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, please send an email to software@bmi.cchmc.org
** 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 cchmc@zones.com
- Desktop office productivity software
- Biobanking 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, 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.
| 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 | Free | 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/ |
Biobanking Software
| Biomaterial Tracking & Management Research System | Software to track and manage biological samples, including freezer location and distribution | Free | http://www.daedalussoftware.com/website/ |
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 |
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
| 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
Sequence and expression analysis
Pathway analysis
| Ingenuity | Pathway analysis tools | BMI Licensed | http://www.ingenuity.com/ |
Pharmacokinetics
| NONMEM | Pharmacokinetics software | Licensed | http://www.iconplc.com/technology/products/nonmem/ |
Protein modeling and crystallography
| 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
| 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
| 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
| 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
| 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 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 | |
| LSF | LSF Scheduler | Licensed | http://www.platform.com |
| LONI Pipeline | LONI Pipeline | Free | http://pipeline.loni.ucla.edu |
Operating systems
| Mac OS X Lion (v. 10.7) | Previos 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 |