= Welcome to the LCBRU Informatics Platform wiki = * Getting agile Starting in January 2014, the LCBRU Informatics team embarked on a journey towards being agile. We're hoping it will make us more responsive, more effective and more productive. We're also hoping it will make us happier while we're at work. The experience of becoming agile will be documented on this trac site, at [[Agile LCBRU]]. * 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 * [[BRICCS]] - where it all began * [[BRICCS Aortic Stenosis Study]] * [[DHF]] - Diastolic Heart Failure * [[DREAM]] - Daily REmote Ischaemic Conditioning Post-Acute Myocardial Infarction * [[EMMACE-4]] - observational study of ACS acute care * [[GENVASC]] - recruitment across primary care * [[GRAPHIC]] - Genetic factors in hypertension * [[HDL ethnicity]] - a study into HDL across ethnic groups * [[MVO]] - Microvascular Obstruction * [[NIHR BioResource]] - contributing to a national facility for translational medicine * [[PRESTIGE]] * [[SCAD]] - Spontaneous Coronary Artery Dissection * [[TOTAL]] - Routine aspiration thrombectomy versus PPCI alone * Planning * [[Integration phase 20101112]] * [[LAMP proposal]] * [[Between now and LAMP]] * [[Northampton Recruitment into BRICCS]] * Component pages * 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 * [[Building & Deploying caTissue application from the source code in Ubuntu]] * [[CiviCRM]] * [[CiviCRM - Upgrading]] * [[CiviCRM - Create a New Report Template]] * [[CiviCRM Genvasc Patient Export]] * [[CiviCRM Graphic 2 Patient Export]] * [[CiviCRM - Rest API]] * [[CiviCRM GP/Practice Update process]] * [[CiviCRM API Development]] * [[CiviCRM Testing]] * [[Drupal Settings Deployment|CiviCRM Settings Deployment]] * ClinicalRegistry * [[Darwin]] * [[Drupal]] * [[Drupal Settings Deployment]] * [[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 import]] * [[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]] * Data * [[Read Codes]] * [[QRISK]] * [[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.