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MareyMap
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.
The Ark
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.
SC Pitch / Sparse Coding Pitch
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.
MSM / Multiple Source Method
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.
WormGender
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.
BCoDE / Burden of Communicable Disease in Europe toolkit
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.
DATA / Dynamic Assessment Treatment Algorithm
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.
CardiacProfileR
New
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.
pulse2percept
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.
Computer Oculomotor Rehabilitation
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.
DAPPER
New
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.
Ebola CARE
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.
NetDSS / Net Decision Support System
Obsolete
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.
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