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Software

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, send an email to software@bmi.cchmc.org

** To request a quote for any software not listed here please contact CCHMC preferred software vendor by sending an email to cchmc@zones.com

 

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 software@bmi.cchmc.org

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.

Name Description Licensed or free Vendor web site
Adobe Acrobat PDF reader/writer BMI Licensed http://www.adobe.com/
Adobe Photoshop Elements Graphic creation and editing software BMI Licensed http://www.adobe.com/
EndNote Bibliographic software BMI Licensed http://www.endnote.com
Mendeley Bibliography creation and research paper management Free http://www.mendeley.com/
The GIMP Open-source graphic creation/editing software Free http://www.gimp.org/
OpenOffice Open-source office productivity software Free http://www.openoffice.org/

Data storage and management software

For basic research studies

Name Description Licensed or free Vendor web site
CERF Electronic lab notebook for biology BMI Licensed http://rescentris.com

For clinical research studies

Name Description Licensed or free Vendor web site
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 http://office.microsoft.com/en-us/infopath/FX100487661033.aspx
http://www.microsoft.com/sharepoint/default.mspx
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 http://www.cardiff-teleform.com/index.html

Database software

Name Description Licensed or free Vendor web site
FileMaker Pro Database software BMI Licensed http://www.filemaker.com/
MS SQL Server Database software Licensed http://www.microsoft.com/sql/
MySQL Relational database software Free http://www.mysql.com/
Toad Database development/admin tool Licensed / Free http://www.toadsoft.com/

Data analysis software

Statistical computing and numerical analysis

Name Description Licensed or free Vendor web site
GraphPad Prism Statistical computing Software BMI Licensed http://www.graphpad.com/prism/Prism.htm
JMP Genomics SAS-based statistical discovery/visualization software designed specially for genomic, microarray and proteomics data BMI Licensed http://www.jmp.com/software/genomics/
Matlab General purpose numerical computing language BMI Licensed http://www.mathworks.com/
Nquery Statistical computing software BMI Licensed http://www.statsol.ie/html/nquery/nquery_home.html
PSPP Free alternative to SPSS Free http://www.gnu.org/software/pspp/
R Statistical computing software Free http://www.r-project.org/
SAS Statistical computing software BMI Licensed http://www.sas.com/
SigmaPlot Statistical computing software BMI Licensed http://www.systat.com/products/sigmaplot/
SPSS Statistical computing software Licensed http://www.spss.com
Stata Statistical computing software BMI Licensed http://www.stata.com/
SUDAAN SAS add-on BMI Licensed http://www.rti.org/sudaan/

Sequence and expression analysis

Name Description Licensed or free Vendor web site
Avadis NGS Data mining and visualization platform BMI Licensed http://www.avadis-ngs.com/
DNAStar Lasergene Sequence analysis software BMI Licensed http://www.dnastar.com/
GenePattern Scientific workflow platform and genomic analysis tools Free http://www.broad.mit.edu/cancer/software/genepattern/
GeneSpring NGS Gene expression analysis software BMI Licensed http://www.agilent.com
IMPUTE and other GWA tools Package of genome-wide association tools Free http://www.stats.ox.ac.uk/~marchini/software/gwas/gwas.html
MacVector Software for sequence editing, primer design, etc. BMI Licensed http://www.macvector.com/
LAMP Software for linkage and association modeling in pedigrees Free http://www.sph.umich.edu/csg/abecasis/LAMP/index.html
Phred/Phrap/Consed DNA assembly software Free http://www.phrap.org/phredphrapconsed.html
Plink/gPlink Whole genome association analysis toolset Free http://pngu.mgh.harvard.edu/~purcell/plink/
PSI-BLAST Sequence alignment software Free http://www.ncbi.nlm.nih.gov/
Education/BLASTinfo/information3.html
RMAExpress Microarray processing software Free http://rmaexpress.bmbolstad.com/
SOLAR Genetic variance components analysis software Free http://www.sfbr.org/Departments/genetics_detail.aspx?p=37
Vector NTI Sequence analysis and molecular biology data management software BMI Licensed http://www.invitrogen.com

Pathway analysis

Name Description Licensed or free Vendor web site
Ingenuity Pathway analysis tools BMI Licensed http://www.ingenuity.com/

Pharmacokinetics

Name Description Licensed or free Vendor web site
NONMEM Pharmacokinetics software Licensed http://www.icondevsolutions.com/nonmem.htm

Protein modeling and crystallography

Name Description Licensed or free Vendor web site
AMoRe Molecular replacement Free http://www.ibs.fr/content/ibs_eng/presentation/
lab/lmes/MR_development/
ARP/wARP Automated refinement and chain tracing Free http://www.embl-hamburg.de/ARP/
AutoDock / MGLTools Automated docking and GUI Free http://autodock.scripps.edu
CCP4 Collaborative computing project Free http://www.ccp4.ac.uk/
CNS Crystallography and NMR system Free http://cns.csb.yale.edu/v1.0/
Discovery Studio Protein modeling and simulation Licensed http://www.accelrys.com/products/dstudio/
DSSP Secondary structure assignment database Free http://swift.cmbi.ru.nl/gv/dssp/
Loopp Fold recognition Free http://cbsuapps.tc.cornell.edu/loopp.aspx
Mascot Search engine that uses mass spectrometry data to identify proteins from primary sequence databases Licensed http://www.matrixscience.com
MOLPRINT 2D Fast fragment-based similarity search method Free http://www.molprint.com
O Macromolecular crystallographic modeling Free http://xray.bmc.uu.se/~alwyn/
Distribution/distrib_frameset.html
PyMOL Molecular graphics and modeling Free http://pymol.sourceforge.net/
RasMol Molecular visualization Free http://www.umass.edu/microbio/rasmol/
SOLVE/RESOLVE Heavy atoms and MAD phasing Free http://www.solve.lanl.gov/
USF Various programs from the USF Free http://xray.bmc.uu.se/usf/

Flow cytometry analysis

Name Description Licensed or free Vendor web site
CellQuest Pro Flow cytometry software Licensed http://www.bdbiosciences.com/features/
products/display_product.php?keyID=46
Cyflogic Flow cytometry software Free http://www.cyflogic.com/
FACS Diva Flow cytometry software Licensed http://www.bdbiosciences.com/features/
products/display_product.php?keyID=93
*FCS Data Reader Flow cytometry software Free http://www.mathworks.com/matlabcentral/fileexchange/
loadFile.do?objectId=9608&objectType=FILE
FCS Express Flow cytometry software Licensed http://www.denovosoftware.com
*FCS Extract Utility Flow cytometry software Free http://research.stowers-institute.org/efg/
ScientificSoftware/Utility/FCSExtract/index.htm
FlowJo Flow cytometry software Licensed http://www.flowjo.com
*Flow Informatics and Computational Cytometry Society Several software packages Free http://www.ficcs.org/software/
IDEAS v3.0 ImageStream analysis software Free http://www.amnis.com/

*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

Name Description Licensed or free Vendor web site
ILOG/CPLEX Optimization software Licensed http://www.ilog.com/
l1svm, l1svr Linear programming SVM/SVR solvers Free N/A
libsvm Chih-Jen Lin's SVM solver Free http://www.csie.ntu.edu.tw/~cjlin/libsvm/
psvm Parallel implementation of a support vector machine Free http://code.google.com/p/psvm/
SNNS Stuttgart Neural Network Simulator Free http://www-ra.informatik.uni-tuebingen.de/SNNS/
Svmlight Thorsten Joachim's SVM solver Free http://svmlight.joachims.org/
Weka Machine learning algorithms for data mining tasks Free http://www.cs.waikato.ac.nz/ml/weka/

Visualization packages

Name Description Licensed or free Vendor web site
GraphViz Graph visualization package Free http://www.graphviz.org
IDL Data visualization and image analysis software Licensed http://www.ittvis.com/

Remote and cluster computing software

Name Description Licensed or free Vendor web site
Environment Modules Tool to manipulate user environment Free http://modules.sourceforge.net/
C3 Tools Cluster utilities Free http://www.csm.ornl.gov/torc/C3/
Citrix ICA Client Client for accessing Citrix servers Free http://www.citrix.com
FreeNX / NX X compression protocol Licensed / Free http://freenx.berlios.de/
http://www.nomachine.com
OpenNX X compression protocol Free http://opennx.net/
Gold Resource accounting and allocation Free http://www.emsl.pnl.gov/docs/mscf/gold/
MPI Parallel programming libraries Free http://www.mpi-forum.org
PBS Tools Cluster tools Free http://www.osc.edu/~troy/pbs/
PVM Parallel virtual machine Free http://www.csm.ornl.gov/pvm/
Totalview Parallel debugger Licensed http://www.roguewave.com/products/totalview-family.aspx
PuTTY Secure Shell client Free http://www.putty.org/
WinSCP SCP/SFTP client Free

http://www.winscp.net/
LSF LSF Scheduler Licensed http://www.platform.com

Operating systems

Name Description Licensed or free Vendor web site
Mac OS X Lion (v. 10.7) Latest version of the Mac OS Licensed http://www.apple.com/macosx/
Mac OS X Snow Leopard (v. 10.6) Previous version of the Mac OS Licensed http://www.apple.com/macosx/
Mac OS X Leopard (v. 10.5) Previous version of the Mac OS Licensed http://www.apple.com/macosx/
VMWare Fusion Virtualization OS Licensed http://www.vmware.com/products/fusion

 

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