Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.


Orly Alter is a Utah Science, Technology, and Research associate professor of bioengineering and human genetics at the Scientific Computing and Imaging Institute1  and the Huntsman Cancer Institute at the University of Utah, the principal investigator of a National Cancer Institute's Physical Sciences in Oncology project,2,3  and the chief technology officer and a co-founder of Eigengene, Inc.4,5  Alter received her Ph.D. in applied physics at Stanford University and her B.Sc. magna cum laude in physics at Tel Aviv University. Her Ph.D. thesis on "Quantum Measurement of a Single System," which was published by Wiley,6,7,8  is recognized as crucial to quantum computing and gravitational wave detection.9,10,11 

Research Interests

Postdoctoral and Graduate Positions at the Genomic Signal Processing Lab

NCI U01 CA-202144: Multi-Tensor Decompositions for Personalized Cancer Diagnostics and Prognostics

Inventor of the "eigengene,"12,13,14,15  Alter formulates comparative spectral decompositions, physics-inspired multi-tensor16,17  generalizations18,19,20,21,22  of the singular value decomposition, to (i) compare and integrate any data types, of any number and dimensions, and (ii) scale with data sizes. Her models (iii) are interpretable in terms of known biology and batch effects and (iv) correctly23  predict24,25,26,27,28  previously unknown mechanisms.29,30  By validating a genome-wide pattern of DNA copy-number alterations in brain31,32,33,34,35  tumors as the best predictor of survival, her retrospective clinical trial36,37  proved that the models (v) discover accurate, precise, and actionable genotype-phenotype relationships, (vi) are relevant to populations based upon whole genomes of small cohorts, and (vii) can be validated. She discovered this, and patterns in lung,38,39  nerve, ovarian,40,41,42,43,44,45  and uterine tumors, in public data. Such alterations were recognized in cancer, yet repeated previous attempts to associate them with outcome failed, demonstrating that Alter's algorithms are uniquely suited to personalized medicine.

  • 26th Annual Meeting of the Society for Neuro-Oncology (SNO) (Boston, MA, November 18–21, 2021).
  • Decade of the Physical Sciences in Oncology Network (PS-ON) at the National Cancer Institute (NCI) Virtual Symposium (September 21–23, 2020).