MapReduce-based tool to remove duplicate DNA reads
MarDRe is a de novo MapReduce-based parallel tool to remove duplicate and near-duplicate DNA reads through the clustering of single-end and paired-end sequences from FASTQ/FASTA datasets. This tool allows bioinformatics to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset. MarDRe is the Big Data counterpart of ParDRe (link above), which employs HPC technologies (i.e., hybrid MPI/multithreading) to reduce runtime on multicore systems. Instead, MarDRe takes advantage of the MapReduce programming model to significantly improve ParDRe performance on distributed systems, especially on cloud-based infrastructures. Written in pure Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for Big Data processing.
Open pharmacovigilance data extraction, mining and analysis tool
OpenVigil provides a webinterface to analyse pharmacovigilance data, i.e., spontanous or systematic collections of treatments (drugs) and observed adverse events ("drug side effects"). FDA Adverse Event Reporting System (AERS) and other pharmacovigilance data (e.g., Canadian or German) are supported. The OpenVigil web-based analysis tools offer several analysis modes like extraction, filtering, mining of data and analyses via measurements of disproportionality like proportional reporting ratio or reporting odds ratios) and export to spreadsheets programs like Microsoft Excel or statistics programs like R. OpenVigil 1 operates on raw data, OpenVigil 2 on cleaned data (using drugbank.ca and drugs@FDA), OpenVigilFDA uses the official FDA online API. OpenVigil 2 supports query for ATC codes or certain chemical moieties. Other tools of the OpenVigil project include a calculator for measurements of disproportionality for a 2x2 contingency table and a drugname mapper using RxNorm.
specific protein interaction networks from transcript expression
Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal alterations in protein connectivity caused by alternative splicing. The original publication can be found on https://bioinformatics.oxfordjournals.org/content/32/4/571 .
A norm calculator for neuropsychological tests for daily use in clinic
Our premise when starting this project was that why do we have to dig through arrays of normative values to find the group our patient belongs to. Then proceed to manually calculate its z score and find out where it is on the percentile graph, when we could have a software that could do it for us. We weren’t able to find one in the literature. Thus came the PsiNorm. Currently only a demo for english exists, while Turkish adapted version is fully functional. If you'd like a version adapted to your patient population/language please contact us at Contact e-mail: firstname.lastname@example.org
PyVE is image analysis and visualization environment
PyVE is image analysis and Visualization Environment focused at clinical use. At the core of it there is a powerful viewer for displaying 3D datasets (MRI, PET, CT) based on VTK. It all comes precompiled allowing painless access to Python (2.x), the ITK toolkit for image analysis, numpy/scipy for numerical calculations, Qt and PyQt4 for the development Graphical User Interfaces. It is what you need for fast prototyping and development of more complex projects.
A web-based minimisation service
Based on MinimPy (http://sourceforge.net/projects/minimpy/), QMinim is a web-based minimization application, for allocation of subject to different arms of a clinical trial. It is an alternative to randomization, with the advantage of balancing arms of trial with respect to preselected prognostic factors. All aspects of minimization procedure including treatments, factors, minimization protocole, and including a preload can be customized using QMinim.
QC tests and patient doses from radiodiagnostic XRay equipment
This software performs various quality control tests for XRay devices used in radiography, mammography, fluoroscopy and CT such as: HVL/tube filtration, high voltage, exposure time, tube output, MTF calculations, film sensitometry, AEC devices and more. It also compute patient doses using an external program based on the GEANT4 simulation toolkit. This program is found here: https://sourceforge.net/projects/doseinhumanbody/ Read the "README" file for details. Source code and documentation included.
Use Apache Pig to process your large sequencing datasets!
SeqPig is a library for Apache Pig for the distributed analysis of large sequencing datasets. It provides import and export functions for file formats commonly used for sequencing data, as well as a collection of Pig user-defined-functions (UDF’s) to help process aligned and unaligned sequence data. Currently SeqPig supports BAM/SAM, FastQ and Qseq input and output. For more information see the manual at http://seqpig.sourceforge.net/
OS X DICOM PACs server and an update to the Conquest server.
A DICOM PACs server for OSX. Just download and run the application. Easy to setup. Conquest is a well known DICOM PACs server in the windows world. In its heart is the dgate server. This is an Mac interface to that server. Several improvements have been made to the dgate server, JPEGLS for one, HL7 work list is another. The dgate code is compiled for Windows and use to replace the current date program in Conquest with the new added features.
Markup Code generator
Classes for generation of not only (X)HTML code. It is possible to create also XML, XSL, SVG and many other - but possibilities are limited by original purpose: creation of HTML code.
A tool for personal trainers and fitness enthusiasts.
Currently: *Source code now available in the form of a Visual Studio 2015 project (zipped).* 1) Calculate BMI, daily caloric intake, target heart rate, maximum and training poundage, and ideal proportions based upon joint measurements. 2) Record and recall measurements and progress using the Basic Information tab. 3) Create, Manage, Export, and Import custom foods/exercises lists using the appropriate tabs. 4) Store and recall workout and diet log records by date. Future Improvements (in the works): * Diet and Workout tab improved functionality.
C-level driver collection for MSP430 and derivatives
ocapi is an open source driver collection for MSP430 and derivative processors. It provides a C language application programming interface (API) for deploying individual processor capabilities. Current modules support serial communication via UART, I2C and SPI, digital I/O (GPIO), analog-to-digital conversion (ADC), Timers and so on. ocapi aims at being independent of the development host platform. So it should work, no matter if you live in the Windows, Linux or Mac world. ocapi is used as the hardware abstraction layer for the MSP430 port of the Takatuka Java virtual machine (JVM). Before it can be used, the library must be built from the sources provided here. The build environment allows for fine grained configuration of the library's functionality and target system.
object-based image analysis framework
Wienert S, Heim D, Kotani M, Lindequist B, Stenzinger A, Ishii M, Hufnagl P, Beil M, Dietel M, Denkert C, Klauschen F. CognitionMaster: an object-based image analysis framework. Diagn Pathol 2013, 8:34
3DBrainExplorer is a lightweight OpenGL-based 3D renderer for scientific visualization of volumetric data (NIfTI) featuring real-time image manipulation, AAL brain labels (Tzourio-Mazoyer et al., 2002), SPM5 statistical images and stereo display.
TTS for Basque Lapurdian dialect
AhoTTS Iparrahotsa is the TTS developed at the Aholab Signal Processing Laboratory of the University of the Basque Country (UPV/EHU) for the Lapurdian dialect of Basque. This dialect is spoken at the Northern area of the Basque speaking area (French region). This project was funded by the Euroregion Aquitaine-Euskadi under grant EUSKADI-2012-004.
Android app to tell simple day and time, e.g. Saturday Afternoon
Designed to run on old Android tablets, TV boxes etc to give a simple display of the current day of the week and time of day (morning, afternoon etc) for people who are suffering from dementia. Highly configurable.
Bioequivalence Model Dependent-Independent Approach
Bioequivalence Model Dependent-Independent Approach scripts for in-vitro dissolution profile comparison as proposed by Sathe et al. in 1996 (Sathe PM, Tsong Y, Shah VP. In-vitro dissolution profile comparison: statistics and analysis, model dependent approach. Pharm Res. 1996 Dec;13(12):1799-803) and Tsong et al. in 1996 (Tsong Y, Hammerstrom T, Sathe P, Shah VP. (1996) Statistical Assessment of Mean Differences between Two Dissolution Data Sets, Drug Info. J. 30:1105-1112).
Tool to search binary biclusters on CUDA-enabled GPUs
CUBiBit is a parallel tool to accelerate the search of biclusters on binary datasets using CUDA-enabled GPUs. This data mining procedure is especially useful for gene expression data. This tool receives as input a file with ARFF extension that contais the binary values of m attributes and n samples and returns a file with the biclustering information. It is able to exploit the parallel capabilities of manycore NVIDIA GPUS. It also makes use of C++11 multithreading support to accelerate one phase of the algorithm on several CPU cores.
La app está programada en Java así que funciona en Windows, Linux, Solaris, Mac, etc. Solo necesitas tener instalado java (http://www.java.com/getjava) Básicamente es una calculadora para medir la Grasa Corporal, Masa Magra (musculatura), Tasa Metabólica Basal (La cantidad de calorías que necesitas consumir por día para subsistir), IMC (indice de Masa Corporal) e índice cintura/altura. Solo tenés que colocar las medidas, peso, altura y edad para que te dé lo que necesitas saber. Presionando en los signos de pregunta vas a obtener datos de referencia y formas de medirte. Modo Personal Trainer También agregué un botón para salvar los datos con diferentes perfiles. De esta forma no solo podés medir tu progreso sino el de tus amigos o clientes (si sos trainer)
Canreg5 is a software package for population based cancer registries
Cancer registries need a tool to input, store, check and analyse their data. If these data are also coded and verified in a standard way, it facilitates the production of comparable analyses across registry populations. The main goal of the CanReg5 project is to provide a flexible and easy to use tool to accomplish these objectives. CanReg5 is a multi user, multi platform, open source tool to input, store, check and analyse cancer registry data. It has modules to do: data entry, quality control, consistency checks and basic analysis of the data It was designed with an emphasis on user friendliness, it has a modern user interface and is easy to navigate. Is available in several languages. (English, French, Spanish, Portuguese, Russian, Turkish, Georgian, and Chinese.)
Coordination Center Software for mobile operation - web based
We moved this project to https://github.com/wrk-fmd/CoCeSo Content on this site is outdated and here just for historic reasons and therefore read-only. CoCeSo is a web application depending on a database which is used by ambulance services for the management of its units at events (concerts, soccer matches,...). It allows you to manage the status of units, create and track interventions and assign units to them. A colorful interface facilitates an overview at a glance. The interface language is german or english (with your contribution any other language can be added).
A web-based launcher into the ConnectingGTA Training Environment
The Training Environment Launcher provides a friendly and secure interface for Trainers, Clinicians (trainees), and Operations personelle to access the Training Environment, which contains no personal health information. While this program is complete, certificates and private keys are not publicly available, and thus cannot be integrated with a regional hub without valid credentials. This program provides the following functions: o Program Trainers at Hospitals can define training courses o Hospital Trainees (Clinicians) can take training courses o Program Operations personelle can add/remove trainers, organizations, and reusable internal accounts. For more information about ConnectingGTA, see the eHealth Ontario website: http://www.ehealthontario.on.ca/en/regional-partners/view/cgta
Creates 24h-Duty-Plans by considering preferences for up to 20 Persons
Diese schlanke und kostenlose Excel-Tabelle erlaubt es, für bis zu 20 Personen einen 24 Stunden Dienstplan zu erstellen. Die Software Berücksichtigt dabei Wünsche, Abwesenheit und Rufbereitschaften der einzelnen Personen. Nachdem eine Übersicht erstellt wurde, wird der Dienstplan mit der optimalen Verteilung der Dienste erstellt. Hierbei werden Feiertage und Wochenenden Berücksichtigt. Die Software ist nutzbar für alle Monate und Jahre.
Pour la médecine fondée sur les faits (Evidence-Based Medicine (EBM)). La technique PICO pour formuler des questions cliniques. Plate-forme web open source pour supporter la création de PICO, la recherche et l'évaluation d'informations.
The Experimental Factor Ontology describing experimental variables
*** Please note this repository is now deprecated as of January 2018. All EFO development and source code has been moved to https://github.com/EBISPOT/efo *** The Experimental Factor Ontology (EFO) available from http://www.ebi.ac.uk/efo is an application focused ontology modeling the experimental factors in ArrayExpress and constructing mappings to multiple existing domain specific ontologies. To submit new terms, features or report bugs please submit a ticket at the following: http://www.ebi.ac.uk/panda/jira/secure/CreateIssue!default.jspa