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NIAID project and sample application standard

The CBIL and EuPathDB groups have participated in developing standards for the representation of metadata associated with projects and samples as part of the NIAID Bioinformatics Resource Centers and Genome Sequencing Centers for Infectious Diseases Metadata Working Group.

Biobank ontology workshop at ICBO 2014

We will be conducting a workshop with Mathias Brochhausen (U. Arkansas) and Melissa Haendel (OHSU) on Starting an OBI-based Biobank Ontology at the 2014 International Conference on Biomedical Ontologies (ICBO) being held in Houston this October.


NIAGADS Genomics Database

The GUS database and WDK Strategies system has been used to deploy the NIAGADS Genomics Database. NIAGADS is the National Institute on Aging Genetics Alzheimer's Disease Data Storage Site run by Li-San Wang and his group. The NIAGADS Genomics Database is a resource of NIAGADS built by us and uses the GUS4 schema optimized for high throughput data and capturing experimental metadata.

Publication on Ontodog in Bioinfomatics

A description of Ontodog, a web-based ontology community view generator, has just been published as an Applications Note in Bioinformatics. Ontodog was developed as a collaboration with Oliver He's group at the University of Michigan.


ICBO2013 Proceedings available on-line

Our paper on "Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations" (Jie Zheng, Elisabetta Manduchi and Christian J. Stoeckert Jr) is now available on-line at:
Also available is:

CBIL student runs premier college hackathon

The Fall semester 2013 PennApps was led by Brynn Claypoole who is studying pancreatic gene networks at CBIL. Brynn is in the Student Spotlight of the October 17, 2013 issue of Penn Current.

Publication on red blood cell gene regulatory networks

A machine learning approach was taken to identify candidate regulators of primitive erythropoiesis by identifying properties of such regulators in adult and fetal definitive erythropoiesis.
Greenfest-Allen E, Malik J, Palis J, Stoeckert CJ Jr. Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis. BMC Syst Biol. 2013 May 15;7:38.
PMID: 23675896

CBIL now part of IBI

The Penn Center for Bioinformatics (PCBI) has undergone a reorganization and become the Institute for Biomedical Informatics (IBI). IBI combines bioinformatics with medical informatics at the Perelman School of Medicine. As a result, CBIL which was part of PCBI is now part of IBI. (but we are still in the same physical location).

CBIL hosts OBI workshop

A workshop was held May 29-31, 2013 to review and discuss core terms in the Ontology for Biomedical Investigations (OBI). Details about what was covered can be found at the Philly2013 wiki page at the OBI web site.

FGED 15th International Conference: Translational Genomics: Applications of Genomics to Clinical Diagnosis and Treatment

The FGED Society is pleased to announce the 15th Annual FGED meeting. FGED15 will focus on clinical applications of genomics to diagnosis and patient care, cancer genomics, big data & bioinformatics to support clinical diagnostics and patient care, and processing of next generation sequencing data. The meeting will take place June 20-22, 2013 at the downtown Seattle Public Library, Seattle, Washington.
See the FGED Seattle Conference site for more details.


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