eAdventure (formerly <e-Adventure>) is an authoring tool for the creation of point-and-click games, especially designed for educational purposes. eAdventure is SCORM compatible so eAdventure games can be integrated with LMS like Moodle. More info at: http://e-adventure.e-ucm.es
The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. More at http://deconseq.sourceforge.net
QuteMol is a real time, high quality molecular visualizer that offers an array of innovative visual effects. QuteMol aims at improving the clarity of rendered images and at offering a better understanding of the molecular 3D shape and spatial structure.
Generalized Radiation Observation Kit. Java toolkit (based on David Clunie's PixelMed DICOM toolkit) for extracting CT radiation dose information from DICOM image archives.
SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.
PL/FLOW is a workflow engine written in Oracle PL/SQL, implementing interfaces 1 and 2 (Process Definition and the client API) as specified by the Workflow Management Coalition. (www.wfmc.org)
The Open PI Initiative and its subprojects offer adapters, modules and tools for SAP’s integration platform SAP® NetWeaver® Process Integration (SAP® NetWeaver® PI, formerly SAP® Exchange Infrastructure).
Chemical structures database & machine learning with web services API
AMBIT offers a cheminformatics data management for chemical substances, structures and nanomaterials. Flexible structure, similarity and study queries storage, descriptor calculation and predictive models building via REST web services.User interface for creating read across assessment and generating reports, aligned with regulatory and industrial requirements. Command line applications also available. Integration with third party tools and databases.
Since 2001 CottageMed™ has been the simplest, most flexible, ruggedly dependable and HIPAA-secure Electronic Medical Records system (EMR/EHR)...with secure wireless networking, mobile support, and prescription writing on Mac and PC (& Linux client)
The aim of the BioWeka project is to add bioinformatics functionalities such as e.g. alignments to the popular machine learning framework Weka.
The project has moved to GitHub: https://github.com/pixmeo/osirix
Security Officers Management and Analysis Project (SOMAP) is all about defining security management work methods and supplying Security Officers with tools to do their job more efficient and following standards easily.
CueMol - Molecular Visualization Framework
R packages for PK/PD modeling, BE/BA, drug stability, ivivc, etc.
These R packages are developed for data analysis of PK/PD modeling, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM). They include bear, ivivc, PKfit, stab and tdm.
Open Source and data mining software
ADaMSoft is a free and Open Source Data Mining software developed in Java. It contains data management methods and it can create ready to use reports. It can read data from several sources and it can write the results in different formats.
Open-source cross-platform spectrometer device driver
SeaBreeze is a device driver library that provides an interface to select Ocean Optics spectrometers. It is written in C/C++ and builds and runs on Windows (XP/7/8), MacOSX, and Linux (x86/x64/ARM).
BioNLP-Corpora is a repository of biomedically and linguistically annotated corpora and biomedical data sources. There are many resources available in separate packages in this project.
WorldVistA EHR is based on and compatible with the U.S. Department of Veterans Affairs (VA) world renowned EHR, VistA (R). Please refer to the WorldVistA website: http://worldvista.org/Software_Download for download and installation instructions
Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.
FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013. For users' convenience, we also make FragGeneScan available at GitHub: (https://github.com/COL-IU/FragGeneScan).
iPath is providing an free and open plattform for "case based collaboration", especially designed for medical applications (telemedicine, etc). The iPath-Server package provides a sort of medical BBS to discuss/consult cases online. Additional modules
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP now is much more than the plugin so we decided to rebrand it as Next Generation Sequencing Experience Platform. NGSEP is an integrated framework for analysis of high throughput sequencing reads with several deployment alternatives for different kinds of users. The main functionality of NGSEP is the variants detector, which allows to make simultaneous discovery of SNVs, indels, and CNVs. We also provide a user interface for bowtie2, alignments sorting, merging of variants from different samples, functional annotation, filtering, format conversion, and several additional features. Note: Since we offer different distribution alternatives for different kinds of users, the quick download (green) button may not lead you to the version of the product that you need. Please visit our web page to choose the distribution of NGSEP that better suits your needs.
EDIReader parses EDI input from ANSI X12 and EDIFACT, including documents for HIPAA compliance. It supports Java JAXP/SAX XML interfaces with a custom implementation of an "XML" parser, allowing access to EDI data with XML tools.
The Tolven platform and ePHR and eCHR applications enable interoperability across electronic health records for consumers and clinicians. Using Java, EJB3, Faces, Facelets, AJAX, relational database, and LDAP for security.
FreeLIMS is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. FreeLIMS is Open Source and Free.