= Welcome to the LCBRU Informatics Platform wiki = [[Lcbru IT Systems]] * About us The LCBRU public / general website is at http://www.le.ac.uk/lcbru/ This is the wiki for the Leicester Cardiovascular BRU informatics team. We use it to document the systems we have in use, the studies we are supporting, and the configurations, settings and other necessary information for keeping everything running smoothly. If you are a member of LCBRU staff, please do help us by editing the wiki regularly - you will need to log in (menu in top right corner of the page) to edit content. Don't be scared of making edits - we can always roll back to a previous version if something goes wrong. We also use this system for recording 'tickets' when work needs to be done. Again, you will need to be logged in to create, edit or view tickets. Please remember that this wiki is visible to anonymous visitors, so that we can share information with collaborators and colleagues outside the LCBRU. But that means we must not include any passwords or usernames in the documentation, or any example data which is not entirely fabricated. Items which must be kept confidential should be recorded in tickets, not in the wiki. * First things, first * [[new_staff|Setting up a new staff member as a user]] * LCBRU studies supported * [[Aneurysms Study]] - Matt Bown's consortium on female screening for aortic aneurysms * [[BRICCS Study]] - where it all began * [[Aortic Stenosis Study]] * [[BRAVE Study]] * [[Exome Sequencing Project]] * [[DHF Study]] - Diastolic Heart Failure * [[DREAM Study]] - Daily REmote Ischaemic Conditioning Post-Acute Myocardial Infarction * [[EDIFY]] * [[EMMACE-4 Study]] - observational study of ACS acute care * [[GENVASC Study]] - recruitment across primary care * [[Global Leaders]] * [[GRAPHIC Study]] - Genetic factors in hypertension * [[HDL Ethnicity Study]] - a study into HDL across ethnic groups * [[MVO Study]] - Microvascular Obstruction * [[NIHR BioResource]] - contributing to a national facility for translational medicine * [[PRESTIGE Study]] * [[SCAD Study]] - Spontaneous Coronary Artery Dissection * [[SCAD and CAE Study]] - Extension of the [[SCAD Study]] study to include patients with Coronary Artery Aneurysms / Ectasia * [[Telomere Length Study]] * [[TMAO Study]] * [[TOTAL Study]] - Routine aspiration thrombectomy versus PPCI alone * Planning * [[Integration phase 20101112]] * [[LAMP proposal]] * [[UoL LAMP Preparation Discussion]] * [[Northampton Recruitment into BRICCS]] * [[i2b2_meeting|Health Data and i2b2 workshop]] * Component pages * [[DataIntegrations]] * CaTissue * [wiki:CaTissueClientAPI API Client - 'Sampler'] * BarCodeReaders - notes on the various input devices reading linear and 2d barcodes * CaTissueUpgrade - notes on the upgrade process to v1.2 * [[CaTissue HowTo Build & Deploying CaTissue from the source code]] * [[CiviCRM]] * [[CiviCRM HowTo Install]] * [[CiviCRM HowTo Create a New Case Type]] * [[CiviCRM HowTo Upgrade]] * [[CiviCRM HowTo Create a New Report Template]] * [[CiviCRM HowTo Use Rest API]] * [[CiviCRM HowTo Develop API]] * [[CiviCRM HowTo Run Tests]] * ClinicalRegistry * [[Darwin]] * [[Drupal]] * [[Drupal HowTo Update]] * [[Drupal HowTo Edit and Deploy Settings]] * [[DAPS]] * [[i2b2]] * [[i2b2 - Cohort Request Procedure]] * [[i2b2 - How Tos]] * [[i2b2 - Debugging and Gotchas]] * [[i2b2 - Plugins]] * [[i2b2 - PDO]] * [[i2b2 Mapped Importer]] * [[i2b2 - Customisations]] * [[i2b2 - caTissue integration]] * [[i2b2 - UHL clinical informatics system integration]] * [[i2b2 - primary care informatics systems integration]] * [[i2b2 Onyx importer]] * [[i2b2 - fixes]] * i2b2 AUG * [[i2b2 - AUG 2013]] * [[Query Tool and Analysis Types]] * Ontology and CRC: * [[i2b2 - Documents]] * [[i2b2 - DB Basics]] * [[i2b2OntologyCRC-1]] Discussion, questions, things discovered * [[Snomed CT]] Discussions regarding mapping legacy data to Snomed CT for data management * [[c_metadataxml]] Column holding metadata associated with lab findings * i2b2 - Web Services * [[i2b2 - Importing data via web services]] * [[i2b2 - web services, switching them on]] * [[i2b2 - The algorithms applied to importing a PDO]] * [[i2b2 - GEM data load for GENVASC]] * IdLabelPrinting * [[MRBS]] * [[Onyx]] * OnyxCode * OnyxQuestionnaire - Developing (and Maintaining) a Questionnaire * OnyxDeployment - Deploying a Questionnaire * OnyxPrismClient * [[Onyx Export and Purge]] * [[OnyxExportOntology]] Discussion on deriving an initial ontology * OnyxTestSystem * OnyxVersions * OnyxDatabaseReporting * OnyxDataValidation * [[Onyx to PDO]] Assumptions underlying importing facts into i2b2 from the BRICCS questionnaire * [[Onyx to CiviCRM]] * [[PMI Lookup]] * RealWorldRecruitment * [[AS Study specific]] * [[REDCap]] * [[REDCap Installation]] * [[REDCap Usage]] * [[REDCap to i2b2]] * [[MySql]] * [[MySql Tips and Tricks]] * Data * [[Read Codes]] * [[QRISK]] * [[DM+D]] * [[ATC Codes]] * [[Office for National Statistics]] * [[Hospital Episode Statistics|Hospital Episode Statistics (HES)]] * [[Secondary Use Service|Secondary Use Service (SUS)]] * [[Genomics Files]] * [[Clinical Coding]] * [[SystemAdmin]] System admin information for the LCBRU server infrastructure. * Infrastructure components * [[Backups]] data backup requirements and processes. * [[DNS]] DNS configuration for {{{briccs.org.uk}}} * [[Eclipse]] development tool kit. * [[JBoss]] Settings, experiences and gotchas from working with the JBoss Application Server * [[Maven]] development tool kit. * [[MS SQL issues]] MS SQL Server commands, gotchas and bugs * [[Oracle]] Oracle commands, gotchas and bugs * [[ServiceDeployment]] recommendations for flexible service deployment. * [[SSH]] ssh keys and configuration. * [[Subversion]] source code repository. * [[Tomcat]] Middleware for the Onyx questionnaire tool. * [[Trac]] issue tracking system. * [[VirtualBox]] !VirtualBox commands and bugs * Components under consideration, or not implemented * [[C3PR]] * [[caAERS]] * [[EDGE - possibly]] * Miscellaneous * WebLinks * GoogleApps * Email [http://mail.briccs.org.uk] * Docs [http://docs.briccs.org.uk] * User pages * DaveMorris * JeffLusted * NickHolden * ChrisGreengrass * VasilStezhka * JasonSelby * NileshSamani * TimBeck = Trac notes = This wiki and issue tracking system is using Trac. Trac is a '''minimalistic''' approach to '''web-based''' management of '''software projects'''. Its goal is to simplify effective tracking and handling of software issues, enhancements and overall progress. All aspects of Trac have been designed with the single goal to '''help developers write great software''' while '''staying out of the way''' and imposing as little as possible on a team's established process and culture. As all Wiki pages, this page is editable, this means that you can modify the contents of this page simply by using your web-browser. Simply click on the "Edit this page" link at the bottom of the page. WikiFormatting will give you a detailed description of available Wiki formatting commands. "[wiki:TracAdmin trac-admin] ''yourenvdir'' initenv" created a new Trac environment, containing a default set of wiki pages and some sample data. This newly created environment also contains [wiki:TracGuide documentation] to help you get started with your project. You can use [wiki:TracAdmin trac-admin] to configure [http://trac.edgewall.org/ Trac] to better fit your project, especially in regard to ''components'', ''versions'' and ''milestones''. TracGuide is a good place to start. Enjoy! [[BR]] ''The Trac Team'' == Starting Points == * TracGuide -- Built-in Documentation * [http://trac.edgewall.org/ The Trac project] -- Trac Open Source Project * [http://trac.edgewall.org/wiki/TracFaq Trac FAQ] -- Frequently Asked Questions * TracSupport -- Trac Support For a complete list of local wiki pages, see TitleIndex.