Dear Researcher,

Thank you for taking the time to complete this short, 17 question, survey.

The PathoSystems Resource Integration Center (PATRIC), at the Virginia Bioinformatics Institute (VBI), is asking for your opinions and feedback. Our goal is to provide the scientific community with a portal of biological information on bacterial pathogenic microorganisms, to facilitate research in the areas of drugs, vaccines and diagnostics.

In order to provide high-quality service to the pathogen communities we are conducting a survey to assess your bioinformatics needs.

Note that responses to any or all of the questions below is optional and will be used solely to assist in planning for our PATRIC Bioinformatics Resource Center.

General Research Interests

1. Please select all areas list below that apply most closely to your lab’s research interests. Please, provide a brief description if you check the “Other” box.

2. Select all NIAID Category A, B, or C bacterial pathogens related to your work.

3. Please identify some of your main bioinformatics analysis needs. Select all that apply.

Data Needs
4. PATRIC will be providing rich and varied data related to bacterial genomes. Choose five of the following data types that are most useful for you work.

5. PATRIC will be extending its bacterial genome annotation to include new annotation feature types. Chose the three annotation feature types that would most benefit your work.

Analysis Tools
6. PATRIC will provide tools for the analysis of data stored in the PATRIC database. Choose three of the following tasks that you would find a tool most useful for.

7. PATRIC website will also provide tools for the analysis of user-supplied data. Choose three of the following tasks that you would find a tool most useful for.

8. Please indicate the data visualization tools that are required for your work. Select all that apply.

9. PATRIC will provide a wide-array of analysis and visualization tools to aid bacterial researchers. Chose three tools from the list below that would most benefit your work.

Website Features
10. PATRIC will allow users to upload their own sequence data to leverage the wealth of PATRIC bacterial data, analysis and website tools. This data could be data you have created (e.g., by sequencing a new bacterial strain), or data you've gathered from other locations.

Select three features you would most likely use to gain insight on your uploaded data. If there is a feature or action not listed, please describe in the “other” field.

11. The ability to customize PATRIC web pages allows users to quickly enter PATRIC and “get to work." This customizable approach is already in use throughout the mainstream web; for example, both Yahoo and iGoogle allow registered users to customize their home page to perform a number of common tasks on a single page.

Select three customization features you would most likely use to expedite your work or pique your interests on PATRIC. If there is a feature not listed, please describe in the “other” field.

12. PATRIC will support a wide range of opportunities for community involvement and social participation. The goal of these features is to provide community-driven value to, and discussion around, PATRIC data.

Select two social and community features you would most likely use to stay informed and/or pique your interest on PATRIC. If there is a feature not listed, please describe in the “other” field.

13. PATRIC will expand the traditional notion of “download data”, by offering access to annotation data, post-genomic data (to, for example, run additional analyses), pathway data, publications, and so on.

Select two methods by which you are most likely to access data from PATRIC.

Outreach Activities

14. The main goal of our outreach efforts is to engage the scientific community into the design, development, use and usability of the resources that we will develop. The main objectives of outreach are to discover and acquire data for inclusion in PATRIC; enhance data quality through data analyses and curation; improve the usefulness and usability of the resource based on the feedback; and enhance the participation by the community through workshops, training, and presentations.

Please select all that applies to your work.

15. Collaborative projects and other outreach activities provide valuable input and use cases for the PATRIC analysis resource and website. We collect these requirements and use them to steer future development to continually improve PATRIC's utility and usability.

Collaborative projects may include (for example) bioinformatics support and analyses of large datasets on bacterial infectious diseases.

Please indicate your collaboration interests in the following:

16. PATRIC has acquired funding to engage the scientific community on Driving Biological Projects (DBPs), which are expected to ‘drive’ the research by the infectious disease research, as well as, the development of PATRIC. We will broadly and openly solicit proposals for and establish four DBPs through a competitive review process, and collaborate with the selected experimental laboratories.

Please indicate your interest in the following:

Contact Information

17. PATRIC will be continuously engaging the bacterial BRC community. If you are interested in participating, please provide your email address below, and then select the notifications and options of interest. All email addresses will be held in confidence, used strictly for PATRIC feedback purposes, and will not be shared with any other organizations.

Email address:

Select all engagement activities that are of interest to you.

Virginia Bioinformatics Institute
Washington Street, Blacksburg, VA 24061
Contact Us
This project has been funded in whole or in part with Federal funds from the
National Institute of Allergy and Infectious Diseases, National Institutes of Health,
Department of Health and Human Services,
under Contract No. HHSN272200900040C