OHSU

Bioinformatics

The Bioinformatics Shared Resource (BISR) is one of several OHSU resources supported by the Knight NCI Cancer Center Support Grant. The grant ensures that management and support services are available for the researchers and programs of the OHSU Knight Cancer Institute.

The mission of the Bioinformatics Shared Resource is to provide investigator-driven advanced algorithm development and implementation, clinical trials management support and reporting, new tools and data management solutions for new technologies being used by Knight shared resources and researchers, as well as training and education.


MEET OUR STAFF

Shannon McWeeney, Ph.D.,  Director?
Associate Professor, Biostatistics & Bioinformatics 
Director, OCTRI BMIP Translational Bioinformatics Program

STAFF

  • Lara Fournier, M.S., C.C.R.P., Project Manager
  • Laura Bradley, M.S.W., Clinical Informaticist
  • Fred Loney, M.S., Senior Informaticist
  • Armand Bankhead, Ph.D.,  Computational Biologist
  • Hollis Wright, Ph.D.,  Post Doc

JOINT OCTRI PERSONNEL IN TRANSLATIONAL BIOINFORMATICS

  • Sophia Jeng, M.S., Developer
  • Sunita Kawane, B.S., Developer
  • Guaming Wu, Ph.D., Developer
  • Beth Wilmot, Ph.D., Senior Staff Scientist, Statistical Genetics
  • Daniel Bottomly, M.S., Developer

Jennifer Teeples, Administrative Contact?
Email: teeples@ohsu.edu
Phone: (503) 494-8382

COMPUTATIONAL RESOURCES

The Bioinformatics Shared Resource (BISR) has access to a wide variety of computing resources to support the informatics needs of cancer research. These include resources for development, project management, clinical trial and data management and statistical analysis.   

Software and web development tools

We have several software and web development applications available including Apache Tomcat, JBoss, JVM, Java, PHP, and Coldfusion, as well as operational tools such as CVS for version control and Bugzilla for issue and bug tracking.  

Databases

In addition to the development tools, OHSU’s computing infrastructure supports MySQL, Oracle and Microsoft SQL Server. These databases are available for use with BISR-supported projects.

Project management and collaboration

Project management and collaborative work applications availableinclude Wiki by Confluence, Plone, Macromedia Breeze for Web meetings and recorded demos, and Microsoft Project and Merlin for project management.

Analysis tools

We develop analytical tools for use by OHSU Knight Cancer Institute researchers. Some of these packages include:
  • Consense (R package): A consensus framework for exploring functional genomics data using multiple clustering methods.
  • TandTraq: An open-source tool for integrated protein identification and quantitation.
  • MetaData
  • SNP Mask from Walter et al (2007)

Clinical trial and data management

We currently utilize Surveyor Perspective Suite (v. 6.0.02, Permedics, Inc.) as our primary clinical trial management and trial registration system. All interventional and noninterventional cancer studies are tracked in this database. In addition to tracking the study activation status, we use Surveyor to track all enrollments for interventional studies and aggregate totals for noninterventional studies.
We also support and administer a local limited-use installation of Velos eResearch (v7.0, Velos, Inc.) to create study-specific data collection forms (CRFs) and collect research data throughout the study.
In addition, we are in the process of implementing a suite of caBIG applications called the Clinical Trials Framework. These include applications to handle adverse event capture and reporting (caAERS), patient registration (C3PR) and patient study calendar building and maintenance (PSC).

Life sciences applications

In addition to the caBIG Clinical Trials Framework, we are also in the process of implementing an additional application bundle called the Life Sciences Framework.  This suite includes applications to handle specimen repositories and tracking (caTISSUE), analyzing genomic data (caArray, geWorkbench, GWAS) and image analysis (NCIA).

Reporting/data extraction

For reporting and data extraction, we use the following tools: Crystal Reports/Crystal Enterprise (v. 10, Business Objects), PL/SQL Developer (v 6x, AllAroundAutomations), Cognos BI (Cognos, Inc) and RazorSQL (Richardson Software, LLC).

FEES

If you have a large-scale project or require novel methodology development, we recommend you to budget FTE for bioinformatics assistance in your grant. Contact us for more details.