The members of NUBIC help to develop biomedical informatics across the NU academic medical enterprise. This page contains a list of all our current and past projects. You can read more about NUBIC on the NUCATS website.
eNOTIS is a web-based study enrollment log that helps to improve safety and security for study participant enrollment. This system is available now. Any biomedical clinical research study that has been approved by the NU IRB is listed in eNOTIS.
Registar is a web-based research registry system used to collect information about potential research study participants and contact them over email.
NUCATS Assist is a web application for managing seed and pilot project solicitations, applications and reviews. It has been used to run the NUCATS pilot awards, the Foundation Dixon awards, and two cycles of the Northwestern Core Facilities Equipment Grants.
The Northwestern Oncology Trial Information System is a web application for tracking patients on clinical trials within the Robert H Lurie Comprehensive Cancer Center and its affiliates. NOTIS also includes an electronic Case Report Form module used to capture patient data while patients are participating in studies.
Patient Study Calendar
Patient Study Calendar is a web application for defining and tracking the activities for a patient on a clinical trial. It is part of the NCI's (National Cancer Institute) caBIG® (cancer Biomedical Informatics Grid) initiative to develop open source software to support cancer research. However, it is not specific to cancer clinical trials and has been successfully adapted to other purposes.
A tool for patient care coordinators to help patients with a serious diagnosis navigate the health care system. The application couples a lightweight patient and provider registry with a protocol and patient-activity management application. The application is based on the NCI's (National Cancer Institute) caBIG® (cancer Biomedical Informatics Grid) Patient Study Calendar (also developed by NUBIC). To use the demo site, login with the username "inavdemo" and use the password "password".
An application to manage the workflow of investigators submitting requests to the Prostate SPORE's disbursement committee for the distribution of biospecimens and/or clinical patient data. Disburser can easily be adapted to the workflow of any group that needs to approve disbursement requests.
Prostate Cancer Follow-up
An online survey for participants of the Prostate SPORE study to directly report their clinical medical histories.
Specialized Program of Research Excellence in Prostate Cancer (Prostate SPORE)
An application to track the clinical medical histories of prostate cancer patients — both manually curated from medical records and automatically extracted form Northwestern's' Enterprise Data Warehouse.
An application to match faculty members of Northwestern's Feinberg School of Medicine to funding opportunities. Faculty Connect developed as a One Northwestern tool for identifying Northwestern faculty who are potentially eligible for funding opportunities, national service positions such as the National Academy of Medicine, and honors. Faculty Connect provides both identification and outcome tracking tools for managing foundation and grant matchmaking, application, and reporting activities. Data is pulled from existing sources such as the FSM Faculty Database, LatticeGrid, Community of Science, and foundation opportunity database subscriptions owned by the University.
LatticeGrid (publications and SNA)
LatticeGrid is an open source publications/collaboration assessment tool. The Feinberg version of this tool leverages data from the FSM Faculty Database, and provides ways to see co-authorship and assess investigator similarity based on existing research activity. It also provides network graphs for viewing direct coauthors or assessing investigators working in a particular area.
SAMPLE is a web application for tracking biospecimens in a laboratory from receipt to shipment. It was developed for the Pathology Core Facility at the Robert H. Lurie Comprehensive Cancer Center, and is being expanded to meet the needs of other groups.
ClearCATS is a reporting tool for NUCATS employees which helps NUCATS keep track of who worked with the several centers and programs. ClearCATS will demonstrate that, with NUCATS' support, investigators have been able to obtain grants, receive awards, publish, and conduct studies.
The Lynn Sage Database
The Lynn Sage Database is a web application for collecting information about patients who come to the Lynn Sage Comprehensive Breast Center for care and who consent to participate in research. The application also contributes to the The National Comprehensive Cancer Network (NCCN), a not-for-profit alliance of the world's leading cancer centers dedicated to improving the quality and effectiveness of care provided to patients with cancer.
dictyBase is the central web portal to access genome information and experimental resources for the model organism Dictyostelium discoideum. This includes a web interface for ordering strains, available from the Dicty Stock Center located at Northwestern, and 'cloned' websites for related organisms, such as Dictyostelium purpureum.
lumi is a Bioconductor R package designed for BeadArray Specific Methods for Illumina Methylation and Expression Microarrays. It provides an integrated solution for Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays.
MassSpecWavelet is a Bioconductor R package designed to perform mass spectrum analysis using wavelet-based algorithms.
CGIporter is an R package for importing CGI (Complete Genomics, Inc.) whole genome sequencing data into Biocondutor and integrating with genome annotation, mutation and CNV analysis. It is an ongoing project.
Surveyor is a Ruby gem and developer tool that brings surveys into Rails applications. Surveys are written in the Surveyor DSL (Domain Specific Language).
Ladle is a developer tool which enables test-driven development of LDAP-backed Ruby software. It spins up an actual LDAP server with the data you specify, so no mocks are needed.
schema_qualified_tables is an ActiveRecord extension that simplifies using ActiveRecord models from several different schemas in the same application.
Bcdatabase is a Ruby library that enables the centralized configuration of database connection parameters across all the applications on a server. This simplifies administration (since a changed password only needs to be updated once per server) and makes the databases more secure (because their credentials are not stored in and deployed with each application, but rather live on the servers alone).
Dagnabit is an ActiveRecord extension for manipulating directed acyclic graphs in PostgreSQL 8.4+. It was originally developed for SAMPLE, but can be applied elsewhere. Dagnabit provides fast reachability queries without burdensome recalculation overhead.
Castanet is a Ruby client library for authentication servers implementing the Central Authentication Service (CAS) 2.0 protocol.