Assists clinicians to establish the optimum revascularisation approach in patients with complex coronary artery disease. Syntax Score is a program that aids decision making between coronary artery bypass graft (CABG) and percutaneous coronary intervention (PCI). This tool includes a calculator to supply doctors an individual, patient-oriented treatment recommendation based on the mortality risk.
Offers well-established, broadly validated measures of phenotypes and exposures relevant to investigators in human genomics, epidemiology, and biomedical research. PhenX Toolkit is a catalog of recommended, standard measures of phenotypes and environmental exposures for use in biomedical research. It provides detailed protocols, information about the measures, and tools to help investigators incorporate PhenX measures into their studies.
Provides a streamlined and simpler platform for estimates of program costs. LiST allows countries and researchers to calculate both the full financial costs and the impacts of maternal, neonatal and child health (MNCH) intervention scale up on morbidity and mortality. It relies on existing intervention inputs and cost databases to ensure consistency with other models which countries may be using.
Estimates recombination rates, has sophisticated interpolation methods and allows complex queries. MareyMap is integrated with physical and genetic maps from different organisms: one vertebrate - Homo sapiens; two invertebrates - Drosophila melanogaster, Caenorhabditis elegans; and one plant Arabidopsis thaliana. It includes sliding window to get local estimation with the slope of the best line fit to the data in a local window. The software is also available as a simplified web service for permitting to get recombination rates from personalized data or a public database.
Serves for selecting optimal cutpoints in diagnostic tests. OptimalCutpoints is an R package that enables end-users to choose from among a considerable number of strategies commonly used in clinical practice for optimal-cutpoint selection. It provides numerical and graphical results and allows optimal levels to be calculated automatically according to levels of certain covariates.
Aims to facilitate the querying of various databases through the BD2K PIC-SURE RESTful API. Rcupcake is a package also containing an assortment of more than 15 functions for descriptive and univariate analysis as well as comorbidities studies. The application was developed for allowing the combination of multiple different variables such as clinical or biochemical information in a unified set, as well as the analysis of multiple layers of data.
Allows researchers to manage health and medical research data for humans and animals without specialized database skills or programming expertise. The Ark provides data management for core research information including demographic, phenotype, biospecimen and pedigree data, in addition to supporting typical investigator requirements such as tracking participant consent and correspondence, whilst also being able to generate custom data exports and reports. The Ark is study generic by design and highly configurable via its web interface, allowing researchers to tailor the system to the specific data management requirements of their study.
Aims to identify the complex relationships between phenotypes and environments. PhenoCurve splits the whole dataset into reliable and unreliable windows based on curve fitting, and then optimizes the results on the unreliable windows using regularized polynomial regression and maximum the posterior estimations. It is 1Qbased on Bayesian theorem and regularized polynomial regression.
Allows researchers and clinicians to collaborate to the elaboration of Computer Assisted Medical Intervention (CAMI) applications. CamiTK permits to regroup knowledge and expertise in various discipline. It introduces some abstraction of the software components, viewers and algorithms in order to ease the full collaboration between CAMI fields. The tool aims to fill the gap between highly specialized software covering different CAMI research aeras.
Extracts pitch cues from the Auditory Nerve (AN) population activity for a given arbitrary stimulus. SC Pitch copes with different pitch phenomena: extracting resolved and non-resolved harmonics, missing fundamental pitches, stimuli with both high and low amplitudes, iterated rippled noises, and recorded musical instruments. It is based on a technique known as sparse coding. The model represents input stimuli as sparse linear combinations of atoms, where each atom is derived from the AN population response to a pure tone.
Provides a platform to experiment with mechanisms that may drive the fracture healing process. Callus Analog Framework executes simulated healing and provides a record of an analog healing process. This software simulates how the histologic appearance of a mouse fracture callus may transition from day 7 to day 10. This method is extensible to other research areas to investigate and explain tissue level phenomena.
Determines an ideal number of clusters and permits users to assess their quality. progenyClust utilizes a technique that constructs new samples out of existing ones by sampling features independently. It permits users to diminish data size for re-clustering. This tool captures true and false classification when new samples are repetitively drawn and clustered using a co-occurrence probability matrix.
Estimates usual dietary intake including episodically consumed foods on the basis of two or more short-term measurements such as 24-h dietary recalls. MSM uses optional information regarding habitual use or non-use of a food. It allows nutritional scientists to calculate usual dietary intakes by combining short-term and long-term measurements (multiple sources). The tool is applicable to nutrient and food intake including episodically consumed foods. It can handle different distributions of food and nutrient data and constructs proper population distributions.
Assists users in picking a suited therapy for neuro-oncology patients. CNS TAP is an algorithm that takes into account drug properties, clinical and pre-clinical data, and patient-specific sequencing data for scoring relevant targeted agents. This program is available through a mobile application and the formula aims to be regularly updated by addition of new agents and published data.
Summarizes the impact of communicable disease in the European Union and European Economic Area Member States. The BCoDE toolkit is a user-friendly software for estimating the burden of communicable diseases. The toolkit facilitates communication between data analysts and users through multiple visualization options, ultimately fostering its value in health policy communication. It computes disease-specific results displayed as Disability-Adjusted Life Years (DALYs) calculated for the selected set of disease models, and based on the incidence values entered by the user. The BCoDE toolkit implements a very generic calculation engine that is not restricted to any specific disease model.
A software package for automatic phenotyping in C. elegans included in QuantWorm. WormGender is designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions include, i) automatic recognition and counting of adult hermaphrodites and males, ii) a manual inspection feature that enables manual correction of errors, and iii) flexibility to use new training images to optimize the software for different imaging conditions. We evaluated the performance of our software by comparing manual and automated assessment of sex ratio. Our data showed that the WormGender software provided overall accurate sex ratio measurements.
Translates person-specific dynamic assessment data into a targeted, modularized treatment plan. DATA permits researchers to identify potential points of strength or weakness under controlled conditions. It can build personalized interventions in psychological science, and one that could be shown to be incorrect. The tool is able to quantify the incremental contributions of every input item to the overall pathology and generate a set of item scores.
Assists users with the analysis in electronic data capture systems (EDCs). ODM-DA provides automatically generated descriptive statistics and completeness analyses. Different access options such as server or Docker instance are provided to perform clinical research data analysis. User can directly upload the clinical data, and its syntax is validated, the completeness of the collected data is determined, and the descriptive statistics and additional charts of nearly all items are generated automatically.
Allows users to manage statistically processed data. Genotype Viewer generates organized web content and provides genotype-oriented summaries across mutant strains or cohorts. It is a part of the Phono-pub platform that integrates workflows for three types of data handling that support the steps from data analysis to publication of mouse phenotypic data obtained in a variety of analyses. Genotype Viewer can serve in phenotyping experiments.
Generates web content with measurement parameter-oriented summaries. Strain Viewer is a part of the Phono-pub platform that integrates workflows for three types of data handling that support the steps from data analysis to publication of mouse phenotypic data obtained in a variety of analyses. It contributes to the promotion of noncentralized phenotypic data dissemination.
Supports individual researchers’ routine statistical workflows. Mou-Stat is a semiautomatic analyser dedicated to mouse phenotyping experiments. It is a part of the Phono-pub platform that integrates workflows for three types of data handling that support the steps from data analysis to publication of mouse phenotypic data obtained in a variety of analyses. This tool can be useful for phenotyping experiments.
Helps expedite and facilitate the transformation of raw phenomic character data into discrete character matrices that can be used in most popular evolutionary inference programs. MatrixConverter facilitates the process of evaluating, scoring, and formatting raw phenomic data so that the data can be used for evolutionary inference.
Allows assessment of dietary intake, as well as for diet planning. OPEN is composed of data from Slovenian, European and, to a limited extent, also American food composition tables. It provides a recipe-calculation procedure tested by using both analytical and calculation techniques. This tool was used on a volunteer group of pregnant women to calculate the energy intake.
Supports the workflow of building, sharing, and validating electronic phenotype algorithms. PheKB is a collaborative environment which has tools to enable cross-site collaboration for algorithm development, validation, and sharing for reuse with confidence. The web application allows to view existing algorithms, enter or create new algorithms, collaborate with others to create or review algorithms and view implementation details for existing algorithms.
Provides access to trustworthy, evidence-based vaccine information for a target audience of healthcare providers, pharmacists, and patients (including parents of children). ReadyVax provides a comprehensive suite of information on the vaccines and the diseases they prevent. It can be used in the event of an emergency to empower public health authorities to convey messages to target populations as quickly as possible.
Predicts the perceptual experience of retinal prosthesis patients across a wide range of implant configurations. pulse2percept provides simulations to evaluate the perceptual experiences likely to be produced across current and future devices. The software predicts the perceptual distortions experienced by "virtual patients" over space and time. It can help to improve stimulation protocols for existing devices, guide reimbursement decisions and help patients and doctors in their decision as to when or whether to be implanted, and which device to select.
Permits users to utilize reliability for study design. relfeas is an R package that approximates the reliability of an outcome measure for new samples based on the results of previous test-retest studies. The software allows for calculation of the characteristics of a sample which would be required for the measure to reach sufficient levels of reliability. It can be useful in study planning and in assessment of the feasibility of new study designs.
Serves for extraction and visualization of heart rate profiles from wearable fitness trackers. CardiacProfileR can detect periods of active exercise from the data, and it constructs a heart rate profile for each period of active exercise. More precisely, this program is able to produce interactive visualization of one or multiple heart rate profiles in two dimensions or three dimensions. This enables aggregation and comparison of data from multiple periods of exercise or comparison between multiple people.
Supports cross-sectional cohort phenotype analyses. PhenoStacks presents phenotypes in context, groups and clusters them, and summarizes them via overviews to support the exploration of phenotype distributions. It can help to identify phenotype patterns, investigate data quality issues, and inform data collection design. The tool is based on feedback from expert genetics researchers. It can be used in other domains where instances of taxonomies or ontologies are analyzed.
Assists users to study mild traumatic brain injurym (TBI)/traumatic brain injury (TBI). COR is an oculomotor rehabilitation program contains: (1) automated assessment of Resource Reservation Protocol (RSVP) errors; (2) a versatile stimulus package; (3) the ability to add a visual and/or auditory distractor to the training to increase difficulty level; (4) automated assessment of visual performance. The utilization of this tool is possible for over a wide range of diagnostic groups manifesting abnormal oculomotor control.
Permits to evaluate deep features and classifiers in digital pathology. DAPPER is a framework based on a data analysis plan developed to predict biomarkers from massive omics data. It is composed of (i) the whole slide images (WSI) preprocessing pipeline, (ii) the deep learning backbone to extract deep features, (iii) the data analysis plan (DAP) for the machine learning models, (iv) the uniform manifold approximation and projection (UMAP) module and other modules for unsupervised analysis.
Serves for a variety of applications at CERN. FLUKA is a program for calculations of particle transport and interactions. It can simulate with high accuracy the interaction and propagation in matter of about 60 different particles, including photons and electrons. It allows management of very complex geometries, using an improved version of the well-known Combinatorial Geometry (CG) package.
Summarizes patient information. Ebola CARE offers a visual representation of the predictive outcome as well as attributing clinical protocols adjusted by demographic parameters. This application selects the appropriate model according to the data provided by the user. It uses the full model if all required clinical symptoms (body temperature, headache, bleeding, diarrhea, jaundice, vomit, abdominal pain, asthenia/weakness), patient age, and initial reverse transcriptase PCR cycle threshold (CT) values are entered.
Classifies patients using patient similarity networks. netDx can perform data integration and model interpretability. It integrates heterogeneous datatypes, including clinical variables, DNA methylation, somatic mutations, mRNA, miRNA and protein expression profiles. This tool was used for survival prediction in kidney, lung, ovarian and brain cancer. It is based on a machine-learning method.
Allows virtual planning of reconstructions. iPlan CMF is a program permitting users to work on complex planning of mid-facial reconstructions and tumor removal, and especially to reproduce three-dimensional imaging of tumor and its surrounding. This tool is useful to observe the virtual osteotomy to highlight several characteristics such as tumor, skull and vessel.
Allows consultation and modification of files according to the North American Association of Central Cancer Registries (NAACCR). XMLExchange Plus has several features such as: conversion of files, validation of contents, or dictionary maintenance.
Allows users to work on Health Level Seven (HL7) files from anatomic pathology laboratories. This tool can produce a pathology laboratory database and contain HL7 data elements or permits users to override any automated decisions about reportability and coding.
Allows to visualize Statewide Planning and Research Cooperative System data. SPARCS data interactive visualization deals with samples sizes of 10, 100, 1000 and 10000 of records for each year. The user can select county and limit and then visualize data results graphically. The results can be filtered easily.
Reviews and explores data produced by continuous positive airway pressure (CPAP) and related machines. SleepyHead is a cross platform, opensource sleep tracking program for CPAP and Oximetry data which are devices used in the treatment of Sleep Disorders like Obstructive Sleep Apnea.
Reaps information about cancer from public internet. Web Plus is a web-based application offering three functions: follow-back efforts, file upload and download, and online abstracting. Its configuration allows users to upload abstracts generated by from death certificate and pathology lab files.
Provides a data acquisition system for ultrasound images of liver ultrasounds. Hepaticus is a medical image data collection server. User can annotate the image for liver texture, liver surface irregularity or add additional remarks.
Permits to simulate effects of different type of color-blindness. dichromat provides 17 color schemes suitable for people with deficient or anomalous red-green vision. It uses a matrix to determine the kind of vision (normal, protan, deutan or tritan).
Provides a well-engineered flexible database system supporting mouse animal husbandry and data management. JCMS is an application composed of four integrated software modules: (1) colony management, (2) experiment management, (3) sample tracking, and (4) reports and queries. It includes several supporting applications, such as a pedigree tracking tool (JPT) or an application that converts provided instances, which can be then used with a relational database management system (RDBMS).
Consists in a central registry database program. CRS Plus has several functions such as: (1) allows users to compare and store data; (2) supplies management reports; and (3) can export data in NAACCR format.
Supports depression care manager activities and facilitates the dissemination of collaborative care models. NetDSS is based on intervention materials used for a randomized trial of depression care management that improved clinical outcomes compared with usual care. It guides the care manager through a self-documenting patient encounter using evidence-based scripts and self-scoring instruments. The tool provides context-specific decision support in real time during encounters with patients by using scripts, self-scoring instruments, and clinical algorithms to identify new trials, treatment phases, and outcome milestones.
Recognizes the causative disease. Phrank scores diseases caused by a patient candidate gene for its ability to explain the set of patient phenotypes. It allows clinicians to accelerate diagnosis of Mendelian diseases. This tool is based on a natural information theoretic formulation that quantifies how informative a phenotype is for diagnosis to determine phenotype sets similarity.
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