Current Projects

From PublicWiki
Jump to: navigation, search

Contents

Current Projects and Demos

Cancer Center Clinical Trials Abstracts production

Cancer Center Members Profiles production requires login

Animal Models of Disease production NU only IPs

Open Source Collaborations and Projects

Oligonucleotide Properties Calculator

Disease Ontology (DO) sourceforge site; DO wiki

lumi Bioconductor package for Illumina microarray data analysis project site wikipedia entry

DOLite gene functional enrichment project

LatticeGrid Collaboration Assessment and Knowledge Management Tool github source site

NUCATS Publications public site

RHLCCC Publications public site includes interaction graphs for Cancer Center members

dictyBase MOD and wiki NIGMS-funded Model Organism Database

nuID data

ER Beta Drug Study

NGS

nuID-based Illumina Associations website

caBIG™ Patient Study Calendar Project demo site gForge site

caBIG™ caGRID Bioconductor Project gForge site developers gForge site

IPBS Prostate SPOREs/caBIG™ caTISSUE Suite Adoption gForge site

NUCATS Assist

caBIG™ activities

  • Developer for the Patient Study Calendar module, a caBIG™ compatible clinical trials patient study calendar software module
  • co-Developer for the caAERS module (cancer Adverse Event Reporting System) - partners with SemanticBits and Akaza Research to build a software module designed to interoperate with the new adverse event reporting systems at the NCI and FDA, with the ability to interoperate with local systems
  • co-Developers and subject matter experts for the caBIG™ CTMS interoperability project. We have been involved in integrating/grid-enabling the Patient Study Calendar and caAERS and defining the use cases and scenarios for interoperating these tools with the patient registry (C3PR), the clinical trials database C3D and caExchange.
  • Adopter of the Clinical Annotations Engine (CAE)- a software system developed by UPMC to pull structured data from clinical anatomical pathology laboratory information systems and structure it according to caBIG harmonized models for attachment to biospecimens
  • Developer/Adopter of the interoperability components for the Inter-prostate Biomarker Study (IPBS). We will use caTissue Suite to provide grid-enabled access to our prostate biospecimen data for sharing samples and data among 11 Prostate SPORE for the IPBS study, and with caGrid users throughout the community.
  • Adopter of the caTissue Suite - an integration of CAE, caTissue, and caTIES. caTissue is designed to capture workflow about biospecimens. caTIES is designed to import textual reports, including pathology reports, into a caBIG compatible format for attachment to biospecimens. The three systems together provide a powerful platform for tissuebanking and biorepositories. The systems do NOT include tracking information about the patient, consents, or studies. That information we use NOTIS to capture and track.
  • Bioconductor Adopter: we are working with the Fred Hutchinson Cancer Research Center to grid enable Bioconductor, so that Bioconductor packages for statistics and high throughput data analysis can be made available on caGRID.
  • caWorkbench/geWorkbench Adopter: we worked with Columbia to release a caBIG compatible version of geWorkbench, for the processing and analysis of high throughput biological data.
  • caArray unfunded adopter: we worked with the NCI contractors for more than two years to vet and improve the performance of caArray for importing, exporting, and transforming microarray data

Current collaborations with Northwestern researchers

Collaborator/PI Project
Yang, Ximing ECOG PCO-RL: Human Specimen Banking
Zeine, Rana ECOG Pathology Coordinating Office-Reference Lab (PCO-RL)
Mirkin, Chad Center of Cancer Nanotechnology Excellence
Budunova, Irina Microarray design and analysis to identify genes responsible for tumor suppressor effect of the glucocorticoid receptor in skin stem cell
Platanias, Leonidas Microarray Analysis to determine genes that are induced/inhibited by by MKK3/6, P38 and Stat1 independent of Interferon
Bergan, Ray ftp & web site setup for µArray data and gene profiling of genistein’s effect in men with Prostate cancer
Bulun, Serdar Illumina µArray analysis, time course
Lee, Chung Correlation of platelet-poor TGF-beta1 with clinical outcomes and TMA analysis to identify markers for predicting Prostate Cancer recurrence
Rosen, Steven µArray analysis of alternative splicing of glucocorticoid receptor
Mayo, Kelly Illumina µArray analysis and pathway analysis of ovarian cell lines
Pope, Richard experimental design and analysis of microarray studies of monocyte development
Scarpulla, Richard experimental design for chIP-on-chip
Hummel, Mary Analysis of pathways for TNF signaling pathway in kidney transplant
Bergan, Ray Proteomics experiment design on prostate cancer
Makoul, Greg Risky Behavior Study
Varga, John Design for µArrays experiment: effect of the ratio of egr-1 and egr-1 inhibitor on down-stream gene expression.
Paul Lindholm Poster presentation: gene expression profiles of PC-3 prostate cancer cell invasion variants with increased RhoA and NF-κB activity.
Hernandez, Rosario Glaucoma study -comparison of incidence in African American and Caucasian American populations

Research Projects

Project Title Collaborators
Development of Disease Ontology, an open source, NCBO and OBO compliant ontology to describe disease Chisholm, Osborne, Kibbe, Wolf, Zhu, Lin
Active involvement in Gene Ontology Chisholm, Kibbe
Using MeSH terms and Gene Ontology to organize microarray results Osborne, Zhu, Lin, Kibbe
Mining GeneRIFs for gene/disease associations Osborne, Kibbe, Lin, Zhu, Chisholm
Literature mining and microarray annotation Lin, Kibbe
Using Disease Ontology to organize disease associations Osborne, Kibbe, Chisholm
Development of nuIDs - a vendor-independent, sequence-specific tagging convention for tracking oligo probes for microarrays Du, Kibbe, Lin
A wavelet-based Proteomics peak detetion tool Du, Kibbe, Lin
A Proteomics baseline removal tool Lin, Du, Kibbe
A Model-based Variance-stabilizing Transformation tool for Illumina microarray data Lin, Du, Kibbe
A pipeline of processing Illumina Microarrays Du, Kibbe, Lin

Other projects and services

  • Development, operation, maintenance of NOTIS, the Northwestern Oncology Trial Information System. NOTIS was developed by Winter, Webb, Kuzel and Kibbe, and is currently being redesigned by Nyberg, and caBIG components are being integrated by Sutphin and Whitaker
  • The LTFU/STAR program database [Zhu, Liao, Kibbe]
  • Biorepository data management, currently focused on Prostate, Breast, and Ovarian cancer, but will reach into other disease areas as we integrate caBIG tools for the management of biorepositories [Zhu, Nyberg, Liao]
  • The NUgene Project information system. NUgene is a large genome-focused biorepository that mines the medical records of participants and associates their clinical history with their genotype [Allen, Winter, Kibbe]
  • The Clinical Enterprise Data Warehous (EDW). The EDW is a multi-institutional initiative spearheaded by Dale Sanders, the CIO of the Northwestern Medical Faculty Foundation. Andrew Winter in our core has been selected as the chief data architect for this project, and we will be leveraging the EDW to provide us with electronic access to the entire spectrum of clinical data on our clinical trial participants as well as for quality improvement and benchmarking of our oncology enterprise. We should start to have access to these data in the fall of 2007. [Winter]
  • TimeTracker: a system in use by the Clinical Research Office and Bioinformatics to track time on projects and on clinical trials [Kibbe]
  • MemberProfiles: This is a system used by all cancer center members to manage their biosketches, collaborations, publications, etc. Primarily for grant preparation, but we have been asked to extend it for use as a way to link faculty together [Kibbe]
  • CoreSurvey: a small application for capturing the level of service RHLCCC cores are providing to Cancer Center members [Kibbe]
  • DO Browser: an application for organizing ICD and CPT data on patients according to disease [Kibbe]
  • GoogleMapsForDisease: an application for plotting cancer patients by diease and location [Winter]
  • SAGE miner: a web application for finding SAGE expression probes by tissue, and tissue expression by probe [Kibbe, Ge, Wang]
  • nuID portal: a web application with web services for converting oligos into nuIDs, and looking up RefSeq annotations for Illumina probes. [Kibbe]
  • NU Animal Models of Disease: a Rails application for tracking animal models that have been developed or used by researchers at NU as cancer disease models [Kibbe]
  • NOTIS Abstracts: a small application used to present IRB approved abstracts and eligibility criteria to the public. [Kibbe]
  • CoreFac: CoreFac is a system that we have built and provide as a recharge to any core facility at the university. It tracks orders, inventory, scheduling and billing, including cancer center member usage reports, for the cores using the system. Those shared facilities currently are Cell Imaging, Flow Cytometry, Transgenic and Targeted Mutagenesis, Genomics, and Monoclonal Antibodies. [Zhu, Kibbe, Nyberg, Garcia]
  • NUDAIS: this is another research support system that provides the cancer center with an IT tool to help it manage the complex financial transactions that it must oversee. [Gordon]
  • Google SoC: Summer student intership program at Robert H. Lurie Comprehensive Cancer Center [Kibbe, Lin and Du]

Other Core services

  • Computing cluster support for Biostatistics and Bioinformatics Cores
  • caGrid node adoption and deployment for Biostats and Bioinformatics
  • Keck Core authentication and automation project
  • Center for Functional Genomics data storage
  • Computing infrastructure support for Cancer Center
Personal tools