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Custom Software Development for Clinical and Basic Research

Custom Software Development for Clinical and Basic Research. When Your Needs Go Beyond Standard Tools. Andrew Rupert Open Source Team Lead John Stullenberger .NET Team Lead. Research IT Services Overview (http://bmi.cchmc.org). System Administrators (Windows, Linux, Mac)

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Custom Software Development for Clinical and Basic Research

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  1. Custom Software Development for Clinical and Basic Research When Your Needs Go Beyond Standard Tools Andrew Rupert Open Source Team Lead John Stullenberger .NET Team Lead

  2. Research IT Services Overview (http://bmi.cchmc.org) • System Administrators (Windows, Linux, Mac) • Storage Administrators • Database Administrators (Oracle, MSSQL, MySQL) • Help Desk • Application Developers (Java, .NET, Open Source) • Data warehouse, i2b2 • Work very closely with CCHMC Information Services.

  3. Research IT - Application Developers • Java – Jeremy Nix • Focus on using the Java programming language for their applications. Heavily involved in the development and setup of i2b2. • .NET – John Stullenberger • Uses the Microsoft .Net Framework for their projects. Also involved with developing custom Sharepoint tools. • Open Source – Andrew Rupert • Uses Open Source languages such as PHP, Perl, Python for their applications. Many projects focus on applications that interface with the computational cluster.

  4. What do the Research IT Application Development groups do? • We develop custom software to make your life easier! • This can range from large scale stand alone software packages to modifications of existing open source tools to suite your needs. • If you have ideas, contact us! Our projects often come from casual chats. help@bmi.cchmc.org

  5. Research IT - Application Developers • Work with a wide variety of divisions • Pediatric Neuroimaging Research Consortium • Sports Medicine • Rheumatology • Psychology • Anderson Center • Etc. • Along with a variety of research cores • Flow Cytometry Core • Confocal Microscopy Core

  6. Research IT - Application Developers • We work on larger grant funded projects when a PI needs entire custom applications developed. • We also help with smaller “one-off” tasks that are made easier with simple scripts or programs. • Most applications are now web based. Can access them from anywhere. No need to install software on every computer!

  7. Research IT - Application Developers • We follow best practices in terms of programming structure and security, e.g. role based access and federation. • We can help with integrating existing systems into your projects, e.g. TimeTracker – CORES, Active Directory authentication, etc. • If you think you have a problem that we can help with, please don’t hesitate to contact us! help@bmi.cchmc.org

  8. Open Source Project Examples - Demos • C-MIND - Cincinnati MR Imaging of NeuroDevelopement • Scott Holland (PI), Michael Wagner (BMI) • Fully custom longitudinal data entry, querying, and processing application for fMRI images. • CASSI – Cincinnati Analytical Suite for Sequencing Informatics • John Harley, Ken Kaufman, Leah Kottyan, Sue Thompson • Repository and processing pipelines for Next-Generation Sequencing data.

  9. Project Examples - Demos, Cont. • Sports Medicine – Sports Medicine Portal • Greg Myer (PI) • Self assessment for risk of knee injury. • Instrument Time Tracker • Andrew Rupert, Michael Wagner • Transparently tracks real time lab instrument usage for the Flow Cytometry and Confocal Microscopy cores. • Scheduling Calendars • Sort Scheduler, MRBS, etc.

  10. Project Examples - Demos, Cont. • GWADB • Sue Thompson (PI), Michael Wagner (BMI) • Database of genotypes from SNP chips. Provides a graphical user interface to the computational cluster for genotype processing.

  11. Acknowledgments (and most of the credit) The Open Source Development Team: Nick Felicelli, Sr. App. Dev. Mojtaba Kohram, App Dev. David Van Horn, App Dev. Michael Taylor, App. Dev.

  12. If you need assistance with the development of custom software tools or help configuring existing software packages, please contact us! help@bmi.cchmc.org Andrew.Rupert@cchmc.org

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