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Software

Our software inventory includes commercially licensed software as well as a large number of open-source packages that are available on our cluster and various workstations.

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:

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, contact Eszter Belcher, business director.

Desktop office productivity software

Name Description Licensed or free Vendor web site
Adobe Acrobat PDF reader/writer Licensed http://www.adobe.com/
Adobe Photoshop Elements Graphic creation and editing software Licensed http://www.adobe.com/
Canvas Technical illustration and graphic design software Licensed http://www.acdsee.com/
EndNote Bibliographic software Licensed http://www.endnote.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 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 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 http://www.iwg-online.org/projects/redcap/index.php

Database software

Name Description Licensed or free Vendor web site
FileMaker Pro Database software 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
DBMS / Copy Statistical computing software Licensed http://www.dataflux.com/Product-Services/Products/dbms.asp
JMP SAS-based statistical discovery/visualization software
Licensed http://www.jmp.com/software/jmp7/
JMP Genomics SAS-based statistical discovery/visualization software designed specially for genomic, microarray and proteomics data
Licensed http://www.jmp.com/software/genomics/
Matlab General purpose numerical computing language Licensed http://www.mathworks.com/
Nquery Statistical computing software Licensed http://www.statsol.ie/html/nquery/nquery_home.html
R Statistical computing software Free http://www.r-project.org/
SAS Statistical computing software Licensed http://www.sas.com/
SigmaPlot Statistical computing software Licensed http://www.systat.com/products/sigmaplot/
Stata Statistical computing software Licensed http://www.stata.com/
SUDAAN SAS add-on Licensed http://www.rti.org/sudaan/

Sequence and expression analysis

Name Description Licensed or free Vendor web site
Beacon Designer PCR primer and probe design software Licensed http://www.premierbiosoft.com/molecular_beacons/index.html
BioPerl Perl tools for bioinformatics Free http://www.bioperl.org/
DNAStar Lasergene
Sequence analysis software Licensed http://www.dnastar.com/
dprime, snpgwa, dandelion Whole genome association tools from Wake Forest University
Free http://www.phs.wfubmc.edu/public_bios/sec_gene/downloads.cfm
GCG Sequence analysis software Licensed http://www.accelrys.com/products/gcg
GeneSpring Gene expression analysis software Licensed http://www.agilent.com
MacVector Software for sequence editing, primer design, etc. 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/
Progeny Pedigree and genetic data management software Licensed http://www.progenygenetics.com
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/

Pathway analysis

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

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/main.html
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
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
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.html

*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/

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/
ImageQuant Software for 1D gel, array and image analysis (v. 5 only)
Licensed http://www.imsupport.com

Remote and cluster computing software

Name Description Licensed or free Vendor web site
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
Gold Resource accounting and allocation Free http://www.emsl.pnl.gov/docs/mscf/gold/
Moab Cluster utilities Licensed http://www.clusterresources.com/pages/
products/moab-cluster-suite.php
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/
Torque / Moab Cluster resource manager / scheduler Licensed / Free http://www.clusterresources.com
Totalview Parallel debugger Licensed http://www.etnus.com

Operating systems

Name Description Licensed or free Vendor web site
Mac OS X Leopard Latest version of the Mac OS Licensed http://www.apple.com/macosx/
openSUSE Linux Desktop OS Free http://www.opensuse.org
VMWare Virtualization OS Licensed http://www.vmware.com
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