Open Source Groovy Scientific/Engineering Software

OpenMRS is a community-developed, open source, enterprise electronic medical record system. Our mission is to improve health care delivery in resource-constrained environments by coordinating a global community to creates and support this software.

TXM is a free and open-source cross-platform Unicode & XML based text analysis environment and graphical client, supporting Windows, Linux and Mac OS X. It can also be used online as a J2EE standard compliant web portal (GWT based) with access control built in. DOWNLOAD LATEST VERSION OF TXM : http://textometrie.ens-lyon.fr/spip.php?rubrique61&lang=en TXM offers a comprehensive range of analysis tools (concordances, collocate search, frequency lists, etc.) based on the powerfull CQP full text search engine (http://cwb.sourceforge.net) and a range of statistical functions (factorial analysis, classification, cooccurrency analysis, etc.) based on R packages (http://www.r-project.org). Read the scientific background at the Textométrie project web site http://textometrie.ens-lyon.fr/?lang=en. Read a full description at the TEI Tools wiki http://wiki.tei-c.org/index.php/TXM.

JLink lets users author flow charts based on ISO 5807 and IBM standards. Developers can use JLink to add flowcharts to applications, serve a flow chart over the web in PDF or PNG, or dynamically create a flowchart with Javascript, Python or Ruby scripts

The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.

BOWS is a generic system based on Web Services which allows programmatic access to applications running on HPC clusters. BOWS allows incorporation of several independent applications since programmers can install them in HPC clusters in any programming language. The lonely requirement is to write a script named “arrow” which calls BOWS back-end services periodically in order to check for new processes and their required parameters. If a new process is found, the “arrow” script should change the requisition status from waiting to running, run the process in the HPC cluster and, when the job is complete, call a BOWS back-end service to send the results. The results will then be available to the requestor. BOWS is called from the front-end by Web Services, therefore a program running in a simple computer can benefit of high performance computation executed elsewhere. doi:10.1186/s13104-015-1190-0

CLADlims is a wed based laboratory information and data management system for animals and their measurement records. It is designed to track the weight and tumour growth of the animals, visualize the data, compare data, inform the user for any alarming measurements as well as keep any other data related to animals, cages and experiments. Users can submit the data directly from the measuring facilities to the database using a mobile device (tablet or phone) or any computer with a modern web browser. Multiple tumours per animal can be tracked. With CLADlims you can improve efficiency by getting rid of the text files or spreadsheets and save time and money.

Combean is a Java framework for mathematical structures and optimization algorithms. Through a set of Java interfaces and JavaBeans-based config, Combean glues optimization codes together - leading to more interoperable, adaptable and flexible solutions.

A Controlled Language Programming (CLP) compiler, runtime engine, and development IDE for writing software in a natural (but somewhat restricted) language that clearly represents the real world concerns and maps to a 3GL (Java/Groovy) for execution.

Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.

ELIA(Eyegaze Language Integration Analysis) supports the analysis of eye-tracking data for studies in language processing. ELIA eases early analysis of data to enable iterative development of experiments in response to spoken language.

An Expert Search System for Enterprise Search based on the Information Retrieval Vector Space Model. Our model builds a weighted profile for each candidate and keeps all the documents, thus allowing to retrieve both people and documents together.

Web-based editor for the Gateway Description Language (GDL).

The GIS Metadata Manager is a simple Java-based desktop application to manage files from geographic information systems (GIS) in a specified directory by grouping files into records, adding metadata and searching the metadata to find files.

This is a collection of tools for IEEE 1516 HLA FOM (FDD) files, including a fom-to-html converter with cross reference and minimal validation.

Identifiers.org is a system providing resolvable and persistent identifiers, in the form of URIs, used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. The resolving services of Identifiers.org rely on the information stored in the MIRIAM Registry.

IRSA is a toolkit for Information Retrieval Service Assessment. It builds upon the Grails Web Framework and is developed at GESIS. It implements two main functionalities: (1) A number of showcases that show the implemented services like a so-called Search Term Recommender and different science-model based ranking mechanisms and (2) an IR assessment module that let's one do an interactive evaluation of the retrieval services. All implemented services are available via well-documented RESTful API. This toolkit is distributed under an Apache License 2.0.

this is a small project which provides several mathematical function useful for a chemist or somebody working with mass specs. The goal is to provide several cuda and c based functions which can be easily accessed using java, groovy and python.

The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.

Maui is the Maltcms User Interface, a rich client application for Chromatography-Mass Spectrometry and related research areas.

Mircrogrid market is a proof-of-concept implementation of a combinatorial heat and power double auction exchange. With this platform energy consumers and producers can buy or sell heat and power resources on demand for certain times of the day.

Myrtle is a simple programmable spreadsheet and statistical analysis software specifically designed for learning statistics. It provides the standard spreadsheet functionality one would expect like multiple tabbed sheets, relative and absolute row and column referencing in formulas, and a large catalog of built-in functions. Functions specific to logic and computer science, mathematics, probability, and statistics are available. Student's can easily create, customize, and update plots and graphical summaries of their analyses. Myrtle offers a unique bookmarking facility which allows students to create and reuse named references to their favorite cell ranges. This can help students focus attention on the important relationships among particular rows or columns of data. Myrtle's graphics and reporting features allow students to report back to their instructors their mastery of course content.

This is a pipeline that is used to store an EST or Genome assembly information including reads and their alignment in a mysql database. Further more, it provides a set of scripts to mine SNPs and other statistics from the assembly.

Nomin is a mapping engine for the Java platform. It provides abilities to transform object trees using declarative mapping rules. Main features are no XML configuration, intuitively looking mapping, using arbitrary expressions/method invocations.

Onco-STS is a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments. The sample tracking system for oncogenomic studies (Onco-STS) is designed to store these data and make them easily accessible to the researchers who work with the samples. The system is a web application, which includes a database and a front-end web page that allows the remote access, submission and updating of the sample data in the database.