List of Hosted Resources

Hosted Web Sites

SharePoint What's this?

SharePoint is available on the Cincinnati Children's internal network only. If you are connected to the Cincinnati Children's network, you can see a complete list of available SharePoint sites by going to http://researchlink.cchmc.org.

Drupal What's this?

Name URL Owner BMI Administrator
Biomedical Informatics Research IT Services http://bmi.cchmc.org BMI Division  
Communication Sciences Research Center http://csrc.cchmc.org Scott Holland, PNRC/IRC  
i2b2 Research Data Warehouse Portal http://i2b2.cchmc.org Keith Marsolo, BMI  
OPQC - Ohio Perinatal Quality Collaborative http://www.opqc.net Ed Donovan, HPCE  
Pluripotent Stem Cell Facility http://research.cchmc.org/stemcell Chris Mayhew, DB  
Quantitative Genomics Seminar Series http://research.cchmc.org/quantgenomics Lisa Martin, DBE  

Stand-alone

Name URL Technologies Owner BMI Administrator
ADHD Collaborative http://research.cchmc.org/adhd   John Simon, Behaviroal Medicine Ron Bryson
CLEAR-ER Stroke Trial http://www.clear-er.org   Arthur Panciolo, UC Emergency Medicine Ron Bryson
Female Adolescent Development Study (FADS) Portal http://fads.cchmc.org PHP Jennie Noll, Behavioral Medicine Ron Bryson
Female Growth and Development Study (FGDS) Portal http://research.cchmc.org/fgds PHP Jennie Noll, Behavioral Medicine Ron Bryson
Gastroenterology, Hepatology and Nutrition - Online Calculators http://gastro.cchmc.org/calculators/pcdai/
http://gastro.chmcc.org/calculators/iaihg/
http://gastro.cchmc.org/calculators/donor-risk-index/
JavaScript Michael Bates, GI  
Genetic Variation and Gene Discovery Core http://dna.cchmc.org PHP/MySQL David Fletcher, Human Genetics  
Imaging Research Center http://irc.cchmc.org, http://www.irc.cchmc.org PHP/MySQL Scott Holland, IRC  
Jegga Lab http://anil.cchmc.org   Anil Jegga, BMI  
Lu Lab http://dragon.cchmc.org   Jason Lu, BMI  
Meller Lab http://folding.cchmc.org   Jarek Meller, BMI  
Pneumocystis Genome Project http://pgp.cchmc.org   Melanie Cushion, VA, and Jarek Meller, BMI  
Porollo eLab http://aplab.cchmc.org   Aleksey Porollo, BMI  
Publication Supplement http://gastro.cchmc.org   Michael Bates, GI Ron Bryson
Publication Supplement http://sp.cchmc.org   Steve Potter, Developmental Biology Ron Bryson
STOP-IT Study http://www.stopitstudy.org   Matthew Flaherty, UC Neurology Ron Bryson
Traumatic Brain Injury (TBI) Study Web Portal http://tbi.cchmc.org   Shari Wade, Pediatric Rehab Ron Bryson

Hosted Web Applications

Basic Research

Name Description/Notes URL Owner BMI Administrator
Cinteny Server for synteny identification and analysis of genome rearrangement; requires Apache 2.0, PHP 5.0, gd 2.0 http://cinteny.cchmc.org Jarek Meller, BMI Prakash Velayutham
CisMols Analyzer Comparative genomics tool http://cismols.cchmc.org Bruce Aronow, Anil Jegga, BMI  
Conserved Cis-Elements Scanner Comparative genomics tool http://concise-scanner.cchmc.org Bruce Aronow, Anil Jegga, BMI  
Flow Cytometry Data Repository Tool for archiving results files from various flow cytometry analysis programs http://research.cchmc.org/FCSData Michael Wagner, BMI  
GATACA Tool for gene associations to anatomy and clinical abnormalities http://gataca.cchmc.org Bruce Aronow, Anil Jegga, BMI  
Genetic Analysis Interfaces   http://genal.cchmc.org Mehdi Keddache, Human Genetics  
GenomeTraFaC Gene regulatory region repository http://genometrafac.cchmc.org Bruce Aronow, Anil Jegga, BMI  
Genotyping Data Repository   http://research.cchmc.org/genotyping Michael Wagner, BMI Nick Felicelli
GWA Database Interface Web interface to the genome wide association database, which among other features, can be used to filter samples, select SNPs and spawn analysis jobs on the Linux cluster http://research.cchmc.org/gwadb Michael Wagner, BMI Andrew Rupert
metaMS meta server for protein identification using Peptide Mass Fingerprinting http://research.cchmc.org/metams Michael Wagner, BMI Michael Wagner, BMI
Microarray Data Repository   http://research.cchmc.org/microarray Michael Wagner, BMI Nick Felicelli
Polydoms Functional genomics server and repository http://polydoms.cchmc.org Bruce Aronow, Anil Jegga, BMI  
Protein Structure Prediction and Visualization Tools   http://sable.cchmc.org, http://minnou.cchmc.org, http://polyview.cchmc.org http://sppider.cchmc.org, http://scorppion.cchmc.org, http://sift.cchmc.org Jarek Meller, BMI Prakash Velayutham
Pulmonary Biology Gene Expression Database Relational database containing multiple microarray experiments collected from investigators in Pulmonary Biology http://research.cchmc.org/pbge/ Yan Xu, Pulmonary Biology  
ToppGene Disease gene prioritization tool http://toppgene.cchmc.org Bruce Aronow, Anil Jegga, BMI  
TraFaC Comparative genomics tool http://trafac.cchmc.org Bruce Aronow, Anil Jegga, BMI  

Clinical Research See also list of supported studies

Name Description/Notes URL Owner BMI Administrator
REDCap Electronic data capture system for GCRC studies https://redcap.research.cchmc.org/ Chris Mastin, Biomedical Informatics Prakash Velayutham
Sports Injury Surveillance System Data capture tool for Sports Medicine Biodynamics Center http://siss.cchmc.org/ Sports Medicine Biodynamics Center  

Administrative tools - institutional use

Name Description/Notes URL Owner BMI Administrator
ATTRAC Attendance tracking system for pediatric residents http://attrac.cchmc.org/ Javier Gonzalez, Emergency Medicine  
Blackboard Online course management software https://blackboard.cchmc.org Education and Training  
LimeSurvey Open-source survey design and administration tool http://research.cchmc.org/limesurvey/ BMI Division Ron Bryson
MRBS/Research Equipment Scheduling System Open-source equipment booking/scheduling software for users with BMI LDAP accounts; based on MRBS version 1.2.6 http://research.cchmc.org/mrbs/ BMI Division Prakash Velayutham

Administrative tools - BMI use only

Name Description/Notes URL Administrator
Horde Centralized authentication management tool http://bmi.cchmc.org/horde/ Prakash Velayutham
Ganglia Cluster monitoring tool http://bmi.cchmc.org/ganglia/ Prakash Velayutham
Gold Allocation manager for cluster resources http://bmi.cchmc.org/gold/ Prakash Velayutham
Mantis Bug tracking software http://bmi.cchmc.org/mantis/  
Mailman Mail list administrator https://mailman.cchmc.org/mailman/listinfo Bob Bader
Moab Access Portal Tool for accessing the Linux cluster http://bmi.cchmc.org/map/ Prakash Velayutham
PBS Cluster statistics tool http://bmi.cchmc.org/pbsstats Prakash Velayutham
RT BMI help desk tool http://bmi.cchmc.org/rt/ Prakash Velayutham

Hosted Databases (without web interfaces)

Name Description/Notes Database Software Primary Server Operating System Owner Principal Administrator
discont Disease Card, Semantic Web Oracle 10g RAC crsprod(bmiorap1,bmiorap2) and crsdev(bmiorad1,bmiorad2) SLES 10 Bruce Aronow, BMI  
hgdata hgpatient application (patient database, result tracking), fosamaxkids application, Cytogenetics lab statistics database (extract from Cerner) Oracle 10g RAC crsprod(bmiorap1,bmiorap2) and crsdev(bmiorad1,bmiorad2) SLES 10 Auvo Reponen, Human Genetics  
IBC Institutional Biosafety Committee Filemaker Pro filemaker.cchmc.org Mac OS X IBC Bob Bader
IRC Support for the Imaging Research Center Filemaker Pro filemaker.cchmc.org Mac OS X IRC Chris Hearn
IRC Support for the Imaging Research Center MySQL bmi-mysql.cchmc.org Linux IRC Chris Hearn
JRA Integrative Genomics Project MySQL galactose.cchmc.org Linux   Prakash Velayutham
JRADB Juvenile Rheumatoid Arthritis, Backend for jradb MySQL cellulose.cchmc.org Linux   Prakash Velayutham
pneumoc Pulmonary Biology Gene Expression (PBGE) Oracle 10g RAC crsprod(bmiorap1,bmiorap2) and crsdev(bmiorad1,bmiorad2) SLES 10 Yan Xu, Pulmonary Biology/BMI  
sequence All applications belonging to Human Genetics Sequencing Core; abidata sequencing core database, Liquid Nitrogen storage database, caepg application(research study database), ipah application (research study database) Oracle 10g RAC crsprod(bmiorap1,bmiorap2) and crsdev(bmiorad1,bmiorad2) SLES 10 Mehdi Keddache and Auvo Reponen, Human Genetics  
trafac & pneumoc BMI in-house research applications: TraFaC, GenomeTraFaC, ToppGene, Semantic Web, Disease Card, Abstrainer, Micro RNA, Polydoms, Promoter SNP, SNP Plot, Gataca, UMLSKS;  Human Genetics online genetics courses application; Human Genetics news feedback application Oracle 10g RAC crsprod(bmiorap1,bmiorap2) and crsdev(bmiorad1,bmiorad2) SLES 10 Bruce Aronow, BMI, and Auvo Reponen, Human Genetics  
UMLS Medical free text annotation with medical concepts for information retrieval and organization MySQL bmidbi1.cchmc.org Linux John Pestian, Pawel Matykiewicz and Malik Spencer, BMI; Robert Kowatch, Psychiatry; Tracy Glauser, Neurology  

 

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