To make it easier to coordinate software purchases and obtain volume or academic discounts whenever possible, the Division of Biomedical Informatics maintains an inventory of commercial and open-source software products being used by researchers at Cincinnati Children's and UC College of Medicine, including:

** Please note Biomedical Informatics has a centralized license for all software listed as BMI licensed.

**If licensing information isn't available or you have other licensing-related questions, please send an email to

** To request a quote for any software not listed here or not BMI Licensed, please call contact CCHMC's preferred software vendor Zones, by sending an email to


Click the software package name for details including access and usage instructions. Packages labeled as Licensed are available to Cincinnati Children's and University of Cincinnati researchers on a cost-share basis, i.e., users must sign up in order to use the software and make annual contributions toward covering the cost of the license. In most cases, you can get details about the costs of using a specific package by clicking the "Licensed" link. If licensing information isn't available or you have other licensing-related questions, send an email to


Desktop office productivity software

For a list of standard software provided on Cincinnati Children's Windows and Mac computers, see the Information Services CenterLink site.

Adobe Acrobat Pro PDF reader/writer BMI Licensed
Adobe Photoshop CC (Creative Cloud) Graphic creation and editing software Licensed
EndNote Bibliographic software Free
Mendeley Bibliography creation and research paper management Free
The GIMP Open-source graphic creation/editing software Free
OpenOffice Open-source office productivity software Free


Biobanking Software

Biomaterial Tracking & Management Research System Software to track and manage biological samples, including freezer location and distribution Free


Data storage and management software

For clinical research studies

CERF CERF is electronic lab notebook software designed for biological researchers. BMI Licensed  
ePAS System for submitting human research protocols to the Cincinnati Children's IRB Free N/A
InfoPath/SharePoint Companion tools for designing and hosting web-based forms BMI Licensed
REDCap Tool for managing research data collection for small and medium (typical GCRC) studies Free  
TeleForms Tool for generating and scanning paper-based data collection forms Licensed


Database software

FileMaker Pro Database software BMI Licensed
MS SQL Server Database software Licensed
MySQL Relational database software Free
Toad Database development/admin tool Licensed / Free


Data analysis software

Statistical computing and numerical analysis

GraphPad Prism Statistical computing Software BMI Licensed
ImageQuant TL Image analysis software (e.g., for Western Blots) Licensed
JMP and JMP Genomics Statistical discovery / visualization software designed specifically for genomic, microarray and proteomics data BMI Licensed
Matlab General purpose numerical computing language BMI Licensed
Mplus Mplus is a latent variable modeling program with a wide variety of analysis capabilities BMI Licensed
Nquery Statistical computing software BMI Licensed
PSPP Free alternative to SPSS Free
R Statistical computing software Free
SAS Statistical computing software BMI Licensed
SigmaPlot Statistical computing software BMI Licensed
SPSS Statistical computing software Licensed
Stat/Transfer Statistical computing software BMI Licensed
Stata Statistical computing software BMI Licensed  


Sequence and expression analysis

Strand NGS (formerly Avadis NGS) Data mining and visualization platform BMI Licensed
DNAStar Lasergene Sequence analysis software BMI Licensed
GenePattern Scientific workflow platform and genomic analysis tools Free
GeneSpring 13 Gene expression analysis software BMI Licensed
Golden Helix Analysis software BMI Licensed
IMPUTE and other GWA tools Package of genome-wide association tools Free
MacVector Software for sequence editing, primer design, etc. BMI Licensed
LAMP Software for linkage and association modeling in pedigrees Free
Phred/Phrap/Consed DNA assembly software Free
Plink/gPlink Whole genome association analysis toolset Free
PSI-BLAST Sequence alignment software Free
RMAExpress Microarray processing software Free
SOLAR Genetic variance components analysis software Free
Vector NTI Sequence analysis and molecular biology data management software BMI Licensed


Pathway analysis

Ingenuity Pathway analysis tools BMI Licensed



NONMEM Pharmacokinetics software Licensed


Protein modeling and crystallography

AMoRe Molecular replacement Free
ARP/wARP Automated refinement and chain tracing Free
AutoDock / MGLTools Automated docking and GUI Free
CCP4 Collaborative computing project Free
CNS Crystallography and NMR system Free
Discovery Studio Protein modeling and simulation Licensed
DSSP Secondary structure assignment database Free
Loopp Fold recognition Free
Mascot Search engine that uses mass spectrometry data to identify proteins from primary sequence databases Licensed
MOLPRINT 2D Fast fragment-based similarity search method Free
O Macromolecular crystallographic modeling Free
PyMOL Molecular graphics and modeling Free
RasMol Molecular visualization Free
SOLVE/RESOLVE Heavy atoms and MAD phasing Free
USF Various programs from the USF Free


Flow cytometry analysis

Cyflogic Flow cytometry software Free
FACS Diva Flow cytometry software Licensed
*FCS Data Reader Flow cytometry software Free
FCS Express Flow cytometry software Licensed
*FCS Extract Utility Flow cytometry software Free
FlowJo Flow cytometry software Licensed
*Flow Informatics and Computational Cytometry Society Several software packages Free
IDEAS v3.0 ImageStream analysis software Free

*If you are interested in running any of these packages on the BMI cluster, send an email to the BMI Help Desk.


Machine learning and optimization

ILOG/CPLEX Optimization software Licensed
l1svm, l1svr Linear programming SVM/SVR solvers Free N/A
libsvm Chih-Jen Lin's SVM solver Free
psvm Parallel implementation of a support vector machine Free
SNNS Stuttgart Neural Network Simulator Free
Svmlight Thorsten Joachim's SVM solver Free
Weka Machine learning algorithms for data mining tasks Free


Visualization packages

GraphViz Graph visualization package Free
IDL Data visualization and image analysis software Licensed


Remote and cluster computing software

Environment Modules Tool to manipulate user environment Free
C3 Tools Cluster utilities Free
Citrix Client Client for accessing Citrix servers Free
FreeNX / NX X compression protocol Licensed / Free
OpenNX X compression protocol Free
Gold Resource accounting and allocation Free
MPI Parallel programming libraries Free
PBS Tools Cluster tools Free
PVM Parallel virtual machine Free
Totalview Parallel debugger Licensed
PuTTY Secure Shell client Free
WinSCP SCP/SFTP client Free

LSF LSF Scheduler Licensed
LONI Pipeline LONI Pipeline Free


Operating systems

Mac OS X Lion (v. 10.7) Previos version of the Mac OS Licensed
Mac OS X Snow Leopard (v. 10.6) Previous version of the Mac OS Licensed
Mac OS X Leopard (v. 10.5) Previous version of the Mac OS Licensed
VMWare Fusion Virtualization OS Licensed


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