Campus alert status is orange: For the latest campus alert status, news and resources, visit

Search Close Search
Search Close Search
Page Menu



Integration of computational technology and biology. Computational innovation accelerates biotechnology innovation. Newly developed software developed at UMassMed can aid diagnosis, care, and research and are now available to the public.







Browse Our Software Innovations:






Title: Adaptive, Multimodal Communication System for Non-Speaking ICU Patients. UMMS15-54; Patent Pending. 

  • This novel communication system is specifically tailored to patients who are restrained and unable to speak permitting communication about topics of ICU relevance. The system consists of 1) a handheld unit, responsive to multiple types of tactile input, which will be accessible to a patient lying in bed; and 2) a tablet displaying visual output and producing synthesized speech output situated above the bed, visible to the patient and to others in the room. The systems most important feature is that both the hardware and software components of the device are completely adaptable to the patients's physical deficits/impairments which vary substantially. Further, the device also produces tactile feedback, e.g. such as producing vibration when an action is initiated and/or completed, a feature shown to benefit those with disabilities.

Title: Methods and System for Optimizing a Control System. UMMS15-40. Patent Pending. 

  • Inducing a switch in neuronal state using energy optimal stimuli is relevant to a variety of problems in neuroscience. Analytical techniques from optimal control theory can identify such stimuli; however, solutions to the optimization problem using indirect variational approaches can be elusive in models that describe neuronal behavior. Here we develop and apply a direct gradient-based optimization algorithm to find stimulus waveforms that elicit a change in neuronal state while minimizing energy usage. Our gradient-based algorithm: 1) enables automated exploration of a wide solution space, using stochastically generated initial waveforms that converge to multiple locally optimal solutions; and 2) finds optimal stimulus waveforms that achieve a physiological outcome condition, without a priori knowledge of the optimal terminal condition of all state variables. Analysis of biological systems using stochastically-seeded gradient methods can reveal salient dynamical mechanisms underlying the optimal control of system behavior. The gradient algorithm may also have practical applications in future work, for example, finding energy optimal waveforms for therapeutic neural stimulation that minimizes power usage and diminishes off-target effects and damage to neighboring tissue. more info.

Title: A Novel Use of Eye Tracking to Improve Radiologists' Diagnostic Accuracy and Training. UMMS15-13; Patent Pending.  

  • This invention provides an eye-tracker and computer software to improve one's ability to observe details in images, particularly radiologic images. The technology is based on the finding that people may believe they have not seen a detail for which they were looking (such as a flaw in a work of art, defect in a machined part, or an abnormality in a tissue sample), when in fact the person may have actually unconsciously detected it. By tracking eye movements the invention provides methods to detect unconscious estimations thereby encouraging the individual to reconsider the initial estimation that the detail was not observed. 

Back To Top



Title: REBISS Score and REBISS Score Calculator. UMMS14-32; Patent Pending. 

  • To prevent misdiagnosis, this technology discloses a clinical scoring system that effectively and efficiently utilizes a number of different data sources to determine a diagnosis of patient conditions. The score is compared to a spectrum of scores in order to identify between disorders, such as Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBSd) or gastroesophageal reflux disease (GERD) and functional dyspepsia for which there are currently no validated scoring systems.

Title: A New Tool for Studying Heterogeneity of Treatment Effects in Longitudinal Translational Research. UMMS14-29; Patent Pending. 

  • The invention generally relates to data analysis. More specifically, the invention relates to analyzing variation in data resulting from clinical trials or observational studies. The invention describes a computer-implemented method for visualizing trajectory pattern recognition of longitudinal data that improves the accuracy and stability of identified patterns, including the structure of high-dimensional (HD) data with missing values. 

Title: iSERF: Intelligent Search, Relation Extraction and Research for Functional Biology. UMMS14-25; Patent Pending.

  • The present invention relates generally to identifying relationships between items. Certain embodiments of the present invention are configurable to identify the probability that a certain event will occur by identifying relationships between items. Certain embodiments of the present invention provide an improved supervised machine learning system.

Back To Top



Title: System and Method for Using Somatic Movement to Improve Prediction and Prevention of Infant Apnea. UMMS13-75; Patent Pending.

  • The present invention relates to methods and systems for inhibiting apneic and hypoxic events. More specifically, the present invention provides methods for monitoring physiological signals of a patient, predicting the occurrence of a life-threatening event such as apnea or hypoxia, and initiating a stimulus to lessen the severity of, or even prevent, the occurrence of the life-threatening event.

Back To Top



Title: UMMS12-06; Patent Pending. 

  • A web-based system for implementing a smoking cessation support therapy that promotes individual, proactive participation by obtaining an initial consent, indicating motivation, from a patient, and linking the patient with a clinician for monitoring, feedback, and direction of subsequent support media based on clinician oversight and the reported motivation of the patient. The disclosed system encompassing self-motivation assessment, reinforcement feedback, and communication linkages to both clinicians and peers provides for a proactive response by a patient to a clinician invitation, thus establishing a minimal motivational level, and gathers statistical and motivational information from the patient for subsequent monitoring by the clinician.

Back To Top



Title: Specifications for Operating Room Hand Hygiene and Surgical Scrub Reminder System. UMMS11-34; Patent 8,633,816. 

  • This technology involves a system and method for monitoring personal protection items of a healthcare worker (gloves, gown, mask and respirator), using a user badge which stores data representing items worn by a worker, wirelessly communicating with the badge before the worker enters a patient zone (such as a patient room, bed area or exam table area), to see whether the worker has the required items. Patient beacons, located near patient room doors, near beds and other locations, store data representing the items required by workers who come in contact with, or close proximity to a patient, and wirelessly communicate with the badge. The patient beacon data can be set for the requirement of the patient, based on patient condition.

    • Inventors: Richard Ellison
    • Applications:
    • Patent Expiration Dates: 2032-03-29


Back To Top


Back To Top



Title: my5C Software. UMMS09-57; Patent Pending. 

  • My5c software is a publicly available computational tool that can be used for 5C-based chromosome structural studies. 5C is a powerful high-throughput method for analyzing chromosome folding. Researchers can upload data obtained from their experiments, either by sequencing or microarray. Using My5C, researchers can obtain a two-dimensional heat map of three-dimensional chromosome structure.

Back To Top




  • This invention builds on the existing non invasive spectroscopic sensor that can detect information from tissues of different thicknesses to aid diagnoses. This invention uses a mathematical approach to calculate capillary SO2, pO2, pH, pCO2, and temperature. The calibration equation for all parameters uses PCA Loading Correction factor to account for subject-to-subject variation that has been used to determine the calibration equation.