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 |