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Research Applications

The applications below are available for Upstate faculty, staff, and students.  Most may be downloaded and installed on Upstate-purchased computers from either the Software Center (PC) or Upstate Apps (Mac).  Some must be requested from the Help Desk or require the purchase of a license. For technical support with these applications, please contact the Help Desk 315-464-4115 so that we may set up an appointment with you.

 

TriNetX

Real-time access to patient populations, driven and refreshed by electronic medical record (EMR) data, to determine protocol feasibility, cohort analysis, site identification and the generation of real-world evidence to support regulatory submissions.

SlicerDicer

SlicerDicer is an advanced reporting interface for exploring Upstate University hospital data. In SlicerDicer, you can investigate a hunch and then refine your searches on the fly by examining trends, drilling down to line-level details, and jumping to related records to follow up.

GraphPad Prism

The preferred analysis and graphing solution purpose-built for scientific research. Join the world’s leading scientists and discover how you can use Prism to save time, make more appropriate analysis choices, and elegantly graph and present your scientific research. This software may be requested from the Help Desk.

FlowJo

FlowJo is a software package for analyzing flow cytometry data. Files produced by modern flow cytometers are written in the Flow Cytometry Standard [1] format with an .fcs file extension. FlowJo will import and analyze cytometry data regardless of which flow cytometer is used to collect the data.
  • Installation is available from the Software Center (PC) or Upstate Apps (Mac) on campus-issued computers
  • Purchase of a license is required, please contact the Help Desk for information.

IBM SPSS

Statistical analysis application
  • Installation is available from the Software Center (PC) or Upstate Apps (Mac) on campus-issued computers

MATLAB

MATLAB is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages.
  • Request installation within Upstate Apps or from the Help Desk.

Snap Gene Viewer

SnapGene Viewer is revolutionary software that allows molecular biologists to create, browse, and share richly annotated DNA sequence files up to 1 Gbp in length.
  • Installation is available from the Software Center (PC) or Upstate Apps (Mac) on campus-issued computers

Tableau Desktop

Connect to almost any database, drag and drop to create visualizations, and share with a click.
  • Installation is available from the Software Center (PC) or Upstate Apps (Mac) on campus-issued computers
  • Training is available from the Moonshot Team

Fiji

Image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
  • Installation is available from Upstate Apps on campus-issued computers

ImageJ

Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.
It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.
  • Installation is available from Upstate Apps on campus-issued computers

Endnote

Provided by the Health Sciences Library,
  • Installation of program and updates are available from the Software Center (PC) and Upstate Apps (Mac) on campus-issued computers

Mendeley

Free citation manager from Elsevier.  See mendeley.com for more information.

RefWorks

Provided by the Health Sciences Library

Zotero

Free citation manager; see zotero.org for more information.

  • Installation is available from the Software Center (PC) and Upstate Apps (Mac) on campus-issued computers

 

  • Installation is available from Upstate Apps on campus-issued computers. Available at https://www.zotero.org/ for your own personal computers.
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