BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format
intracranial electrodes localization toolbox
iElectrodes is an open source toolbox to obtain intracranial electrode coordinates in a semiautomatic way with minimal user intervention. It uses MRI and CT coregistered images. It is possible to add brain parcellations and brain surfaces. It works in the native or normalized MNI space The toolbox is capable to work with ECoG (subdural grids and strips) and SEEG (depth) electrodes. In the presurgical evaluation of patients with drug resistant epilepsy is of great importance to know the intracranial electrodes coordinates and the anatomical description of these locations. Additionally, you can plan depth electrode implantation and then compare it with the real locations. Visit iElectrodes Wiki tab to learn more about the toolbox. Please report any bugs to firstname.lastname@example.org We are trying to make iElectrodes a great toolbox everyday! Thanks for your help! Additional scripts are provided to make image corregistations using SPM software.
ICD10CM ICD10PCS NDC (Drug Codes USA) LOINC
PubMed Central browser. Source code: http://github.com/dualword/dualword-pmc/
Enterprise telephony recording and retrieval system
Enterprise telephony recording and retrieval system with web based user interface. The project currently supports recording voice from VoIP SIP, Cisco Skinny (aka SCCP), raw RTP and audio sound device and runs on multiple operating systems and database systems. It can record audio from most PBX and telephony systems such as BroadWorks, Metaswitch, Asterisk, FreeSwitch, OpenSIPS, Avaya, Nortel, Mitel, Siemens, Cisco Call Manager, Cosmocom, NEC, etc... It is amongst others being used in Call Centers and Contact Centers for Quality monitoring (QM) purposes.
Analyze and visualize tours in many variations, which are recorded with a GPS device, bike-, exercise- or ergometer-computer. Some highlights: Tools are available to adjust recorded data, GPS tours can be visualized in customizable maps, ...
JasperReports Server is a powerful, yet flexible and lightweight reporting server. Generate, organize, secure, and deliver interactive reports and dashboards to users with a web based BI Platform. Available as an open source community edition download as well as a commercially licensed, enterprise-grade business intelligence solution.
OpenHospital - Hospital Information System
This application is the first of a set of software products that ISF* has developed to support the management and the activities of the St. Luke Hospital in Angal (Uganda). After that mission, the St. Luke Hospital has become only the first one of a long list of hospitals that found this software useful. All the work was realized as an open-source project using only open-source development software. * Informatici Senza Frontiere
CueMol - Molecular Visualization Framework
BioSig is a software library for processing of biomedical signals (EEG, ECG, etc.) with Matlab, Octave, C/C++ and Python. A standalone signal viewer supporting more than 30 different data formats is also provided.
(Q)SAR Model Reporting Format Inventory
In the regulatory assessment of chemicals (e.g. under REACH), Quantitative Structure Activity Models (QSAR) are playing an increasingly important role in predicting properties for hazard and risk assessment. This implies both a need to be able to identify relevant QSARs and to use them to derive estimates and/or have access to their precalculated estimates. To help meet these needs, the JRC QSAR Model Database is established and freely accessible through http://qsardb.jrc.ec.europa.eu/qmrf The QSAR Model Reporting Format (QMRF) is a harmonised template for summarising and reporting key information on QSAR models, including the results of any validation studies. The information is structured according to the OECD validation principles. Download the QMRF Editor in order to describe your models in QMRF format and send the descriptions to JRC-COMPUTOX@ec.europa.eu to have them included in the database. More at http://qmrf.sourceforge.net/
Download data from medical device interfaces in ICU & Anaesthesia
A C# .NET app to download or capture data from several medical device interfaces such as Datex AS3 S/5 Anesthesia, Philips Intellivue, GE Dash, Mindray patient monitors, GE Engstrom, Draeger (Medibus), Maquet ventilators, Fresenius Agilia syringe and volumetric pumps. Requires Visual Studio 2015, .NET 4 or Xamarin Studio to compile. Android version requires Xamarin Studio, Android SDK to compile. Support for capture from other monitors is planned in future.
Easy-to-Use business intelligence (BI) for all
Pentaho tightly couples data integration with business analytics in a modern platform that brings together IT and business users to easily access, visualize and explore all data that impacts business results. Use it as a full suite or as individual components that are accessible on-premise in the cloud or on-the-go (mobile). Pentaho Kettle enables IT and developers to access and integrate data from any source, and deliver it to your business applications, all from within an intuitive and easy to use graphical tool.
UMLS::Query is an umbrella for projects that create measures of semantic similarity for the biomedical domain. Our current project is UMLS-Interface and UMLS-Similarity. Our JBI-2007 article was based on Semantic-Similarity and Snomed-Interface.
Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
Quantum universal object system with referencing and genetics
Jack LIRE (Linked Record) is a quantum database-backed life-long text record diary with referencing (linking) between records, and a data library for life-long keeping of files such as documents, photographs, music and more. The diary records are fully searchable. Files can be mentioned in diary records to preserve memories, document knowledge and ideas, and more. Massive numbers of diary records and files can be permanently kept. A database located on one computer can be accessed from another computer across a computer network or the Internet, and multiple people can sign into and work on the same database at the same time and share the diary records, files and other objects in the database.
Reporting, Dashboarding, Analytic, Self-service BI, Ad-hoc reporting
Active Intelligence Server 2 (AIS) is a data visualization tool and fully featured reporting server which enable users from open source community to host any reports created using BIRT, Jasper and Pentaho community edition allowing organization to leverage open source technologies and enable them to use AIS as a reporting server to deploy their existing and new reports seamlessly onto AIS for secure sharing the information in different file formats and schedule to make system automation and much more. AIS comes with self-service BI capabilities enabling end users to make the data-driven decision at the right time, all with minimal IT dependency. Tightly integrated user and role management ensure correct information distribution that prevents unauthorized access to information, collaboration is ever so easy with AIS that people with no BI knowledge can start real-time collaboration in minutes. AIS 2 is also available from the website http://activeintelligence.co.uk/download
Rapid data integration framework
Java based data integration framework; can be used to transform/map/manipulate data in various formats (CSV,FIXLEN,XML,XBASE,COBOL,LOTUS, etc.); can be used standalone or embedded(as a library). Connects to RDBMS/JMS/SOAP/LDAP/S3/HTTP/FTP/ZIP/TAR.
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.
Patient vital sign simulator for medical emergency training purposes
The vital sign simulator simulates a patient monitor and is intended for use in medical emergency training simulations. In combination with a (cheap) cpr-manikin, it offers a low-cost alternative to commercial high-tech patient simulation manikins. It is used with a dual monitor system, one monitor with controls for the operator and one providing the vital signs to the trainees. Heart rate, oxygen saturation, etCO2, respiratory rate, blood pressure and various moving ecg-samples can be set and changed at any time by the operator. The trainee-side interface allows automatic/manual defibrillation, cardioversion and pacing.
NGSEP (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: The quick download (green) button will provide you the jar file for command line usage. For other usage alternatives including the Eclipse plugin, please visit the wiki (https://sourceforge.net/p/ngsep/wiki/Home/)
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.
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 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).
Document Management System and Content Management System
OpenKM is a electronic document management system and record management system EDRMS ( DMS, RMS, CMS ). It provides modern and flexible architecture that meet today's IT demands, based on open technology (Java, Tomcat, GWT, Lucene, Hibernate, Spring and jBPM), powerful and scalable multiplatform application. OpenKM is a Web 2.0 application that works with Internet Explorer, Firefox, Safari and Opera. Can be configured in major DMBS like Oracle, PostgreSQL and MySQL among others. Due to its technological architecture design, OpenKM meets the document management needs of businesses of all sizes (from SMEs to big corporations). Thanks to its elegant and intuitive interface, OpenKM transforms complex operations into easy tasks. The most relevant functions of OpenKM is the indexing of the most common types of files: text, Office, Office 2007, OpenOffice, PDF, HTML, XML, MP3, JPEG, etc. For a complete feature list take a look at http://goo.gl/au8cQy