Public Health Informatics:
"...the application of information, computer science, and technology to public health practice, research, and learning. Application of the principles and practices of public health informatics enables the development and use of interoperable information systems for public health functions such as biosurveillance, outbreak response, and electronic laboratory reporting."
-National Center for Public Health Informatics, CDC (2010)
Biomedical and Health Informatics:
"...has to do with all aspects of understanding and promoting the effective organization, analysis, management, and use of information in health care. ...biomedical and health informatics has developed its own areas of emphasis and approaches that have set it apart from other disciplines and specialties."
Boslaugh, S. (2007). Secondary data sources for public health: a practical guide. Cambridge: Cambridge University Press.
Braveman, P. (2006) Health disparities and health equity: concepts and measurement. Annu. Rev. Public Health, 27, 167-94.
Ewles, L. (2005). Key topics in public health: essential briefings on prevention and health promotion. Edinburgh: Elsevier Churchill Livingstone.
Harper, S., Lynch, J. (2005). Methods for measuring cancer disparities: using data relevant to healthy people 2010 cancer-related objectives. Bethesda: National Cancer Institute. NIH Publication No. 05-5777.
Institute of Medicine (IOM). (2005). Implications of genomics for public health: workshop summary. Washington, D.C.: The National Academies Press.
Last, J.M. (2007). A dictionary of public health. Oxford: Oxford University Press.
Liebowitz, J., Schieber, R.A., Andreadis, J.D. (2010) Knowledge management in public health. Boca Raton: CRC Press.
Milail, C.N. (2008). Public health genomics: the essentials. San Francisco: Jossey-Bass.
Miner, K.R., Richter, D.L. (2008). Curricular innovation and the science of public health education: a call to action. Public Health Rep., 123(Suppl 2), 1-4.
National Research Council (NRC). (2006). Reaping benefits of genomic and proteomic research intellectual property rights, innovation, and public health. Washington, D.C.: The National Academies Press.
Stewart, A., Brice, P., Burton, H., Pharoah, P., Sanderson, S., Zimmerman, R. (2007). Genetics, health care, and public policy: an introduction to public health genetics. Cambridge: Cambridge University Press.
Clinical Avatars
Peter Tonellato's labs have developed a methodology for creating virtual representations of people for the purpose of conducting personalized medicine simulations. We call these virtual representations, "Clinical Avatars". Avatars can be configured so that their statistical distribution matches the requirements of a particular population.
Initially, we have used clinical avatars to better understand complicated genomic-based drug dosing regiments. We selected the drug warfarin as our first use-case example. In addition to the warfaring propject, clinical avatars are used in some other running projects on breast cancer risk assessment tools and bladder cancer nomograms.
Link to Clinical Avatar's website: http://clinicalavatars.org/#/?model=warfarin
i2b2 (Informatics for Integrating Biology and the Bedside)
The i2b2 is a scalable informatics framework that enables clinical researchers to use existing clinical data for discovery research and clinical decision support. It allows researchers to perform self-service queries of de-identified data for HIPAA-compliant cohort discovery and hypothesis testing. Sponsored by the NIH, i2b2 is used by research and academic centers across the country for research and clinical performance improvement initiatives.
The i2b2 framework has been adopted by the LPHIG team for a few number of projects such as "Anti-Coagulate Pharmacogenetic Clinical Trial Simulations to Predict Improved Patient Outcomes".
The LPHIG team is open to share its knowledge and expertise on installing, administering, maintaining, and using this tool with the other UWM research groups.
Link to i2b2 website: https://www.i2b2.org/
LPHIG Cloud and Galaxy
LPHIG currently employs Amazon Web Services (AWS) as its cloud computing framework; primary usage is split between two applications—the Elastic Computing Cloud (EC2) and the Simple Storage Service (S3). In EC2, users may initiate new instances of single [or multiple] processors to accomplish tasks; the capacity to attach as many “child” nodes as desired to a “parent” instance allows for virtually unparalleled computing capacity—a key component in addressing the challenge of “Big Data”. S3, meanwhile, provides stable long-term storage for project data and EC2 results. Instance and storage management policies have been designed and will be implemented for all AWS users; instances will be appropriately named, storage on S3 will be correctly tracked, and all usage of AWS will be recorded within an electronic logbook for administrative tracking.
Galaxy is an open-source, web-based framework for conducting transparent, reproducible bioinformatics experiments. Its compatibility with AWS, particularly in the form of the CloudMan virtual machine image, serves as a great asset to LPHIG. Galaxy will be employed in the construction of a cloud-based pipeline for next-generation sequencing (NGS) analysis of transgenerational gene alterations induced in Zebrafish through environmental exposure to methyl mercury (MeHg). The capacity to combine NGS analysis tools with a cloud computing environment holds great promise for future NGS pipelines.
AVI
LPHIG members have access to Avi cluster. Avi is a nickname for a large HPC research cluster located at UWM. It has 142 nodes, each with 8 Intel Nehalem cores (1,136 cores in total). Each node has 24 gigabytes. Avi is very stable, offers good support, and has various applications already installed (e.g. Matlab, R). Disadvantages include: can be very heavily used on weekdays, and cannot be accessed off campus.
More information about Avi can be found at: http://www4.uwm.edu/hpc/about/. Information on high performance computing at UWM can be found here. All new users should review this.
REDCap
REDCap is a secure, web-based application for building and managing online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using
1) The online method from your web browser using the Online Designer; and/or
2) The offline method by constructing a 'data dictionary' template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods.
REDCap provides automated export procedures for seamless data downloads to Excel and common statistical packages (SPSS, SAS, Stata, R), as well as a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields.
REDCap Features
·Build online surveys and databases quickly and securely -Create and design your project rapidly using secure web authentication from your browser. No extra software is required.
·Fast and flexible -Conception to production-level survey/database in less than one day.
·Export data to common data analysis packages -Export your data to Microsoft Excel, PDF, SAS, Stata, R, or SPSS for analysis.
·Ad Hoc Reporting -Create custom queries for generating reports to view or download.
·Scheduling - Utilize a built-in project calendar and scheduling module for organizing your events and appointments.
·Easily manage a contact list of survey respondents or create a simple survey link - Build a list of email contacts, create custom email invitations, and track who responds, or you may also create a single survey link to email out or post on a website.
·Save your data collection instruments as a PDF to print - Generate a PDF version of your forms and surveys for printing to collect data offline.
·Advanced features - Auto-validation, calculated fields, branching/skip logic, and survey stop actions.
REDCap is currently being used in the lab to collect data on the Moroccan population of women. The survey will cover general breast cancer risk factors as well as Moroccan-specific risk factors to help build a data set, which will be used to create a model that stratifies women into risk groups in hopes of creating a more personalized treatment approach to women of high risk.
NOTICE: If you are collecting data for the purposes of human subject research, review and approval of the project is required by your Institutional Review Board (IRB).
Training Resources
If you would like to view some quick video tutorials of REDCap in action and an overview of its features, please see the Training Resources page.
ArcGIS
ArcGis is a desktop application that links maps and geographic information and enable creation of interactive maps and applications.
ArcGIS provide three GIS products with ArcGis Desktop- ArcView, ArcEditer, and ArcInfo-with each product providing different levels of functionality.
Features
·Ready to Use-No extra software installation or setup is needed to use this software. It is delivered as a service with tools needed to create or publish maps/applications.
·Sharing-You can easily share your maps and data on blogs or web apps, to Facebook or Twitter.
·Go Mobile-The ArcGIS app is available to use for Smartphones and tablets.
·Ready-to-Use Content- There is a rich collection of base maps, geographic maps, image services, and data that you can use as a foundation for your work.
·Easily Add Data- Data can be easily created with content-rich intelligent maps that can be easily shared with other users.
·Create Maps Directly in Excel- Maps can be created in Excel using Esri Maps . You can share your map in ArcGIS online with other users.
·Data in the Cloud- you can easily turn your data into web-enabled services that can be easily used with your organization.
·A Platform for Building Applications- Custom applications are built using ArcGIS APIs and SDKs to create either web or mobile applications
Contact
If you require assistance or have any questions about ArcGIS, please contact Customer Service.