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:
- Desktop office productivity software
- Data storage and management software
- Data analysis software
- Remote and cluster computing software
- Operating systems
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
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 | Licensed | http://www.adobe.com/ |
| Adobe Photoshop Elements | Graphic creation and editing software | Licensed | http://www.adobe.com/ |
| EndNote | Bibliographic software | Licensed | http://www.endnote.com |
| Medeley |
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 | 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 |
| TeleForms | Tool for generating and scanning paper-based data collection forms | Licensed | http://www.cardiff.com/products/teleform/index.html |
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 |
|---|---|---|---|
| Statistical computing software |
Licensed |
http://www.dataflux.com/Product-Services/Products/dbms.asp | |
| GraphPad Prism |
Statistical computing Software | Licensed | http://www.graphpad.com/prism/Prism.htm |
| 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 |
| 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 | Licensed | http://www.sas.com/ |
| SigmaPlot | Statistical computing software | Licensed | http://www.systat.com/products/sigmaplot/ |
| SPSS | Statistical computing software | Licensed | http://www.spss.com |
| Stata | Statistical computing software | Licensed | http://www.stata.com/ |
| SUDAAN | SAS add-on | Licensed | http://www.rti.org/sudaan/ |
Sequence and expression analysis
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 |
| 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.html |
| IDEAS v3.0 | ImageStream analysis software | Free | http://www.amnis.com/IDEAS30Release.asp |
*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/ |
| 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 |
|---|---|---|---|
| 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 |
| 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 |
| PuTTY | Secure Shell client | Free | http://www.putty.org/ |
| WinSCP | SCP/SFTP client | Free | http://www.winscp.net/ |
Operating systems
| Name | Description | Licensed or free | Vendor web site |
|---|---|---|---|
| Mac OS X Snow Leopard (v. 10.6) | Latest 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/ |
| openSUSE Linux | Desktop OS | Free | http://www.opensuse.org |
| VMWare | Virtualization OS | Licensed | http://www.vmware.com |
