
|in catface of living / living with catface containing
|
|-
|in center of rotten / rotten center containing
|
|-
|in clump of / clump containing
|
|-
|in cocoon of / cocoon containing
|
|-
|in colony of / colony containing
|
|-
|in culture of / culture containing
|
|-
|in dead log of / dead log containing
|
|-
|in decaying / decayed containing
|
|-
|in decaying bark of / decayed bark containing
|
|-
|in decaying fruit, nut, seed of / decayed fruit, nut, seed containing
|
|-
|in decaying log of / decayed log containing
|
|-
|in decaying mulch of / decayed mulch containing
|
|-
|in decaying root of / decayed root containing
|
|-
|in decaying tree stump of / decayed tree stump containing
|
|-
|in duff of / duff containing
|
|-
|in dunnage of / dunnage containing
|
|-
|in fallen of / fallen containing
|
|-
|in field with / in field with
|
|-
|in flower head of / flower head containing
|
|-
|in gall of / gall containing
|
|-
|in gall of flowering / flowering with gall containing
|
|-
|in galleries of / galleries containing
|
|-
|in leaf nest of / leaf nest containing
|
|-
|in leaf sheath of / leaf sheath containing
|
|-
|in litter of / litter containing
|
|-
|in litter of treehole of / litter of treehole containing
|
|-
|in litter under log of / litter under log containing
|
|-
|in litter with / in litter with
|
|-
|in log of / log containing
|
|-
|in log with / in log with
|
|-
|in manure (feces) of / manure (feces) containing
|
|-
|in mine of / mine containing
|
|-
|in moist decayed log of / moist decayed log containing
|
|-
|in nest of / nest containing
|
|-
|in nest on body of / body in nest containing
|
|-
|in nest with dead chick of / dead chick within nest with
|
|-
|in nest within / containing nest with
|
|-
|in nose of / nose containing
|
|-
|in paneling of / paneling containing
|
|-
|in petiole of / petiole containing
|
|-
|in roast of / roast containing
|
|-
|in roost of / roost containing
|
|-
|in root / root containing
|
|-
|in rotten / rotten containing
|
|-
|in rotten stump of / rotten stump containing
|
|-
|in scat of / scat containing
|
|-
|in shell of / shell containing
|
|-
|in silk tube of / silk tube containing
|
|-
|in soil with / in soil with
|
|-
|in soil with bulb of / bulb in soil with
|
|-
|in soil with root of / root in soil with
|
|-
|in square of / square containing
|
|-
|in stable with / stable containing
|
|-
|in stand of / stand containing
|
|-
|in stem of / stem containing
|
|-
|in stem gall of / stem gall containing
|
|-
|in stomach of / stomach containing
|
|-
|in straw of / straw containing
|
|-
|in stubble of / stubble containing
|
|-
|in subterranean dump of / subterranean dump containing
|
|-
|in thicket of / thicket containing
|
|-
|in treehole of / treehole containing
|
|-
|in trunk of / trunk containing
|
|-
|in tunnel of / tunnel containing
|
|-
|in vein on underside of leaf of / vein on under of leaf containing
|
|-
|in water with / in water with
|
|-
|in web of / web containing
|
|-
|in young leaf of / young leaf containing
|
|-
|infected by / infecting
|
|-
|inhabits / habitat for
|
|-
|internal parasite of / internal host of
|
|-
|larval parasite of / host larva of
|
|-
|larval parasitoid of / host larva of
|
|-
|larval predator of / prey larva of
|
|-
|living in / lived in by
|
|-
|living in colon of / lived within colon by
|
|-
|living in hypodermis of / lived within hypodermis by
|
|-
|living in pitcher of / lived within pitcher by
|
|-
|living in synovial fluid of / lived within synovial fluid by
|
|-
|living in treehole of / lived within treehole by
|
|-
|living on / lived on by
|
|-
|living on bark of / lived on bark by
|
|-
|living on body of / lived on body by
|
|-
|living on branch of / lived on branch by
|
|-
|living on bud of / lived on bud by
|
|-
|living on bulb of / lived on bulb by
|
|-
|living on feather of / lived on feather by
|
|-
|living on flower of / lived on flower by
|
|-
|living on fruit, nut, seed of / lived on fruit, nut, seed by
|
|-
|living on hair follicle of / lived on hair follicle by
|
|-
|living on hair of / lived on hair by
|
|-
|living on head of / lived on head by
|
|-
|living on leaf of / lived on leaf by
|
|-
|living on log of / lived on log by
|
|-
|living on male cone of / lived on male cone by
|
|-
|living on mosaic infected / (mosaic infected) lived on by
|
|-
|living on nut, seed of / lived on nut, seed by
|
|-
|living on pupa of / lived on pupa by
|
|-
|living on root of / lived on root by
|
|-
|living on sapflow of / lived on sapflow by
|
|-
|living on seed of / lived on seed by
|
|-
|living on shoot of / lived on shoot by
|
|-
|living on stem of / lived on stem by
|
|-
|living on tail of / lived on tail by
|
|-
|living on tree trunk of / lived on tree trunk by
|
|-
|living on twig, branch of / lived on twig, branch by
|
|-
|living on wash of / lived on wash by
|
|-
|living on wing of / lived on wing by
|
|-
|living under bark of / lived under bark by
|
|-
|living under bark of dead / lived under bark by
|
|-
|living under bark of fallen / lived under bark by
|
|-
|living under bark of living / lived under bark by
|
|-
|living under bark of rotten trunk of / lived under bark of rotten trunk by
|
|-
|living under chips of cut / lived under chips by
|
|-
|living with / living with
|
|-
|mother parasitic on / host of mother of
|
|-
|nest containing / in nest of
|
|-
|on abdomen of / abdomen containing
|
|-
|on aphid infested / aphid infested containing
|
|-
|on ball of / ball containing
|
|-
|on bark of / bark containing
|
|-
|on bark of dead / dead with bark containing
|
|-
|on bark of living / living with bark containing
|
|-
|on bloom of / bloom containing
|
|-
|on blossom of / blossom containing
|
|-
|on body of / body containing
|
|-
|on branch of / branch containing
|
|-
|on bulb of / bulb containing
|
|-
|on cadaver of / cadaver containing
|
|-
|on cone of / cone containing
|
|-
|on cone flower of / cone flower containing
|
|-
|on coppice of / coppice containing
|
|-
|on corrigated & crumpled leaf of dwarfed / (dwarfed) corrigated & crumpled leaf containing
|
|-
|on dead / dead containing
|
|-
|on dead branch of / dead branch containing
|
|-
|on dead leaf of / dead leaf containing
|
|-
|on dead limb of / dead limb containing
|
|-
|on dead limb or trunk of / dead limb or trunk containing
|
|-
|on dead or dying twig of / dead or dying twig containing
|
|-
|on dead remains of / upon dead remains by
|
|-
|on dead twig of / dead twig containing
|
|-
|on dead vine of / dead vine containing
|
|-
|on dead, standing / dead, standing containing
|
|-
|on decayed / decayed containing
|
|-
|on decayed log of / decayed log containing
|
|-
|on decayed stump of / decayed stump containing
|
|-
|on decaying of / decaying containing
|
|-
|on deep sear of living / living with deep sear containing
|
|-
|on dense growth of / dense growth containing
|
|-
|on dry / dry containing
|
|-
|on dry dung of / dry dung containing
|
|-
|on dung of / dung containing
|
|-
|on ear of / ear containing
|
|-
|on egg of / egg containing
|
|-
|on egg sac of / egg sac containing
|
|-
|on eye of / eye containing
|
|-
|on female adult of / female adult containing
|
|-
|on fire scorched of / fire scorched containing
|
|-
|on flower bud of / flower bud containing
|
|-
|on flower of / flower containing
|
|-
|on flowering / flowering containing
|
|-
|on flowerless / flowerless containing
|
|-
|on foliage of / foliage containing
|
|-
|on fresh wound of / fresh wound containing
|
|-
|on freshly cut / freshly cut containing
|
|-
|on frond of / frond containing
|
|-
|on fruit of / fruit containing
|
|-
|on fruiting / fruiting containing
|
|-
|on gills of / gills containing
|
|-
|on guano of / guano contaning
|
|-
|on heavily curled leaf of / heavily curled leaf containing
|
|-
|on inflorescence of / inflorescence containing
|
|-
|on lamina of / lamina containing
|
|-
|on large, hollow / large, hollow containing
|
|-
|on leaf axil of / leaf axil containing
|
|-
|on leaf of / leaf containing
|
|-
|on leaf petiole of / leaf petiole containing
|
|-
|on leaflet of / leaflet containing
|
|-
|on log of / log containing
|
|-
|on midrib of / midrib containing
|
|-
|on moldy, shelled / moldy, shelled containing
|
|-
|on needle of / needle containing
|
|-
|on or near / containing or near
|
|-
|on or near flowering / flowering containing or near
|
|-
|on or near flowers of / flowers containing or near
|
|-
|on overripe fruit of / overripe fruit containing
|
|-
|on paddy edge of / paddy edge containing
|
|-
|on paddy of / paddy containing
|
|-
|on pod of / pod containing
|
|-
|on rosette / rosette containing
|
|-
|on rotten / rotten containing
|
|-
|on rotten fruit of / rotten fruit containing
|
|-
|on rotten log of / rotten log containing
|
|-
|on rotting / rotting containing
|
|-
|on scrub / scrub containing
|
|-
|on seed of / seed containing
|
|-
|on seedling of / seedling containing
|
|-
|on short / short containing
|
|-
|on skin of / skin containing
|
|-
|on stalk of / stalk containing
|
|-
|on stem of / stem containing
|
|-
|on sticky seed of / sticky seed containing
|
|-
|on stomach of cadaver of / stomach of cadaver containing
|
|-
|on stored product of / stored product containing
|
|-
|on stump of / stump containing
|
|-
|on thorax of / thorax containing
|
|-
|on top of flower of / top of flower containing
|
|-
|on tree of / tree containing
|
|-
|on trunk of / trunk containing
|
|-
|on trunk of dead / dead with trunk containing
|
|-
|on trunk of dying / dying with trunk containing
|
|-
|on twig of / twig containing
|
|-
|on underside of frond of / underside of frond containing
|
|-
|on unflowered / unflowered containing
|
|-
|on vine of / vine containing
|
|-
|on wild of / wild containing
|
|-
|on wing of / wing containing
|
|-
|on wound of twig of / wound of twig containing
|
|-
|on young / young containing
|
|-
|ovipositing into bud of / host bud of
|
|-
|ovipositing into egg of / host egg of
|
|-
|ovipositing into gall of / host gall of
|
|-
|ovipositing into young sprout of / young sprout containing
|
|-
|paraphage on / host of
|
|-
|parasite of / host of
|
|-
|parasitic in ear of / host ear of
|
|-
|parasitic in nose of / host nose of
|
|-
|parasitic in skin of / host skin of
|
|-
|parasitic on abdomen of / host abdomen of
|
|-
|parasitic on body of / host body of
|
|-
|parasitic on branchial chamber of / host branchial chamber of
|
|-
|parasitic on cloaca of / host cloaca of
|
|-
|parasitic on coxa of / host coxa of
|
|-
|parasitic on ear of / host ear of
|
|-
|parasitic on egg of / host egg of
|
|-
|parasitic on eye of / host eye of
|
|-
|parasitic on genitalia of / host genitalia of
|
|-
|parasitic on gills of / host gills of
|
|-
|parasitic on hair follicle of / host hair follicle of
|
|-
|parasitic on hair of / host hair of
|
|-
|parasitic on head of / host head of
|
|-
|parasitic on hypodermis of / host hypodermis of
|
|-
|parasitic on larva of / host larva of
|
|-
|parasitic on limb of / host limb of
|
|-
|parasitic on lung of / host lung of
|
|-
|parasitic on mouth of / host mouth of
|
|-
|parasitic on nipple of / host nipple of
|
|-
|parasitic on nose of / host nose of
|
|-
|parasitic on pupa of / host pupa of
|
|-
|parasitic on quill feather (covert) of / host quill feather (covert) of
|
|-
|parasitic on quill feather (flight feather) of / host quill feather (flight feather) of
|
|-
|parasitic on quill feather (tail feather) of / host quill feather (tail feather) of
|
|-
|parasitic on quill feather of / host quill feather of
|
|-
|parasitic on sentinel egg of / host sentinel egg of
|
|-
|parasitic on shoot of / host shoot of
|
|-
|parasitic on skin of / host skin of
|
|-
|parasitic on stomach of / host stomach of
|
|-
|parasitic on tail of / host tail of
|
|-
|parasitic on thorax of / host thorax of
|
|-
|parasitic on trachea of / host trachea of
|
|-
|parasitic on wash of / host wash of
|
|-
|parasitic on wing of / host wing of
|
|-
|parasitic under elytra of / under elytral host of
|
|-
|parasitic under scales of / under scales host of
|
|-
|parasitoid of / host of
|
|-
|patolling on / patrolled by
|
|-
|phoretic on / host of
|
|-
|phoretic on abdomen of / host abdomen of
|
|-
|phoretic on alate / alate host of
|
|-
|phoretic on antenna of / host antenna of
|
|-
|phoretic on body of / host body of
|
|-
|phoretic on coxa of / host coxa of
|
|-
|phoretic on eye of / host eye of
|
|-
|phoretic on hair follicle of / host hair follicle of
|
|-
|phoretic on head of / host head of
|
|-
|phoretic on leg of / host leg of
|
|-
|phoretic on limb of / host limb of
|
|-
|phoretic on tail of / host tail of
|
|-
|phoretic on thorax of / host thorax of
|
|-
|phoretic on wing of / host wing of
|
|-
|phoretic under elytra of / under elytral host of
|
|-
|phoretic under supra-anal plate of / under supra-anal plate host of
|
|-
|pollinating / pollinated by
|
|-
|predator of / prey of
|
|-
|prey of / predator of
|
|-
|pupa of / adult of
|
|-
|recorded in background with / in background for recording of
|
|-
|solitary egg parasitoid of / host egg of
|
|-
|stinging neck of / neck being stung by
|
|-
|stomach parasite of / host stomach of
|
|-
|subcortically living in dead / dead subcortically living in by
|
|-
|subcutaneous parasite of / subcutaneous host of
|
|-
|subcutaneously living in / subcutaneously lived in by
|
|-
|tracheal parasite of / tracheal host of
|
|-
|under bark of / under bark by
|
|-
|under bark of dead / dead under bark by
|
|-
|under bark of dead or dying twig or branch / dead or dying twig or branch under bark by
|
|-
|under bark of trunk of dead / dead under bark of trunk by
|
|-
|under dead / under dead by
|
|-
|under dead stem of / under dead stem by
|
|-
|under loose bark of / under loose bark by
|
|-
|under manure (feces) of / under manure (feces) by
|
|-
|under rocks with / under rocks with
|
|-
|under seed of / under seed by
|
|-
|unspecified association / unspecified association
|
|-
|wing parasite of / host wing of
|
|-
|with eggs of / eggs with
|
|-
|with roots of / roots with
|
|}

[[Category:Data Entry Assistant]]
[[Category:xBio:D Controlled Vocabularies]]

User:Hemly.1

2015-08-05T16:54:49Z

Jcora: Creating user page for new user.

My name is Sara Hemly. I am a curatorial technician in the C. A. Triplehorn Insect Collection at The Ohio State University in Columbus, Ohio. My name is Sara Hemly. I am a curatorial technician in the C. A. Triplehorn Insect Collection at The Ohio State University in Columbus, Ohio.

User talk:Hemly.1

2015-08-05T16:54:49Z

Jcora: Welcome!

'''Welcome to ''xBio:D Wiki''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:Jcora|Jcora]] ([[User talk:Jcora|talk]]) 12:54, 5 August 2015 (EDT)

XBio:D Applications

2015-08-03T18:03:42Z

Jcora: /* Applications */

XBio:D Applications

2015-08-03T18:02:29Z

Jcora: Protected "XBio:D Applications" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

XBio:D Applications

2015-08-03T18:02:05Z

Jcora: Created page with "---- '''xBio:D Applications''' This section provides basic information on the structure of xBio:D web applications and links to pages for each individual application. The a..."

Collection (OSUC) Private Portal

2015-08-03T17:55:24Z

Jcora: /* Infrastructure */

Available Software on the OBCP Cluster

2015-08-03T15:07:50Z

Jcora: /* Phylogenetic Software */

'''Available Software on the OBCP Cluster'''

This section of the wiki is designed to help a user locate particular software that is present on the OBCP cluster. Send any software requests to [mailto:cora.1@osu.edu Joe Cora].

== Introduction ==
Standard software packages that are present on most Linux operating systems like Python, Perl, R, etc. are already installed on the OBCP cluster. Some software are designed to be run in parallel by using the message passing interface (MPI) and/or through thread support built into the software. For more information on running programs in parallel, visit the [[Multiple Processor Runs on the OBCP Cluster]] page.

== Datasets ==
=== NCBI - nr Database ===
* ''Path'': /data/shared/seq_dbs/nr/
* ''Notes'':

=== NCBI - nt Database ===
* ''Path'': /data/shared/seq_dbs/nt/
* ''Notes'':

=== Pfam HMMs ===
* ''Path'': /data/shared/seq_dbs/Pfam/HHMs/
* ''Notes'':

=== UniProt - Swiss-Prot Database ===
* ''Path'': /data/shared/seq_dbs/Swiss-Prot/
* ''Notes'':

=== UniProt - UniRef90 Database ===
* ''Path'': /data/shared/seq_dbs/UniRef90/
* ''Notes'':

== Phylogenetic Software ==
=== Agalma ===
* ''Filename'': agalma
* ''Version'': 0.5.0
* ''Parallel'': Yes
* ''Notes'':

=== BAMM ===
* ''Filename'': bamm
* ''Version'': 2.3.1
* ''Parallel'': Yes
* ''Notes'':

=== Bayesian Serial SimCoal ===
* ''Filename'': BayeSSC
* ''Version'':
* ''Parallel'': No
* ''Notes'':
=== BEAST ===
* ''Filename'': beast (BEAST v2) / beast1 (BEAST v1)
* ''Version'': 2.2.1 / 1.8.2
* ''Parallel'': BEAGLE threading
* ''Notes'': BEAST v2 is installed in /opt/beast2/; BEAST v1 is installed in /opt/beast1/; see [http://www.beast2.org/wiki/index.php/BEAST_Features this page] for a comparison between the two version

=== BEAUti ===
* ''Filename'': beauti (BEAST v2) / beauti1 (BEAST v1)
* ''Version'': 2.2.1 / 1.8.2
* ''Parallel'': No
* ''Notes'': This program is a BEAST plugin

=== Bioinformatics Brew ===
* ''Filename'': bib
* ''Version'': ---
* ''Parallel'': ---
* ''Notes'': See information on web - http://bib.bitbucket.org/

=== BUCKy ===
* ''Filename'': bucky & mbsum
* ''Version'': 1.4.3
* ''Parallel'': No
* ''Notes'':

=== B2G4PIPE ===
* ''Filename'': see notes
* ''Version'': 2.5.0
* ''Parallel'': Java threading
* ''Notes'': Must change into the B2G4PIPE directory (/etc/b2g4pipe/), then follow instructions (http://www.blast2go.com/b2glaunch/resources).

=== FastCodeML ===
* ''Filename'': fast
* ''Version'': 1.1.0
* ''Parallel'': OpenMP threading
* ''Notes'':

=== hBayeSSC ===
* ''Filename'': hBayeSSC.py
* ''Version'':
* ''Parallel'': No
* ''Notes'':

=== jmodeltest2 ===
* ''Filename'': java -jar /opt/jmodeltest/jModelTest.jar
* ''Version'': 2.1.7
* ''Parallel'': Java threading
* ''Notes'': The program must be run with the full path to the executable

=== LASTZ ===
* ''Filename'': lastz & lastz_D
* ''Version'': 1.03.54
* ''Parallel'': No
* ''Notes'':

=== MrBayes ===
* ''Filename'': mb
* ''Version'': 3.2.5
* ''Parallel'': MPI-enabled
* ''Notes'': This version of MrBayes now works on Linux kernels using MPI

=== MUSCLE ===
* ''Filename'': muscle
* ''Version'': 3.8.31
* ''Parallel'': No
* ''Notes'':

=== PAML ===
* ''Filename'': multiple executables
* ''Version'': 4.8a
* ''Parallel'': No
* ''Notes'': copy configuration files from /opt/paml/

=== PHASE ===
* ''Filename'': multiple executables
* ''Version'': 2.0
* ''Parallel'': No
* ''Notes'':

=== ProtTest ===
* ''Filename'': java -jar /opt/prottest/prottest.jar
* ''Version'': 3.4
* ''Parallel'': Java threading
* ''Notes'': The program must be run with the full path to the executable

=== pyRAD ===
* ''Filename'': pyRAD
* ''Version'': 3.0
* ''Parallel'': threading
* ''Notes'':

=== RaxML ===
* ''Filename'': raxml
* ''Version'': 8.1.16
* ''Parallel'': Pthreads threading
* ''Notes'':

=== RaxML Light ===
* ''Filename'': raxmlLight
* ''Version'': 1.0.8
* ''Parallel'': Pthreads threading
* ''Notes'':

=== SINA ===
* ''Filename'': /etc/sina/sina
* ''Version'': 1.2.11
* ''Parallel'': No
* ''Notes'': The program must be run with the full path to the executable

=== SNAPP ===
* ''Filename'': snapp
* ''Version'': 1.1.1
* ''Parallel'': BEAGLE threading
* ''Notes'': This program is a BEAST plugin

=== TNT ===
* ''Filename'': tnt
* ''Version'': 1.1
* ''Parallel'': No
* ''Notes'': Use the command ''cp /etc/tnt/.passwordfile.tnt ~/'' prior to the first run of TNT

=== USEARCH ===
* ''Filename'': usearch
* ''Version'': 6.0.307
* ''Parallel'': threading
* ''Notes'':

=== VSEARCH ===
* ''Filename'': vsearch
* ''Version'': 1.0.7
* ''Parallel'': threading
* ''Notes'':

== Genomic/Transcriptomic Software ==
=== ABySS ===
* ''Filename'': abyss-pe
* ''Version'': 1.3.4
* ''Parallel'': MPI-enabled
* ''Notes'': see documentation on how to run in parallel: http://www.bcgsc.ca/downloads/abyss/doc/#parallelprocessing

=== AlignGraph ===
* ''Filename'': AlignGraph & Eval-AlignGraph
* ''Version'': n/a
* ''Parallel'': No
* ''Notes'':

=== ALLPATHS-LG ===
* ''Filename'': multiple executables
* ''Version'': 52188
* ''Parallel'': threaded
* ''Notes'':

=== AUGUSTUS ===
* ''Filename'': augustus
* ''Version'': 3.0.3
* ''Parallel'': No* ''Notes'':

=== Burrows-Wheeler Aligner (BWA) ===
* ''Filename'': bwa
* ''Version'': 0.7.8-r455
* ''Parallel'': No
* ''Notes'':

=== Barrnap ===
* ''Filename'': barrnap
* ''Version'': 0.6
* ''Parallel'': threading
* ''Notes'':

=== CASAVA ===
* ''Filename'': multiple executables
* ''Version'': 1.8.2
* ''Parallel'': Pthreads threading
* ''Notes'':

=== CEGMA ===
* ''Filename'': cegma
* ''Version'': 2.5
* ''Parallel'': Pthreads threading
* ''Notes'':

=== Circos ===
* ''Filename'': circos
* ''Version'': 0.67-7
* ''Parallel'': No
* ''Notes'':

=== Cufflinks ===
* ''Filename'': cufflinks
* ''Version'': 2.2.1
* ''Parallel'': PThreads threading
* ''Notes'':

=== DISCOVAR de novo ===
* ''Filename'': DiscovarDeNovo
* ''Version'': 52325
* ''Parallel'': Pthreads threading
* ''Notes'':

=== FASTX Toolkit ===
* ''Filename'': multiple executables
* ''Version'': 0.0.12
* ''Parallel'': Unknown
* ''Notes'':

=== GATK ===
* ''Filename'': java -jar /usr/local/bin/GenomeAnalysisTK.jar
* ''Version'': 3.1-1
* ''Parallel'': Unknown
* ''Notes'':

=== GENSCAN ===
* ''Filename'': genscan
* ''Version'': ??
* ''Parallel'': No
* ''Notes'':

=== Glimmer ===
* ''Filename'': glimmer3
* ''Version'': 3.02
* ''Parallel'': No
* ''Notes'':

=== GMAP ===
* ''Filename'': gmap & other executables
* ''Version'': 2014-02-20
* ''Parallel'': No
* ''Notes'':

=== GSNAP ===
* ''Filename'': gsnap
* ''Version'': 2014-02-20
* ''Parallel'': No
* ''Notes'':

=== Infernal ===
* ''Filename'': multiple executables
* ''Version'': 1.1.1
* ''Parallel'': Threading
* ''Notes'':

=== KmerGenie ===
* ''Filename'': kmergenie
* ''Version'': 1.6741
* ''Parallel'': Threading
* ''Notes'':

=== MAKER ===
* ''Filename'': maker
* ''Version'': 2.31.8
* ''Parallel'': MPI-enabled
* ''Notes'':

=== MinCED ===
* ''Filename'': minced
* ''Version'': 0.1.6
* ''Parallel'': Java threading
* ''Notes'':

=== MIRA ===
* ''Filename'': mira
* ''Version'': 4.0
* ''Parallel'': No
* ''Notes'':

=== msBayes ===
* ''Filename'': msbayes.pl
* ''Version'': 20140305
* ''Parallel'': No
* ''Notes'':

=== Oases ===
* ''Filename'': oases
* ''Version'': 0.2
* ''Parallel'': OpenMP threading
* ''Notes'': Default parameters were used. Oases (as with Velvet) should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.

=== PEAR ===
* ''Filename'': pear
* ''Version'': 0.9.5
* ''Parallel'': threading
* ''Notes'':

=== Picard ===
* ''Filename'': java -jar /etc/picard-tools/[command].jar
* ''Version'': 1.111
* ''Parallel'': Java threading
* ''Notes'': [command] is replaced with the specific picard command you would like to run

=== Prodigal ===
* ''Filename'': prodigal
* ''Version'': 2.6.2
* ''Parallel'': No
* ''Notes'':

=== Prokka ===
* ''Filename'': prokka
* ''Version'': 1.11
* ''Parallel'': Yes
* ''Notes'':

=== PyMsBayes ===
* ''Filename'': multiple executables
* ''Version'': 0.2.4
* ''Parallel'': Yes
* ''Notes'':

=== QDD ===
* ''Filename'': multiple executables
* ''Version'': 3.0 (beta)
* ''Parallel'': threading
* ''Notes'': Must change into the QDD directory (/usr/local/qdd), then follow instructions (http://net.imbe.fr/~emeglecz/qdd_run.html) for running the program from there.

=== RNAmmer ===
* ''Filename'': rnammer
* ''Version'': 1.2
* ''Parallel'': unknown
* ''Notes'':

=== RSEM ===
* ''Filename'': multiple executables
* ''Version'': 1.2.19
* ''Parallel'': unknown
* ''Notes'':

=== SAMtools ===
* ''Filename'': samtools
* ''Version'': 0.1.19+
* ''Parallel'': No
* ''Notes'':

=== Seqtk ===
* ''Filename'': seqtk
* ''Version'': 1.0-r75-dirty
* ''Parallel'': No
* ''Notes'':

=== SignalP ===
* ''Filename'': signalp
* ''Version'': 4.1c
* ''Parallel'': unknown
* ''Notes'':

=== SISRS ===
* ''Filename'': sisrs
* ''Version'': 1.6
* ''Parallel'': yes
* ''Notes'':

=== SOAPaligner ===
* ''Filename'': soap and 2bwt-builder
* ''Version'': 2.21
* ''Parallel'': Pthreads threading
* ''Notes'':

=== SOAPdenovo ===
* ''Filename'': SOAPdenovo-127mer and SOAPdenovo-63mer
* ''Version'': 2.04
* ''Parallel'': Pthreads threading
* ''Notes'':

=== SPAdes ===
* ''Filename'': spades.py
* ''Version'': 3.5.0
* ''Parallel'': threading
* ''Notes'':

=== Structure ===
* ''Filename'': structure
* ''Version'': 2.3.4
* ''Parallel'': No
* ''Notes'': uses this command 'structure -m /usr/local/bin/mainparams -e /usr/local/bin/extraparams' to run with default parameter files

=== tbl2asn ===
* ''Filename'': tbl2asn
* ''Version'': 11-12-2014
* ''Parallel'': unknown
* ''Notes'':

=== TMHMM ===
* ''Filename'': tmhmm
* ''Version'': 2.0c
* ''Parallel'': unknown
* ''Notes'':

=== TopHat ===
* ''Filename'': tophat
* ''Version'': 2.0.13
* ''Parallel'': Threading
* ''Notes'':

=== Trimmomatic ===
* ''Filename'': java -jar /usr/local/bin/trimmomatic.jar
* ''Version'': 0.32
* ''Parallel'': Java threading
* ''Notes'':

=== Trinotate ===
* ''Filename'': Trinotate
* ''Version'': r20131110
* ''Parallel'': unknown
* ''Notes'': Trinotate directory is located at '/etc/trinotate' if needed. The NCBI sequence databases are located in '/data/shared/seq_dbs/'

=== Trinity ===
* ''Filename'': /etc/trinity/Trinity
* ''Version'': 2.0.6
* ''Parallel'': Threading
* ''Notes'': Use the argument "--bypass_java_version_check" to ignore checking for a specific, earlier Java version

=== Velvet ===
* ''Filename'': velveth & velvetg
* ''Version'': 1.2.09
* ''Parallel'': OpenMP threading
* ''Notes'': Default parameters were used with the exception of enabling OpenMP. Velvet should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.

=== VCFtools ===
* ''Filename'': multiple executables
* ''Version'': 0.1.12a
* ''Parallel'': No
* ''Notes'':

=== VelvetOptimiser ===
* ''Filename'': VelvetOptimiser.pl
* ''Version'': 2.2.5
* ''Parallel'': Threading
* ''Notes'':

=== vtBuilder ===
* ''Filename'': vt-builder.jar
* ''Version'': unknown (preview)
* ''Parallel'': Threading
* ''Notes'': run from command line as '''java -jar -Xmx97152M /usr/local/lib/vt-builder.jar -a n -d ./output.txt -e ./log.txt -f 32 -g 150 -h 250 -j 96'''

== Population Genetic/Genomic Software ==
=== BP&P ===
* ''Filename'': bpp
* ''Version'': 2.1b
* ''Parallel'': No
* ''Notes'':

=== ∂a∂i ===
* ''Filename'': python package
* ''Version'': 1.6.3
* ''Parallel'': No
* ''Notes'':

=== IMa2 ===
* ''Filename'': IMa2
* ''Version'': 8.27.12
* ''Parallel'': No
* ''Notes'': version is the date of release (August 27, 2012)

=== Migrate-N ===
* ''Filename'': migrate-n
* ''Version'': 3.6.11
* ''Parallel'': MPI-enabled
* ''Notes'':

=== Migrate-N (beta) ===
* ''Filename'': migrate-n-beta
* ''Version'': 3.4.4
* ''Parallel'': MPI-enabled
* ''Notes'': This is a beta version

=== ms ===
* ''Filename'': ms
* ''Version'': 3.13.2014
* ''Parallel'': No
* ''Notes'':

=== RTD ===
* ''Filename'': multiple executables
* ''Version'': 06-10-2013
* ''Parallel'': GNU parallel
* ''Notes'':

=== Stacks ===
* ''Filename'': multiple executables
* ''Version'': 1.24
* ''Parallel'': OpenMP threading
* ''Notes'':

== Ecological Modelling Software ==

=== Maxent ===
* ''Filename'': java -jar /usr/local/lib/maxent.jar
* ''Version'': 3.3.3k
* ''Parallel'': Java threading
* ''Notes'':

=== Mothur ===
* ''Filename'': mothur
* ''Version'': 1.33
* ''Parallel'': MPI-enabled
* ''Notes'':

== R Packages ==
=== akima ===
* ''Version'': 0.5-11

=== ape ===
* ''Version'': 3.1-1

=== bGMYC ===
* ''Version'': 1.0.2

=== genalg ===
* ''Version'': 0.1.1

=== rlecuyer ===
* ''Version'': 0.3-3

=== VGAM ===
* ''Version'': 0.9-3

== Python Packages ==
=== ACOR ===
* ''Version'': 1.1.1

=== BCBio ===
* ''Version'': 0.6.1

=== BioPython ===
* ''Version'': 1.6.3

=== Geneland ===
* ''Version'': 4.0.5

=== NumPy ===
* ''Version'': 1.8.2

=== PypeR ===
* ''Version'': 1.1.2

=== OJ_Break ===
* ''Version'': 0.1

=== QIIME ===
* ''Version'': 1.8.0

=== scatR ===
* ''Version'': 0.1

[[Category:OBCP]]

Available Software on the OBCP Cluster

2015-07-30T14:14:17Z

Jcora: /* Phylogenetic Software */

'''Available Software on the OBCP Cluster'''

This section of the wiki is designed to help a user locate particular software that is present on the OBCP cluster. Send any software requests to [mailto:cora.1@osu.edu Joe Cora].

== Introduction ==
Standard software packages that are present on most Linux operating systems like Python, Perl, R, etc. are already installed on the OBCP cluster. Some software are designed to be run in parallel by using the message passing interface (MPI) and/or through thread support built into the software. For more information on running programs in parallel, visit the [[Multiple Processor Runs on the OBCP Cluster]] page.

== Datasets ==
=== NCBI - nr Database ===
* ''Path'': /data/shared/seq_dbs/nr/
* ''Notes'':

=== NCBI - nt Database ===
* ''Path'': /data/shared/seq_dbs/nt/
* ''Notes'':

=== Pfam HMMs ===
* ''Path'': /data/shared/seq_dbs/Pfam/HHMs/
* ''Notes'':

=== UniProt - Swiss-Prot Database ===
* ''Path'': /data/shared/seq_dbs/Swiss-Prot/
* ''Notes'':

=== UniProt - UniRef90 Database ===
* ''Path'': /data/shared/seq_dbs/UniRef90/
* ''Notes'':

== Phylogenetic Software ==
=== Agalma ===
* ''Filename'': agalma
* ''Version'': 0.5.0
* ''Parallel'': Yes
* ''Notes'':

=== Bayesian Serial SimCoal ===
* ''Filename'': BayeSSC
* ''Version'':
* ''Parallel'': No
* ''Notes'':

=== BEAST ===
* ''Filename'': beast (BEAST v2) / beast1 (BEAST v1)
* ''Version'': 2.2.1 / 1.8.2
* ''Parallel'': BEAGLE threading
* ''Notes'': BEAST v2 is installed in /opt/beast2/; BEAST v1 is installed in /opt/beast1/; see [http://www.beast2.org/wiki/index.php/BEAST_Features this page] for a comparison between the two version

=== BEAUti ===
* ''Filename'': beauti (BEAST v2) / beauti1 (BEAST v1)
* ''Version'': 2.2.1 / 1.8.2
* ''Parallel'': No
* ''Notes'': This program is a BEAST plugin

=== Bioinformatics Brew ===
* ''Filename'': bib
* ''Version'': ---
* ''Parallel'': ---
* ''Notes'': See information on web - http://bib.bitbucket.org/

=== BUCKy ===
* ''Filename'': bucky & mbsum
* ''Version'': 1.4.3
* ''Parallel'': No
* ''Notes'':

=== B2G4PIPE ===
* ''Filename'': see notes
* ''Version'': 2.5.0
* ''Parallel'': Java threading
* ''Notes'': Must change into the B2G4PIPE directory (/etc/b2g4pipe/), then follow instructions (http://www.blast2go.com/b2glaunch/resources).

=== FastCodeML ===
* ''Filename'': fast
* ''Version'': 1.1.0
* ''Parallel'': OpenMP threading
* ''Notes'':

=== hBayeSSC ===
* ''Filename'': hBayeSSC.py
* ''Version'':
* ''Parallel'': No
* ''Notes'':

=== jmodeltest2 ===
* ''Filename'': java -jar /opt/jmodeltest/jModelTest.jar
* ''Version'': 2.1.7
* ''Parallel'': Java threading
* ''Notes'': The program must be run with the full path to the executable

=== LASTZ ===
* ''Filename'': lastz & lastz_D
* ''Version'': 1.03.54
* ''Parallel'': No
* ''Notes'':

=== MrBayes ===
* ''Filename'': mb
* ''Version'': 3.2.5
* ''Parallel'': MPI-enabled
* ''Notes'': This version of MrBayes now works on Linux kernels using MPI

=== MUSCLE ===
* ''Filename'': muscle
* ''Version'': 3.8.31
* ''Parallel'': No
* ''Notes'':

=== PAML ===
* ''Filename'': multiple executables
* ''Version'': 4.8a
* ''Parallel'': No
* ''Notes'': copy configuration files from /opt/paml/

=== PHASE ===
* ''Filename'': multiple executables
* ''Version'': 2.0
* ''Parallel'': No
* ''Notes'':

=== ProtTest ===
* ''Filename'': java -jar /opt/prottest/prottest.jar
* ''Version'': 3.4
* ''Parallel'': Java threading
* ''Notes'': The program must be run with the full path to the executable

=== pyRAD ===
* ''Filename'': pyRAD
* ''Version'': 3.0
* ''Parallel'': threading
* ''Notes'':

=== RaxML ===
* ''Filename'': raxml
* ''Version'': 8.1.16
* ''Parallel'': Pthreads threading
* ''Notes'':

=== RaxML Light ===
* ''Filename'': raxmlLight
* ''Version'': 1.0.8
* ''Parallel'': Pthreads threading
* ''Notes'':

=== SINA ===
* ''Filename'': /etc/sina/sina
* ''Version'': 1.2.11
* ''Parallel'': No
* ''Notes'': The program must be run with the full path to the executable

=== SNAPP ===
* ''Filename'': snapp
* ''Version'': 1.1.1
* ''Parallel'': BEAGLE threading
* ''Notes'': This program is a BEAST plugin

=== TNT ===
* ''Filename'': tnt
* ''Version'': 1.1
* ''Parallel'': No
* ''Notes'': Use the command ''cp /etc/tnt/.passwordfile.tnt ~/'' prior to the first run of TNT

=== USEARCH ===
* ''Filename'': usearch
* ''Version'': 6.0.307
* ''Parallel'': threading
* ''Notes'':

=== VSEARCH ===
* ''Filename'': vsearch
* ''Version'': 1.0.7
* ''Parallel'': threading
* ''Notes'':

== Genomic/Transcriptomic Software ==
=== ABySS ===
* ''Filename'': abyss-pe
* ''Version'': 1.3.4
* ''Parallel'': MPI-enabled
* ''Notes'': see documentation on how to run in parallel: http://www.bcgsc.ca/downloads/abyss/doc/#parallelprocessing

=== AlignGraph ===
* ''Filename'': AlignGraph & Eval-AlignGraph
* ''Version'': n/a
* ''Parallel'': No
* ''Notes'':

=== ALLPATHS-LG ===
* ''Filename'': multiple executables
* ''Version'': 52188
* ''Parallel'': threaded
* ''Notes'':

=== AUGUSTUS ===
* ''Filename'': augustus
* ''Version'': 3.0.3
* ''Parallel'': No* ''Notes'':

=== Burrows-Wheeler Aligner (BWA) ===
* ''Filename'': bwa
* ''Version'': 0.7.8-r455
* ''Parallel'': No
* ''Notes'':

=== Barrnap ===
* ''Filename'': barrnap
* ''Version'': 0.6
* ''Parallel'': threading
* ''Notes'':

=== CASAVA ===
* ''Filename'': multiple executables
* ''Version'': 1.8.2
* ''Parallel'': Pthreads threading
* ''Notes'':

=== CEGMA ===
* ''Filename'': cegma
* ''Version'': 2.5
* ''Parallel'': Pthreads threading
* ''Notes'':

=== Circos ===
* ''Filename'': circos
* ''Version'': 0.67-7
* ''Parallel'': No
* ''Notes'':

=== Cufflinks ===
* ''Filename'': cufflinks
* ''Version'': 2.2.1
* ''Parallel'': PThreads threading
* ''Notes'':

=== DISCOVAR de novo ===
* ''Filename'': DiscovarDeNovo
* ''Version'': 52325
* ''Parallel'': Pthreads threading
* ''Notes'':

=== FASTX Toolkit ===
* ''Filename'': multiple executables
* ''Version'': 0.0.12
* ''Parallel'': Unknown
* ''Notes'':

=== GATK ===
* ''Filename'': java -jar /usr/local/bin/GenomeAnalysisTK.jar
* ''Version'': 3.1-1
* ''Parallel'': Unknown
* ''Notes'':

=== GENSCAN ===
* ''Filename'': genscan
* ''Version'': ??
* ''Parallel'': No
* ''Notes'':

=== Glimmer ===
* ''Filename'': glimmer3
* ''Version'': 3.02
* ''Parallel'': No
* ''Notes'':

=== GMAP ===
* ''Filename'': gmap & other executables
* ''Version'': 2014-02-20
* ''Parallel'': No
* ''Notes'':

=== GSNAP ===
* ''Filename'': gsnap
* ''Version'': 2014-02-20
* ''Parallel'': No
* ''Notes'':

=== Infernal ===
* ''Filename'': multiple executables
* ''Version'': 1.1.1
* ''Parallel'': Threading
* ''Notes'':

=== KmerGenie ===
* ''Filename'': kmergenie
* ''Version'': 1.6741
* ''Parallel'': Threading
* ''Notes'':

=== MAKER ===
* ''Filename'': maker
* ''Version'': 2.31.8
* ''Parallel'': MPI-enabled
* ''Notes'':

=== MinCED ===
* ''Filename'': minced
* ''Version'': 0.1.6
* ''Parallel'': Java threading
* ''Notes'':

=== MIRA ===
* ''Filename'': mira
* ''Version'': 4.0
* ''Parallel'': No
* ''Notes'':

=== msBayes ===
* ''Filename'': msbayes.pl
* ''Version'': 20140305
* ''Parallel'': No
* ''Notes'':

=== Oases ===
* ''Filename'': oases
* ''Version'': 0.2
* ''Parallel'': OpenMP threading
* ''Notes'': Default parameters were used. Oases (as with Velvet) should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.

=== PEAR ===
* ''Filename'': pear
* ''Version'': 0.9.5
* ''Parallel'': threading
* ''Notes'':

=== Picard ===
* ''Filename'': java -jar /etc/picard-tools/[command].jar
* ''Version'': 1.111
* ''Parallel'': Java threading
* ''Notes'': [command] is replaced with the specific picard command you would like to run

=== Prodigal ===
* ''Filename'': prodigal
* ''Version'': 2.6.2
* ''Parallel'': No
* ''Notes'':

=== Prokka ===
* ''Filename'': prokka
* ''Version'': 1.11
* ''Parallel'': Yes
* ''Notes'':

=== PyMsBayes ===
* ''Filename'': multiple executables
* ''Version'': 0.2.4
* ''Parallel'': Yes
* ''Notes'':

=== QDD ===
* ''Filename'': multiple executables
* ''Version'': 3.0 (beta)
* ''Parallel'': threading
* ''Notes'': Must change into the QDD directory (/usr/local/qdd), then follow instructions (http://net.imbe.fr/~emeglecz/qdd_run.html) for running the program from there.

=== RNAmmer ===
* ''Filename'': rnammer
* ''Version'': 1.2
* ''Parallel'': unknown
* ''Notes'':

=== RSEM ===
* ''Filename'': multiple executables
* ''Version'': 1.2.19
* ''Parallel'': unknown
* ''Notes'':

=== SAMtools ===
* ''Filename'': samtools
* ''Version'': 0.1.19+
* ''Parallel'': No
* ''Notes'':

=== Seqtk ===
* ''Filename'': seqtk
* ''Version'': 1.0-r75-dirty
* ''Parallel'': No
* ''Notes'':

=== SignalP ===
* ''Filename'': signalp
* ''Version'': 4.1c
* ''Parallel'': unknown
* ''Notes'':

=== SISRS ===
* ''Filename'': sisrs
* ''Version'': 1.6
* ''Parallel'': yes
* ''Notes'':

=== SOAPaligner ===
* ''Filename'': soap and 2bwt-builder
* ''Version'': 2.21
* ''Parallel'': Pthreads threading
* ''Notes'':

=== SOAPdenovo ===
* ''Filename'': SOAPdenovo-127mer and SOAPdenovo-63mer
* ''Version'': 2.04
* ''Parallel'': Pthreads threading
* ''Notes'':

=== SPAdes ===
* ''Filename'': spades.py
* ''Version'': 3.5.0
* ''Parallel'': threading
* ''Notes'':

=== Structure ===
* ''Filename'': structure
* ''Version'': 2.3.4
* ''Parallel'': No
* ''Notes'': uses this command 'structure -m /usr/local/bin/mainparams -e /usr/local/bin/extraparams' to run with default parameter files

=== tbl2asn ===
* ''Filename'': tbl2asn
* ''Version'': 11-12-2014
* ''Parallel'': unknown
* ''Notes'':

=== TMHMM ===
* ''Filename'': tmhmm
* ''Version'': 2.0c
* ''Parallel'': unknown
* ''Notes'':

=== TopHat ===
* ''Filename'': tophat
* ''Version'': 2.0.13
* ''Parallel'': Threading
* ''Notes'':

=== Trimmomatic ===
* ''Filename'': java -jar /usr/local/bin/trimmomatic.jar
* ''Version'': 0.32
* ''Parallel'': Java threading
* ''Notes'':

=== Trinotate ===
* ''Filename'': Trinotate
* ''Version'': r20131110
* ''Parallel'': unknown
* ''Notes'': Trinotate directory is located at '/etc/trinotate' if needed. The NCBI sequence databases are located in '/data/shared/seq_dbs/'

=== Trinity ===
* ''Filename'': /etc/trinity/Trinity
* ''Version'': 2.0.6
* ''Parallel'': Threading
* ''Notes'': Use the argument "--bypass_java_version_check" to ignore checking for a specific, earlier Java version

=== Velvet ===
* ''Filename'': velveth & velvetg
* ''Version'': 1.2.09
* ''Parallel'': OpenMP threading
* ''Notes'': Default parameters were used with the exception of enabling OpenMP. Velvet should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.

=== VCFtools ===
* ''Filename'': multiple executables
* ''Version'': 0.1.12a
* ''Parallel'': No
* ''Notes'':

=== VelvetOptimiser ===
* ''Filename'': VelvetOptimiser.pl
* ''Version'': 2.2.5
* ''Parallel'': Threading
* ''Notes'':

=== vtBuilder ===
* ''Filename'': vt-builder.jar
* ''Version'': unknown (preview)
* ''Parallel'': Threading
* ''Notes'': run from command line as '''java -jar -Xmx97152M /usr/local/lib/vt-builder.jar -a n -d ./output.txt -e ./log.txt -f 32 -g 150 -h 250 -j 96'''

== Population Genetic/Genomic Software ==
=== BP&P ===
* ''Filename'': bpp
* ''Version'': 2.1b
* ''Parallel'': No
* ''Notes'':

=== ∂a∂i ===
* ''Filename'': python package
* ''Version'': 1.6.3
* ''Parallel'': No
* ''Notes'':

=== IMa2 ===
* ''Filename'': IMa2
* ''Version'': 8.27.12
* ''Parallel'': No
* ''Notes'': version is the date of release (August 27, 2012)

=== Migrate-N ===
* ''Filename'': migrate-n
* ''Version'': 3.6.11
* ''Parallel'': MPI-enabled
* ''Notes'':

=== Migrate-N (beta) ===
* ''Filename'': migrate-n-beta
* ''Version'': 3.4.4
* ''Parallel'': MPI-enabled
* ''Notes'': This is a beta version

=== ms ===
* ''Filename'': ms
* ''Version'': 3.13.2014
* ''Parallel'': No
* ''Notes'':

=== RTD ===
* ''Filename'': multiple executables
* ''Version'': 06-10-2013
* ''Parallel'': GNU parallel
* ''Notes'':

=== Stacks ===
* ''Filename'': multiple executables
* ''Version'': 1.24
* ''Parallel'': OpenMP threading
* ''Notes'':

== Ecological Modelling Software ==

=== Maxent ===
* ''Filename'': java -jar /usr/local/lib/maxent.jar
* ''Version'': 3.3.3k
* ''Parallel'': Java threading
* ''Notes'':

=== Mothur ===
* ''Filename'': mothur
* ''Version'': 1.33
* ''Parallel'': MPI-enabled
* ''Notes'':

== R Packages ==
=== akima ===
* ''Version'': 0.5-11

=== ape ===
* ''Version'': 3.1-1

=== bGMYC ===
* ''Version'': 1.0.2

=== genalg ===
* ''Version'': 0.1.1

=== rlecuyer ===
* ''Version'': 0.3-3

=== VGAM ===
* ''Version'': 0.9-3

== Python Packages ==
=== ACOR ===
* ''Version'': 1.1.1

=== BCBio ===
* ''Version'': 0.6.1

=== BioPython ===
* ''Version'': 1.6.3

=== Geneland ===
* ''Version'': 4.0.5

=== NumPy ===
* ''Version'': 1.8.2

=== PypeR ===
* ''Version'': 1.1.2

=== OJ_Break ===
* ''Version'': 0.1

=== QIIME ===
* ''Version'': 1.8.0

=== scatR ===
* ''Version'': 0.1

[[Category:OBCP]]

XBio:D Data Management

2015-07-27T21:44:11Z

Jcora:

----

'''xBio:D Data Management'''

This section provides instructions on performing common data management tasks on the xBio:D database that are not privy to general users. These tasks are not available through web applications and must either be performed by running a script or a database procedure.

== Change Occurrence (Specimen) Record CUID ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC updateSpmID(old_cuid, new_cuid);</code>. The procedure will only produce output when a problem occurred.

== Remove Occurrence (Specimen) Record ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC removeSpm(cuid);</code>. The procedure will only produce output when a problem occurred.

== Merged/Remove Locality Name ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC change_locality(obsolete_loc_name, valid_loc_name);</code>. The procedure removes the obsolete locality and places all of the occurrence records from the obsolete locality into the valid locality name. There is also an additional, optional parameter ''coll_date'', which accepts the format DD-MON-YYYY, that will change the functioning of this procedure to change only those occurrence records that were collected on that particular date. If all of the occurrences were collected on that day, the locality is removed. The procedure will only produce output when a problem occurred.

== Add Collection Records or Taxon Checklist as a Project to the xBio:D IPT ==
# Log into the database server (''osuc.biosci.ohio-state.edu'') via SSH and open DwC-A collection export script, ''export_dwca_collections.py''. This script is set to run every Sunday at 8PM.
## <code>ssh [username]@osuc.biosci.ohio-state.edu</code>
## <code>sudo nano /var/www/cgi-bin/export_dwca_collections.py</code>
# Go to the ''handleDwCAExport'' function and add the taxon or collection you would like to export.
## The ''exportDwCA'' function of the OJ_Exporter package takes the collection ''Storage_Regime_ID'' as the identifier.
## The ''exportTaxonDwCA'' function of the OJ_Exporter package takes the taxon ''tnuid'' as the identifier.
# Execute the ''export_dwca_collections.py'' script immediately or wait until after the weekly export execution
# Download the DwC-A file created for the new collection or checklist
## Collection records example: ''http://osuc.biosci.ohio-state.edu/data_exports/dwca_1.zip''
## Taxon checklist example: ''http://osuc.biosci.ohio-state.edu/data_exports/dwca_tax_195000.zip''
# Create project in xBio:D IPT for the data you will be disseminating.
## Log into IPT and go to ''Manage Resources''
## Scroll to the bottom to ''Create New Resource'', specify a short name and resource type, then upload the previously exported file and create resource
## Fill in the metadata section of the resource with the appropriate values for provider, owner, etc.
# Log into the hymfiles server (''osuc.biosci.ohio-state.edu'') via Remote Desktop and open IPT DwC-A import script, ''populate_ipt.py''. The Python script is located in ''C:\backup_scripts''.
# Go to the ''handlePopulateIPT'' function and add the taxon or collection you would like to export.
## The numeric identifiers are the same as defined in the ''export'' step above
## The second parameter for the populate script is the resource short name specified above.
# Register and publish the new project. The resource will now be available on GBIF and can be shared with other data aggregators like iDigBio, VertNet, etc.

== Aggregation Update ==
Many DB queries use tables that are aggregated from many separate tables to speed up processing. These aggregation tasks are performed automatically every Saturday under the DB job named ''aggregation_update''. These tasks include the following:
* '''''processDescriberIDs''''' - Goes through each taxonomic concept that does not already have a describer specified within the ''Protonym'' table and attempts to infer from an original description or replacement name literature annotation the author of the taxon. If a match is found, then the individual describer or describer party is added to the ''Protonym'' table.
* '''''update_people_stats''''' - Builds the ''AGGR_Person_Stats'' table that contains the # of occurrences collected, # of papers published, # of determinations made, # of distinct events collected, and the total # of contributions for each person.
* '''''update_genera_stats''''' - Builds the ''AGGR_Genus_Stats'' table that contains the # of occurrences determined, # of papers published, # of images taken, # of collections deposited, and distinct events collected for each tnuid.
* '''''update_place_children''''' - Builds the ''AGGR_Place_Children'' table that contains a place along with each subordinate place at any lower position within the geopolitical hierarchy.
* '''''update_taxon_children''''' - Builds the ''AGGR_Taxon_Children'' table that contains a tnuid along with each subordinate tnuid at any lower position within the taxonomic hierarchy. Species-group taxa are excluded as parent taxa within this table.
* '''''update_fossil_taxa''''' - Builds the ''AGGR_Fossil_Taxa'' table that contains a tcid for each taxon concept that is a fossil. Fossil status is only applied to species-group taxa, so this procedure also added taxa in which all of its subordinate taxa are fossils.
* '''''update_recordings''''' - Builds the ''AGGR_Taxon_Recordings'' table that contains a tnuid and recording info id for any recording that is contained within the taxon.
* '''''update_images''''' - Builds the ''AGGR_Taxon_Images'' table that contains a tnuid and image id for any specimen or taxon image that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_habitats''''' - Builds the ''AGGR_Habitat'' table that contains a tnuid and habitat for any occurrence that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_taxon_contributors''''' - Builds the ''AGGR_Taxon_Contribs'' table that contains a tnuid, contributor, and contribution flags for every contribution from the contributor within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_inst_tcids''''' - Builds the ''AGGR_Inst_Tcids'' table that contains the tcids for every collection where an occurrence is present. Species-group taxa are excluded as parent taxa within this table.
* '''''update_associations''''' - Builds the ''AGGR_Taxon_Assocs'' table that contains a tnuid and associated tnuid for every taxon that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.

[[Category:OSUC Private]]

OBCP Cluster Management

2015-07-27T15:02:43Z

Jcora:

----

'''OBCP Cluster Management'''

== Add New User ==

# Go to ''johnsonlab'' folder.
## <code>$ cd /data/johnsonlab/</code>
# Modify ''addUser.sh'' by changing ''NEW_USER'' variable at top to the new username. Exit and save when finished.
## <code>$ sudo nano addUser.sh</code>
## <code>... NEW_USER=[username] ...</code>
# Execute ''addUser.sh'' and enter password for new user. Enter full name of user when prompted. The rest of the options before the disk quota can be ignored.
## <code>$ sudo ./addUser.sh</code>
# When the disk quotas configuration is displayed, change the soft limits for the number of blocks and inodes allowed by the user on the OS filesystem to 1GB.
## Move the cursor to the first ''0'', which is the third column, and change the value to ''1000000''.
## Move the cursor to the next to the last ''0'', which is the sixth column, and change the value to ''1000000''.

== Initiate OBCP Cluster iSCSI Connection ==

Command: <code>sudo iscsiadm -m node -T iqn.1991-05.com.microsoft:d2l7t6v1-obcp-nas-target -p 192.168.5.2:3260 --login</code>

== Mount iSCSI Volumes ==

Command: <code>sudo mount /dev/sdb1 /data</code>

Command: <code>sudo mount /dev/sdc1 /data2</code>

== Add Capacity to OBCP Cluster NAS ==

# Insert hard disk with caddy into next available slot within NAS
# Within the NAS Windows OS, open Dell Open Manage Server Administrator
## Initialize the new physical disk
## Reconfigure the virtual disk (RAID-6) to include the new disk
## Re-initialize the virtual disk to prepare for added capacity
# Within the NAS Windows OS, open Windows Computer Management
## In Disk Management, extend the virtual disk volume to use the added capacity
## In iSCSI Software Management, go to Device and extended the virtual disk volume to use the added capacity
# Within the cluster Ubuntu OS, prepare to extend the iSCSI partition and filesystem
## Kill any processes accessing the iSCSI interface
## Logout from the iSCSI connection and unmount the iSCSI filesystem (<code>umount /dev/sdb1</code> - may require a restart)
## Within the Ubuntu GUI, open GParted and extend the partition stored on the NAS
## Log back into the iSCSI connection and remount the iSCSI filesystem (<code>mount -a</code>)
# The cluster is now ready to use the additional storage capacity

[[Category:OSUC Private]]

Hymfiles Server Management

2015-07-22T19:58:56Z

Jcora: Protected "Hymfiles Server Management" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

XBio:D Database Server Management

2015-07-22T19:51:47Z

Jcora: /* Applications / Services */

----

'''xBio:D Database Server Management (osuc.biosci.ohio-state.edu)'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API - http://xbiod.osu.edu/OJ_Break/
* Database Gateway - http://osuc.biosci.ohio-state.edu/hymDB/
* LSID / GUID Metadata Handler - http://bioguid.osu.edu/
* xBio:D Javascript Library - http://xbiod.osu.edu/xbiod_lib/xbiod.js
* HOL - http://hol.osu.edu/
* vSysLab - http://vsyslab.osu.edu/
* DB Manager - http://osuc-mgr.osu.edu/
* HNS - http://hns.osu.edu/
* Platy site - osuc.biosci.ohio-state.edu/hymDB/eol_scelionidae.home
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database: $ <code>dbstart $ORACLE_HOME</code>
# Start the database listener: $ <code>lsnrctl start</code>

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]

XBio:D Javascript Library Reference

2015-07-22T19:33:16Z

Jcora: /* Loading the xBio:D JavaScript Library */

'''Introduction'''

The xBio:D JavaScript library offers the functionality to create rich, dynamic, and interactive features for use with the [[OJ_Break API Reference|OJ_Break API]]. The OJ_Break API provides procedures to retrieve data within the xBio:D database, and the xBio:D JS library is how that data gets presented. Users planning on working with the xBio:D JS library should be familiar with JavaScript programming and object-oriented programming.

== API Access ==

All functionality in the xBio:D JS library depends on access of data from the OJ_Break API. See [[OJ_Break API Access]] for an overview of the API and how to obtain an [[OJ_Break API Access#key|API access key]].

== Example ==

An easy way to become familiar with the xBio:D JS library is to see a simple example of a web application which uses two xBio:D methods. The first is a Google Maps widget which takes data from the OJ_Break method [[OJ_Break API Reference#getLocalities|getLocalities]] for a specified [[OJ_Break API Data Type Glossary#tnuid_2|tnuid]] and displays the data onto an interactive map. Read more about the [https://developers.google.com/maps/documentation/javascript/tutorial Google Maps JavaScript API]. The second method used in the example is a listing of included taxa for a specified tnuid by using the OJ_Break method [[OJ_Break API Reference#getIncludedTaxa|getIncludedTaxa]].

[[File:wiki-test.png|alt=source code for a simple xBio:D web application.|Simple example of web application.]]



There are a few things to note about this example:
* The '''<!DOCTYPE html>''' tag is necessary for HTML 5 applications (line 1)
* Jquery 1.8 library is included with a '''<script>''' tag (line 7)
* Jquery UI 1.10.4 library is included with a '''<script>''' tag (line 8)
* The Google Map API JavaScript library is included with a '''<script>''' tag (line 9)
* The xBio:D JS library is included with a '''<script>''' tag (line 10)
* A function called ''loader'' intializes the xBio:D resources when the web page has finished loading (line 15)
* Two objects where created to access the xBio:D components called ''visual'' and ''taxon'' (line 22 - 23)
* The applications are created by calling there respective methods via the xBio:D library components (line 26 & 29 - 30)
* In the '''<body>''' there are two '''<nowiki><div></nowiki>''' elements which create areas to hold the widgets. The first is called ''map_id'' and the second is ''included_id''. (line 43 - 44)

These steps will be explained below.

=== Declaring Application as HTML 5 ===
It is recommended for any web application to be declared as a true ''DOCTYPE''. This can easily be done by using the HTML 5 ''DOCTYPE'' as seen below. This allows the application to be more cross-browser compliant. Please refer to the [https://developers.google.com/maps/documentation/javascript/tutorial#HTML5 Google Maps Documentation on HTML 5] for more info.

<!DOCTYPE html>

=== Loading JQuery Library ===
<script type="text/javascript" src=<nowiki>"http://ajax.googleapis.com/ajax/libs/jquery/1.8/jquery.min.js"</nowiki>></script>

The URL in the '''<script>''' tag above is the location of the JavaScript file which allows [http://en.wikipedia.org/wiki/JQuery JQuery] 1.8 to run on the web application. JQuery is used in the xBio:D JS library to get methods from the OJ_Break API and other scripts. It is a necessary component of any web app that intends to use xBio:D functionality.

=== Loading the Google Maps API ===
<script type="text/javascript" src=<nowiki>"https://maps.googleapis.com/maps/api/js?sensor=false"</nowiki>></script>

The URL in the '''<script>''' tag above is the location of the JavaScript file which will load all the necessary defintions to allow access to the Maps API. Normally, an access key would need to be provided in order to use the Maps library. See [https://developers.google.com/maps/documentation/javascript/tutorial#Loading_the_Maps_API Loading the Maps API] for more info. This script file is necessary for web apps that use Google Maps as part of the application. It is a necessary file to have in this simple example, but is not required for all xBio:D applications.

=== Loading the xBio:D JavaScript Library ===
<script type="text/javascript" src=<nowiki>"http://xbiod.osu.edu/xbiod_lib/xbiod.js"</nowiki>></script>

The URL in the '''<script>''' tage above is the location of the xBio:D JavaScript Library which is a required file for this simple example and any web application that will be using xBio:D applications.

=== Initializing the xBio:D JS Library ===
<script>
// Call the loader for the current page
$(document).ready(loader); 
function loader() { 
// Initialize xBio:D library
xbiod.init(['visual','taxon'], /*API_KEY*/, function(){

To begin using the xBio:D library, first the components need to be loaded. This is done through the xBio:D ''init'' function which takes three parameters: an array of the components to be loaded, an API access key, and a callback function. In this example, the '''visual''' and '''taxon''' resources are passed to the ''init'' function for loading (all resources and their methods can be found in the [[XBio:D Javascript Library Reference#Reference|Reference]] section below). This example also shows where a user would provide an OJ_Break API access key. See [[OJ_Break API Access]] for more information on access keys. Lastly, a callback method needs to be provided which will create the component objects.

==== Component Objects ====
// Load xBio:D components
var visual = new xbiod.visual();
var taxon = new xbiod.taxon();

An object derived from a class is instatiated using the '''new''' keyword and a namespace's constructor. The JavaScript namespace that represents the xBio:D visual applications is the '''visual''' namespace/component and similarly the namespace that represents the xBio:D taxon applications is the '''taxon''' namespace/component. Access to functionality from either of these components requires an object with a reference to that component. These objects allow methods from each component to be called to the web page.

==== Calling Application Methods ====
// Load map
visual.showGoogleMap('map_id', tnuid);

// Load included taxa
taxon.showIncludedTaxa('included_id', tnuid, {show_num_spms: 'Y', taxonFormat: '<a href="test.html?tnuid=%tnuid%">%taxon%</a> %author% - %num_spms%'});

Each application has a method associated with it which takes several parameters which will dictate what data it loads, where it will be contained, and options for how it should be presented. These methods and requirements can be found in the [[XBio:D Javascript Library Reference#Reference|Reference]] section.

In the above example, the '''visual''' method ''showGoogleMap'' gets passed a '''<nowiki><div></nowiki>''' element ID string which decides where it will be contained and a tnuid which will dictate which taxon data the map will locate.

The '''taxon''' method ''showIncludedTaxa'' gets passed similar parameters (a specified '''<nowiki><div></nowiki>''' element ID string and a tnuid) however it also gets additional options in the form of a [http://www.w3schools.com/js/js_objects.asp JavaScript object literal]. In this example, the option ''[[OJ_Break API Data Type Glossary#show_num_spms|show_num_spms]]'' is given the [[OJ Break API Data Type Glossary#Boolean_Flag| Boolean_flag]] 'Y' signifying that the application should display the number of specimens for that particular taxon and ''taxonFormat'' is assigned to present the data as links using the '''<a>''' tag.

==== Element Containers ====
Each method requires one or more unique '''<nowiki><div></nowiki>''' tag IDs as string parameters (seen in the example '''<body>''' below). This will be used to specify where the resource will be contained in the web page.

<body>
<div id="map_id"/>
<div id="included_id"/>
</body>

== Reference ==
=== Agent ===
==== showAgentInfo ====
===== Description =====
Displays information about an agent, including name, contact information, and a short biography.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* [[OJ_Break v2 Agent Reference#agent_id|agent_id]]
* options
===== Options =====
* widget_options - Object

==== showAgentOccurrences ====
===== Description =====
Displays collected occurrences for a specified agent on a Google Map. Creates two windows.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* agent_id ([[OJ_Break API Data Type Glossary#collector_id_2|?]])
* options

===== Options =====
* info_element_id - ID String (defaults to element_id parameter)
* generalFormat - HTML String
* markers - String ('spiderfy' or undefined). Requires additional dependencies (see below).
* offset - Number
* limit - Number
* icons - Object
* widget_options

===== Additional Requirements =====
* [https://developers.google.com/maps/documentation/javascript/ Google Maps API v3]
* [https://github.com/jawj/OverlappingMarkerSpiderfier Overlapping Marker Spiderfier]

==== showAgentOccurrenceLocalityInfo ====
===== Description =====
Displays locality information for a certain agent's collecting occurrence.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* loc_id ([[OJ_Break API Data Type Glossary#loc_id_2|?]])
* options
===== Options =====
None

==== showDescribedTaxa ====
===== Description =====
Displays all taxa described by the specified agent.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* author_id ([[OJ_Break API Data Type Glossary#author_id_2|?]])
* options
===== Options =====
* taxonFormat - String
* useTaxonItalics - Boolean
* limit - Number
* offset - Number
* widget_options - Object

==== showPublications ====
===== Description =====
Displays all publications for a specified agent.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* author_id ([[OJ_Break API Data Type Glossary#author_id_2|?]])
* options
===== Options =====
* limit - Number
* offset - Number
* widget_options - Object

=== Occurrence ===
==== showBiologicalInfo ====
===== Description =====
Displays both the habitat and associations for a selected occurrence identifier.

===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* occurrence_id ([[OJ_Break API Data Type Glossary#occurrence_id|?]])
* options
===== Options =====
* widget_options - Object

==== showOccurrenceInfo ====
===== Description =====
Displays collecting trip info for a specified occurrence.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* occurrence_id ([[OJ_Break API Data Type Glossary#occurrence_id|?]])
* options
===== Options =====
* widget_options - Object

==== showDeterminations ====
===== Description =====
Displays determinations for a specified occurence.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* occurrence_id ([[OJ_Break API Data Type Glossary#occurrence_id|?]])
* options
===== Options =====
* widget_options - Object

==== showLocalityInfo ====
===== Description =====
Displays locality info for a specified occurrence.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* occurrence_id ([[OJ_Break API Data Type Glossary#occurrence_id|?]])
* options
===== Options =====
* widget_options - Object

==== showSpecimenInfo ====
===== Description =====
Displays specimen info for a specified occurrence.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* occurrence_id ([[OJ_Break API Data Type Glossary#occurrence_id|?]])
* options
===== Options =====
* widget_options - Object

=== Search ===
==== showSearch ====
===== Description =====
A JQuery UI autocomplete search bar which can search for taxa, occurrences, institutions, agents, journals, localities, and places.

===== Parameters =====
* element_id
* options

===== Options =====
* search - the type of search to execute. Controls the passing of URL parameters to methods. Can be specified a either 'id' or 'name'. Defaults to 'id'
* domains - array of the below object elements
** type - a domain keyword for which data gets searched for
** handler_url - a URL that will be passed the ID of the selected type option

===== Additional Information =====
====== Category Options Formatting ======
Below is an example of how the categories should be input:

// Load search
search.showSearch('search_id', {domains: [{type: 'taxon', handler_url: '<nowiki>http://domain.url/index.html</nowiki>'}, {type: 'occurrence', handler_url: '<nowiki>http://domain.url/occurrence.html</nowiki>'}]});

=== Taxon ===
==== showAssociations ====
===== Description =====
Displays all associations for a specified taxon.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* basic_only - Boolean_flag
* limit - Number
* offset - Number
* widget_options

==== showInstitutions ====
===== Description =====
Displays institutions for which specimens of the selected taxon level belong.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* limit - Number
* offset - Number
* widget_options - Object

==== showContributors ====
===== Description =====
Displays all contributing agents related to the occurrence, taxonomy, literature, and media of a taxon.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* inst_id
* widget_options

==== showDeterminers ====
===== Description =====
Displays determiners for a specified taxon.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* limit - Number
* offset - Number
* inst_id
* widget_options

==== showHabitats ====
===== Description =====
Displays all identified habitats for a selected taxon.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* limit - Number
* offset - Number
* widget_options

==== showIncludedTaxa ====
===== Description =====
Displays taxa directly included within a taxon but not synonymous with it.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* inst_id
* show_syns
* show_fossiles
* types_only
* useTaxonItalics - Boolean
* limit - Number
* offset - Number
* widget_options

==== showLiterature ====
===== Description =====
Displays relevent publications for a specified taxon with links to the literature when available.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* show_children - Boolean_flag
* show_bib - Boolean_flag
* useTaxonItalics - Boolean
* limit - Number
* offset - Number
* widget_options

==== showSubordinateTaxa ====
===== Description =====
Displays the count of valid taxa levels available below the current taxon rank.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* inst_id
* widget_options

==== showSynonyms ====
===== Description =====
Displays all taxa which are objectively or subjectively synonymous with a selected taxon.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* show_fossils
* useTaxonItalics - boolean
* limit - Number
* offset - Number
* widget_options

==== showTaxonMedia ====
===== Description =====
Displays a table of all media associated to a specific taxon rank.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* inst_id
* row_count - Number
* media_type
* limit - Number
* offset - Number
* widget_options

==== showTypes ====
===== Description =====
Displays information and specimen types for a specified taxon.
===== Parameters =====
* [[xBio:D Javascript Library Reference#Element_Containers|element_id]]
* tnuid
* options
===== Options =====
* show_children
* inst_id
* primary_only - Boolean_flag
* basic_only - Boolean_flag
* offset - number
* limit - number
* useTaxonItalics - boolean
* widget_options

=== Visual ===
==== showGoogleMap ====
===== Description =====
A Google map which displays locality markers for a specified taxon.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* tnuid ([[OJ_Break API Data Type Glossary#tnuid_2|?]])
* options
===== Options =====
* place_id - Number
* inst_id - Number
* use_sex_icons - Boolean_flag
* show_children - Boolean_flag
* limit - Number
* offset - Number
* markers - Number
* widget_options - Object

===== Additional Requirements =====
* [https://developers.google.com/maps/documentation/javascript/ Google Maps API v3]
* [https://github.com/jawj/OverlappingMarkerSpiderfier Overlapping Marker Spiderfier]

==== showTaxonHierarchy ====
===== Description =====
An interactive, tree-based animation which allows a user to navigate through a selected taxon's hierarchy and all taxa available through the OJ_Break API.
===== Parameters =====
* element_id ([[xBio:D Javascript Library Reference#Element_Containers|?]])
* tnuid ([[OJ_Break API Data Type Glossary#tnuid_2|?]])
* requestedNode
* options

===== Options =====
* show_num_spms - Boolean_flag
* inst_id - Number
* show_syns - Boolean_flag
* show_fossils - Boolean_flag
* types_only - Boolean_flag
* nodeColor - string or hexadecimal number
* backgroundColor - string or hexadecimal number
* handler_url - File path string/URL
* size - JavaScript object with two string properties:
** width - either a number or string in pixels
** height - either a number of string in pixels
* imagePath - string of relative path to a folder containing necessary images.
* widget_options - Object

===== Additional Requirements =====
* [http://en.wikipedia.org/wiki/Processing.js Processing.js] 1.4.1+
* Pass requestedNode parameter a value of '''null''' when calling function. See below:
// Load taxon hierarchy
visual.showTaxonHierarchy('canvas_id', tnuid, null, { /*options*/ });

===== Additional Information =====
====== URL Handler Option ======
The ''handler_url'' option can be used to allow the nodes to have links attached to them, so that a user may follow the link for more information on that specific taxon.

// Load taxon hierarchy
visual.showTaxonHierarchy('canvas_id', tnuid, null, {nodeColor: 'cyan', backgroundColor: '#FFFFFF', handler_url: '<nowiki>http://hol.osu.edu/index.html</nowiki>'});

In this example, a default web page URL is given (note the use of http:// at the beginning). When provided a URL, the taxon hierachy animation will present a link button to the top right of the node that is currently being highlighted (see image below). This link will not be present if a URL is not specified. If this button is clicked, the ''handler_url'' link will be followed.

====== Size Option ======
The taxon hierarchy application can be resized in one of two ways: via [http://en.wikipedia.org/wiki/Cascading_Style_Sheets CSS] (preferred) or by inputting the dimensions of the HTML canvas into the API method call as options. One way this can be done is by specifying the width and height as numbers:

// Load taxon hierarchy
visual.showTaxonHierarchy('canvas_id', tnuid, null, {size: {width: 300, height: 900}});

The dimensions of the canvas can also be input as pixels:

// Load taxon hierarchy
visual.showTaxonHierarchy('canvas_id', tnuid, null, {size: {width: "300px", height: "900px"}});

Both of these methods (CSS and parameter passing) are valid, but they should never both be used at the same time since unexpected errors may occur.

====== Image Path Option ======
Due to security restrictions, Processingjs is limited in its function to request images. As a consequence, any user wishing to use the animation must have copies of the required images available locally on their server. To access these images, a relative directory path must be input in the form of a optional parameter. The call may look something like this:

// Load taxon hierarchy
visual.showTaxonHierarchy('canvas_id', tnuid, null, {imagePath: "media/images/"});

<hr>


[[Category:xBioD Library]]
[[Category:APIs]]

Portions of this page are modifications based on work created and [https://developers.google.com/readme/policies/ shared by Google] and used according to terms described in the [http://creativecommons.org/licenses/by/3.0/ Creative Commons 3.0 Attribution License].

Hymfiles Server Management

2015-07-22T19:28:42Z

Jcora: Created page with "---- '''Hymfiles Server Management (hymfiles.biosci.ohio-state.edu)''' == General Locations == * IIS Web Directory: ''C:\inetpub\wwwroot'' * xBio:D IPT Directory: ''C:\ipt..."

Collection Server Management

2015-07-22T19:21:51Z

Jcora:

----

'''Collection Server Management (delong.biosci.ohio-state.edu)'''

== General Locations ==
* IIS Web Directory: ''D:\wwwroot''
* DEA Home Directory: ''D:\python_projects\dea''
* Backup Scripts Directory: ''C:\backup_scripts''

== Applications / Services ==
* DEA - http://xbiod.osu.edu/dea/
* Specimage - http://specimage.osu.edu
* xBio:D Gateway (Redirects)
* Collection Web Site - http://bugs.osu.edu
* Collection Web Site (Wordpress) - http://osuc.osu.edu/osuc-wp/
* xBio:D Wiki - http://xbiod.osu.edu/wiki/
* NFJ Lab Web Site - http://wasps.osu.edu
* BLB mp3 storage - http://osuc.osu.edu/blbmp3s/

== DEA Database Backup ==
The database is backup up daily at 9PM via the mysql_backup.bat script. This script create a database dump and transfers saves this file to the ''dumpfiles'' directory of the web directory.

[[Category:OSUC Private]]

Collection Server Management

2015-07-22T19:18:43Z

Jcora:

XBio:D Database Server Management

2015-07-22T19:12:23Z

Jcora:

----

'''xBio:D Database Server Management (osuc.biosci.ohio-state.edu)'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API
* Database Gateway
* LSID / GUID Metadata Handler
* xBio:D Javascript Library
* HOL
* vSysLab
* DB Manager
* HNS
* Platy site
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database: $ <code>dbstart $ORACLE_HOME</code>
# Start the database listener: $ <code>lsnrctl start</code>

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]

Collection Server Management

2015-07-22T19:11:50Z

Jcora:

----

'''Collection Server Management (delong.biosci.ohio-state.edu)'''

== General Locations ==
* IIS Web Directory: ''D:\wwwroot''
* DEA Home Directory: ''D:\python_projects\dea''
* Redmine Home Directory: ''D:\redmine''
* Backup Scripts Directory: ''C:\backup_scripts''

== Applications / Services ==
* DEA
* Specimage
* xBio:D Gateway (Redirects)
* Collection Web Site
* Collection Web Site (Wordpress)
* xBio:D Wiki
* NFJ Lab Web Site
* Redmine Bug Tracker/Project Manager

== DEA Database Backup ==
The database is backup up daily at 9PM via the mysql_backup.bat script. This script create a database dump and transfers saves this file to the ''dumpfiles'' directory of the web directory.

[[Category:OSUC Private]]

Collection Server Management

2015-07-22T17:24:10Z

Jcora: Protected "Collection Server Management" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

----

'''Collection Server Management'''

== General Locations ==
* IIS Web Directory: ''D:\wwwroot''
* DEA Home Directory: ''D:\python_projects\dea''
* Redmine Home Directory: ''D:\redmine''
* Backup Scripts Directory: ''C:\backup_scripts''

== Applications / Services ==
* DEA
* Specimage
* xBio:D Gateway (Redirects)
* Collection Web Site
* Collection Web Site (Wordpress)
* xBio:D Wiki
* NFJ Lab Web Site
* Redmine Bug Tracker/Project Manager

== DEA Database Backup ==
The database is backup up daily at 9PM via the mysql_backup.bat script. This script create a database dump and transfers saves this file to the ''dumpfiles'' directory of the web directory.

[[Category:OSUC Private]]

Collection Server Management

2015-07-22T17:21:52Z

Jcora:

Collection Server Management

2015-07-22T17:12:01Z

Jcora: Created page with "---- '''Collection Server Management''' == General Locations == * IIS Web Directory: ''D:\wwwroot'' * DEA Home Directory: ''D:\python_projects\dea'' * Redmine Home Directo..."

----

'''Collection Server Management'''

== General Locations ==
* IIS Web Directory: ''D:\wwwroot''
* DEA Home Directory: ''D:\python_projects\dea''
* Redmine Home Directory: ''D:\redmine''
* Backup Scripts Directory: ''C:\backup_scripts''

== Applications / Services ==
* DEA
* Specimage
* xBio:D Gateway (Redirects)
* Collection Web Site
* Collection Web Site (Wordpress)
* xBio:D Wiki
* NFJ Lab Web Site

== DEA Database Backup ==
The database is backup up daily at 9PM via the mysql_backup.bat script. This script create a database dump and transfers saves this file to the ''dumpfiles'' directory of the web directory.

[[Category:OSUC Private]]

XBio:D Database Server Management

2015-07-21T21:33:38Z

Jcora: /* Applications / Services */

----

'''xBio:D Database Server Management'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API
* Database Gateway
* LSID / GUID Metadata Handler
* xBio:D Javascript Library
* HOL
* vSysLab
* DB Manager
* HNS
* Platy site
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database: $ <code>dbstart $ORACLE_HOME</code>
# Start the database listener: $ <code>lsnrctl start</code>

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]

Collection (OSUC) Private Portal

2015-07-21T20:47:36Z

Jcora:

----

'''Welcome to the OSUC Private Portal'''

This section of the wiki is private for users associated with the C.A. Triplehorn Insect Collection (OSUC). All subsequent pages, in order to be private, must be protected. Protect new pages by clicking the down arrow next to "View history" at the top, then select "Protect". When the protection setting page is loaded, choose "OSUC users group" from the "Edit" box to reject all users who are not part of the OSUC users group from editing or reading the page.

== General ==
* [[Miscellaneous Publications]]

== Infrastructure ==
* [[xBio:D Data Management]]
* [[xBio:D Database Server Management]]
* [[Collection Server Management]]
* [[Hymfiles Server Management]]
* [[Macroteleia Server Management]]
* [[Tyrannoscelio Server Management]]
* [[Initiate ASC Offsite Backup]]
* [[OBCP Cluster Management]]

== Bioinformatics ==
* [[Data Validation]]

[[Category:OSUC Private]]

XBio:D Database Server Management

2015-07-21T20:40:43Z

Jcora:

----

'''xBio:D Database Server Management'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API
* Database Gateway
* xBio:D Javascript Library
* HOL
* vSysLab
* DB Manager
* HNS
* Platy site
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database: $ <code>dbstart $ORACLE_HOME</code>
# Start the database listener: $ <code>lsnrctl start</code>

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]