custom software development for clinical and basic research when your needs go beyond standard tools...
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![Page 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](https://reader035.vdocuments.us/reader035/viewer/2022062801/56649e725503460f94b71d9b/html5/thumbnails/1.jpg)
Custom Software Development for Clinical and Basic Research
When Your Needs Go Beyond Standard Tools
Andrew RupertOpen Source Team Lead
John Stullenberger.NET Team Lead
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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.
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• 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.
Research IT - Application Developers
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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.
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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
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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!
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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!
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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.
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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.
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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.
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Acknowledgments (and most of the credit)
The Open Source Development Team:
Nick Felicelli, Sr. App. Dev.
Mojtaba Kohram, App Dev.
Michael Taylor, App. Dev.
David Van Horn, App Dev.
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If you need assistance with the development of custom software tools or help configuring existing software packages, please contact us!