BBMap short read aligner, and other bioinformatic tools.
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s. BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file. ...and more!
Entrainer is a Java program (JRE 1.8.0_40+ required, available from http://java.sun.com/javase/downloads/index.jsp) which creates binaural beat frequencies with sound, light and animations for the purpose of entraining one's brain waves.
ProtoMol is an object-oriented component based framework for molecular dynamics simulations.
ECMOjo is a simulator and trainer for extracorporeal membrane oxygenation (ECMO). ECMOjo consists of a graphical user interface to allow interaction and train ECMO practitioners.
import and store ECG, associate to clinical data, automatic HRV
http://www.youtube.com/watch?v=AOzpNMC-FXU This multi-platform application will enable the user to import digital CSV ECGs at any sampling rate and store them in an encrypted local DB along with relevant clinical data of the patient. It also performs automatic QRS complex detection and RR interval classification showing the output in a visual chart that the user can edit to correct sources with artifacts or pats with bad detections. This project was developed using Netbeans 7.3 IDE. For further questions or feature requests please contact me at email@example.com Please read wiki for initial setup
Intellect Modeling Kit - full intellect-based apps development suite
Intellect Modeling Kit is an alternative to traditional Artificial Intelligence, intended to build apps assisting human intellect on the steps of its activity: * Observation * Producing propositions based on knowledge * Elimination of impossible propositions * Selection and verification of the most appropriate propositions * Memorizing - converting data to information and new knowledge item creation * Abstraction finding – building artificial objects, representing group of real objects featuring typical signs of group Any human knowledge written and spoken can be uploaded to IMK in a straight way by any expert not familiar with software coding. The IMK components are designed to create ready-to-use software application using simple text files provided by people. IMK accepts human knowledge and develops new knowledge together with people. The activity of IMK could be verified by human expert on every stage. IMK assists intellectual activity, but does not replace us.
XNBC is a graphic application to simulate biologic neural networks.
XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows. Web site : http://ticemed-sa.upmc.fr/xnbc/ All recent versions are on this site.
Sampsize computes sample size and power for surveys, comparative studies including non-inferiority trials and case-control studies.
Open Source and Portable object oriented software for 3D digital image segmentation and visualization. Pipes and Filters Architechture. Implemented in C++, and uses FLTK, VTK, ITK, TCL (plugins), and pipeline filters implemented in XML. DICOM support.
The 3D Slicer is freely available, open-source software for visualization, registration, segmentation, and quantification of medical image data. Follow the link for more info: http://slicer.org
Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)
This project provides a web location for CUG members to share code or links to utilities, scripts, or procedures for managing Cray systems.
Real-time EEG data acquisition and control software for event related potential (ERP) researchers. Writes data in ERPSS (UCSD) raw and log format and displays, in real time, in X windows.
A set of games and other applications for the Hoppolek platform, a research project aimed at giving gravely handicapped children a possibility to move and play, while also helping to strengthen their bone structure and normalize their muscle tonus.
Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program. It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data.
XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
Electronic Health Records
MitosEHR (Electronic Health Records) is a Open source Web-Based Software for: Medic Practice management Electronic Medical Records Prescription writing and medical billing application And it can be installed on the following systems: Unix-like systems (Linux, UNIX, and BSD systems) Microsoft systems Mac OS X And other platforms that can run Apache Web server, MySQL
MoodTrack keeps track of medications administered, medication changes, user defined observations, notes and events that affect mood and behavior.
The OBO-Annotator is a semantic NLP tool that is designed to give its end-users a great deal of flexibility to combine any number of OBO ontologies from the OBO foundry regardless of their format and use them to annotate text-bases.
HIPAA compliant medical billing, scheduling, and account management system. Integrated with x12 standard electronic transactions, OpenBilling XML standards, and hcfa-1500 legacy support. Complete cross platform performance with java 2 standards.
Pennington Firm OpenEMR - Practice management, electronic medical record (EMR), prescription writing and medical billing software licensed under the GPL. OpenEMR supports ANSI X12 medical billing, HL7, and customization of the open source EHR.
SPRING is a real-time surgical simulation system with soft-tissue modeling and networked haptics. SPRING is cross-platform (Unix, Windows, and OS X.) Written in C++ with OpenGL, SPRING reads many common 3-D file formats and supports parallel processing.
TIDAL is a collection of data acquisition and processing tools for research in respiratory physiology. It provides a high-level language for specifying experimental protocols and required computations.
Two Dimensional NOesy simulation (TDN) implementents an algorithm that creates a time-domain 2D NOesy spectrum. TDN does not calculated the nOe peak intensities, Therefore, you will need the CORMA (Complete nuclear Overhauser Relaxation Matrices).
froi (FS-FAST ROI) is a suite of Perl scripts and modules to provide easy slice-, volume-, and surface-based ROI analysis of functional MRI (fMRI) data analyzed by FS-FAST and Freesurfer (http://surfer.nmr.mgh.harvard.edu).