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List of Hosted Resources

List of web sites, web applications and databases hosted by BMI.

Hosted Web Sites

SharePoint What's this?

Name URL Owner BMI Administrator
Asthma Innovation Lab http://bmiappprod1:5911/AIL Stacy Rechner, DSIOP John Stullenberger
Bariatric Surgery http://bmiappprod1:13600/sites/BI Stacy Rechner, DSIOP Ryan Walters
Biostatistics and Epidemiology Labs
 http://biostats.researchlink.cchmc.org Todd Nick, DBE Ron Bryson
Cancer Center DSMB http://bmiappprod1:17000/HemOnc/CCDSMB Tom Ford, Hem/Onc Ryan Walters
Cincinnati Center for Eosinophilic Disorders (CCED) Project Management http://bmiappprod1:15000/dept/cced Maggie Palazzolo, CCED John Stullenberger
Clinical Research Professionals Advisory Committee http://bmiappprod1:13500/sites/CRPAC Mary Sue Wentzel, Hem/Onc Ryan Walters
Disease Specific Innovations & Outcomes (DSIOP) Project Management http://bmiappprod1:32050/DSIOP Stacy Rechner, DSIOP John Stullenberger
DocSite Registry http://bmiappprod1:32050/DocSite Andrea Booth, DSIOP John Stullenberger
eForms Study Portal
 http://eforms.researchlink.cchmc.org Rob Rasnake, DBE Ron Bryson
GI Division http://bmiappprod1:13400/sites/GI John Bucuvalas, Gastro Ryan Walters
HPCE Data Center http://bmiappprod1:9760/hpce/data-center Ralph Brueggemann, HPCE Ron Bryson
HPCE Operations http://bmiappprod1:9760/hpce/data-center David Buten, HPCE Ron Bryson
Human Genetics Internal Pilot
 http://bmiappprod1:15744/HG Auvo Reponen, Human Genetics
 John Stullenberger

Plone What's this?

Name URL Owner BMI Administrator
Biomedical Informatics Research IT Services http://bmi.cchmc.org BMI Division Ron Bryson
Developmental Biology Imaging
 http://research.cchmc.org/dbimaging
 Matt Kofron, DB
 Ron Bryson
Developmental Biology Stem Cell Core
 http://research.cchmc.org/stemcell Chris Mayhew, DB
 Ron Bryson
Flow Cytometry Core
 http://research.cchmc.org/flow Sherry Thornton, Rheumatology
 Ron Bryson
Hegde Lab, Developmental Biology
 http://research.cchmc.org/hegde Rashmi Hegde, DB Ron Bryson
i2b2 Research Data Warehouse Portal
 http://i2b2.cchmc.org Keith Marsolo, BMI Ron Bryson
Quantitative Genomics Seminar Series http://research.cchmc.org/quantgenomics Lisa Martin, DBE Ron Bryson

Stand-alone

Name URL Technologies Owner BMI Administrator
Bioinformatics Resource Center http://brc.cchmc.org PHP/MySQL John Hutton, BMI Ron Bryson
CLEAR-ER Stroke Trial http://www.clear-er.org   Arthur Panciolo, UC Emergency Medicine Ron Bryson
CMGCC http://cmgcc.cchmc.org   Bruce Aronow, Anil Jegga, BMI Anil Jegga
Computational Medicine Center http://www.computationalmedicine.org PHP/MySQL John Pestian, BMI Ron Bryson
Female Adolescent Development Study (FADS) Portal http://fads.cchmc.org 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 Chris Mastin
Genetic Variation and Gene Discovery Core http://dna.cchmc.org PHP/MySQL Mehdi Keddache, Human Genetics Jerry Phillips
Imaging Research Center http://irc.cchmc.org, http://www.irc.cchmc.org PHP/MySQL Scott Holland, IRC Prakash Velayutham
International Society for Heart Research 2008 North American Section Meeting http://www.ishr2008.org PHP/MySQL Jeff Robbins, MCB Prakash Velayutham
Jegga Lab http://anil.cchmc.org   Anil Jegga, BMI Jerry Phillips
Lu Lab http://dragon.cchmc.org   Jason Lu, BMI Prakash Velayutham
Meller Lab http://folding.cchmc.org   Jarek Meller, BMI Prakash Velayutham
Mentored Patient-Oriented Career Development Award (K23) http://jgp.cchmc.org   Jacqueline Grupp-Phelan, Emergency Medicine Jerry Phillips
NF1 Microarray Consortium http://nf1.cchmc.org   Bruce Aronow, BMI Ron Bryson
Pneumocystis Genome Project http://pgp.cchmc.org   Melanie Cushion, VA, and Jarek Meller, BMI Prakash Velayutham
Porollo eLab http://aplab.cchmc.org   Aleksey Porollo, BMI Prakash Velayutham
Publication Supplement http://gastro.cchmc.org   Michael Bates, GI Ron Bryson
Publication Supplement http://sp.cchmc.org   Steve Potter, Developmental Biology Ron Bryson
SimCenter http://bmiappprod1.cchmc.org/simcenter ASP.NET using Silverlight and .NET AJAX Randy Woodward, Center for Simulation and Research John Stullenberger
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
Abstrainer Text-processing tool http://abstrainer.cchmc.org Bruce Aronow, Anil Jegga, BMI Jerry Phillips
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 Jerry Phillips
Conserved Cis-Elements Scanner Comparative genomics tool http://concise-scanner.cchmc.org Bruce Aronow, Anil Jegga, BMI Karen Noel
GATACA Tool for gene associations to anatomy and clinical abnormalities http://gataca.cchmc.org Bruce Aronow, Anil Jegga, BMI Karen Noel
GeneChip Chip data storage and visualization tool http://genechip.cchmc.org/cgi-bin/gbrowse/ddrdc/ Anil Jegga, BMI Karen Noel
Genet Collaborative expression data analysis tool http://genet.cchmc.org Bruce Aronow, BMI Karen Noel
Genetic Analysis Interfaces   http://genal.cchmc.org Mehdi Keddache, Human Genetics Karen Noel
Genomatix Gene regulation software and databases http://keymaker.chmcc.org/cgi-bin/genomatix/gems/launch.pl Bruce Aronow, Anil Jegga, BMI Karen Noel
GenomeTraFaC Gene regulatory region repository http://genometrafac.cchmc.org Bruce Aronow, Anil Jegga, BMI Jerry Phillips
Interactions Human PPI data miner and visualizer http://keymaker.cchmc.org:10081/Interactions2/test.jsp Anil Jegga, BMI Karen Noel
LOVD
 Hearing loss mutation database http://bmi.cchmc.org/LOVD/ Ammar Husami Prakash Velayutham
Polydoms Functional genomics server and repository http://polydoms.cchmc.org Bruce Aronow, Anil Jegga, BMI Jerry Phillips
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 Rrelational database containing multiple microarray experiments collected from investigators in Pulmonary Biology http://pbge.cchmc.org Yan Xu, Pulmonary Biology Jerry Phillips
ToppGene Disease gene prioritization tool http://toppgene.cchmc.org Bruce Aronow, Anil Jegga, BMI Karen Noel
TraFaC Comparative genomics tool http://trafac.cchmc.org Bruce Aronow, Anil Jegga, BMI Jerry Phillips

Clinical Research See also list of supported studies

Name Description/Notes URL Owner BMI Administrator
REDCap Electronic data capture system for GCRC studies http://redcap.cchmc.org Cathy McGraw, GCRC Prakash Velayutham
Sports Injury Surveillance System Data capture tool for Sports Medicine Biodynamics Center http://siss.cchmc.org/ Sports Medicine Biodynamics Center Chris Mastin
Symptom Surveillance Project Data capture tool for Cincinnati Pediatric Research Group http://ssp.cchmc.org Lea Alae, General & Community Pediatrics Chris Mastin

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 Chris Mastin
Blackboard Online course management software http://blackboard.cchmc.org/ Education and Training Jerry Phillips
BMI Calendar Open-source calendar software for users with BMI LDAP accounts; based on WebCalendar version 1.0.x; time zone support as fixed offset (does not account for DST), so some recurrent events might be off by one hour in ics export. http://bmicalendar.cchmc.org BMI Division Prakash Velayutham
Education & Research Calendar Calendar of education and training events at Cincinnati Children's http://calendar.cchmc.org/ Sharon Sapienz, Education and Training Ron Bryson
Hyperion Web Portal Database reporting tool http://matrix-c.cchmc.org:81/Hyperion/browse Decision Support Services/BMI Division Debi Crowder
LimeSurvey Open-source survey design and administration tool http://research.cchmc.org/limesurvey/ BMI Division Ron Bryson
MeetingMaker Licensed calendar software http://meetingmaker.cchmc.org BMI Division Bob Bader
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
BMI Time Tracker Time tracking tool for BMI IT staff http://bmiappprod1:14000/dept/BMI/Time%20Tracker/default.aspx John Stullenberger
Horde Centralized authentication management tool http://bmi.cchmc.org/horde/ Prakash Velayutham
InterMapper BMI systems monitoring tool http://intermapper.cchmc.org Bob Bader
Ganglia Cluster monitoring tool http://bmi.cchmc.org/ganglia/ Prakash Velayutham
GLPI BMI inventory management tool http://irm.cchmc.org Prakash Velayutham
Gold Allocation manager for cluster resources http://bmi.cchmc.org/gold/ Prakash Velayutham
Mantis Bug tracking software http://bmi.cchmc.org/mantis/ Chris Mastin
Mailman Mail list administrator http://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://ribosome.cchmc.org/pbsstats/, http://galactose.cchmc.org/pbsstats Prakash Velayutham
RT BMI help desk tool http://bmi.cchmc.org/rt/ Prakash Velayutham
TUTOS Defect and issue tracking tool for software development projects http://keymaker.cchmc.org/tutos/php Chris Mastin

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 Mihir Mishra
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 Mihir Mishra
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 Mihir Mishra
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 Mihir Mishra
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 Mihir Mishra
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
 Karen Noel
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