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EuPathDB Bioinformatics Resource Center contract renewed

Read the Penn press release announcing the renewal of the NIAID Bioinformatics Resource Center at Penn and the University of Georgia. The contract supports the Eukaryotic Pathogen Genomics Database (EuPathDB).

Ontology for Biobanking is now a GitHub project

The Ontology for Biobanking (OBIB) has been set up as a GitHub project at
The first release of the OBIB is called: biobank-omiabis_merged.owl
Presentations from the ICBO 2014 Workshop on Starting an OBI-based Biobank ontology are also available.


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).


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