List of Hosted Resources
List of web sites, web applications and databases hosted by BMI.
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/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 |
| Human Milk Program Project | http://research.cchmc.org/hmpp | Ardythe Morrow, DBE/Neonatology | Ron Bryson |
| Human Performance Lab |
http://research.cchmc.org/hpl | Kevin Ford, Sports Medicine | Ron Bryson |
| i2b2 Research Data Warehouse Portal |
http://i2b2.cchmc.org | Keith Marsolo, BMI | Ron Bryson |
| OPQC - Ohio Perinatal Quality Collaborative | http://www.opqc.net | Ed Donovan, HPCE | Ron Bryson |
| Pediatric Functional Neuroimaging Research Network | http://research.cchmc.org/pfnrn | Michael Wagner, BMI | Michael Wagner |
| Pluripotent Stem Cell Facility |
http://research.cchmc.org/stemcell | Chris Mayhew, DB |
Ron Bryson |
| Quantitative Genomics Seminar Series | http://research.cchmc.org/quantgenomics | Lisa Martin, DBE | Ron Bryson |
| REGID - Registry for Eosinophilic Gastrointestinal Disorders Portal | http://www.regid.org | Marc Rothenberg, Allergy James Franciosi, GI |
Ron Bryson |
| Riazuddin and Ahmed Research Labs | http://research.cchmc.org/riazuddin http://research.cchmc.org/ahmed |
Zubair Ahmed, Pediatric Ophthalmology Saima Riazuddin, Pediatric Otolaryngology |
Ron Bryson |
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 | |
| 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 |
| 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 | Chris Mastin |
| Genetic Variation and Gene Discovery Core | http://dna.cchmc.org | PHP/MySQL | Mehdi Keddache, Human Genetics | Karen Noel |
| Imaging Research Center | http://irc.cchmc.org, http://www.irc.cchmc.org | PHP/MySQL | Scott Holland, IRC | Prakash Velayutham |
| Jegga Lab | http://anil.cchmc.org | Anil Jegga, BMI | Karen Noel | |
| Lu Lab | http://dragon.cchmc.org | Jason Lu, BMI | Prakash Velayutham | |
| Meller Lab | http://folding.cchmc.org | Jarek Meller, BMI | Prakash Velayutham | |
| 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 |
| 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 |
|---|---|---|---|---|
| Abstrainer | Text-processing tool | http://abstrainer.cchmc.org | Bruce Aronow, Anil Jegga, BMI | Karen Noel |
| 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 | Karen Noel |
| Conserved Cis-Elements Scanner | Comparative genomics tool | http://concise-scanner.cchmc.org | Bruce Aronow, Anil Jegga, BMI | Karen Noel |
| Flow Cytometry Data Repository | Tool for archiving results files from various flow cytometry analysis programs | http://research.cchmc.org/FCSData | Michael Wagner, BMI | Chris Mastin |
| 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 | Karen Noel |
| 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 |
| 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 |
| 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 | Karen Noel |
| 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 | Karen Noel |
| 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 | Karen Noel |
Clinical Research See also list of supported studies
| Name | Description/Notes | URL | Owner | BMI Administrator |
|---|---|---|---|---|
| REDCap | Electronic data capture system for GCRC studies | https://research.cchmc.org/redcap/ | Cathy McGraw, CCTST | 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 | Karen Noel |
| 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 | Mihir Mishra |
| 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 |
| 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 |
| 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://bmi.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 |
