Open Source Flex Scientific/Engineering Software

Xschem is a schematic capture program, it allows to create a hierarchical representation of circuits with a top down approach . By focusing on interconnections, hierarchy and properties a complex system (IC) can be described in terms of simpler building blocks. A VHDL, Verilog or Spice netlist can be generated from the drawn schematic, allowing the simulation of the circuit. Key feature of the program is its drawing engine written in C and using directly the Xlib drawing primitives; this gives top speed performance, even on very big circuits. I have succesfully managed to simulate complete VLSI projects with this tool, both digital (Verilog / VHDL) and analog (Spice). Schematics can be printed in SVG, PNG, PDF, formats. XSCHEM runs on Linux or other Unix-likes with Xorg server and on Windows with the Cygwin layer and required tools installed. Can be found also on github: https://github.com/StefanSchippers/xschem

Our source code is now on GitHub: https://github.com/hci-gnomex/gnomex. Please refer to GitHub for the latest code. GNomEx is Genomic LIMS and Data Repository. It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. Experiment platforms supported include Illumina HiSeq, MiSeq, iScan, ABI Sanger sequencing, Affy and Agilent Microarrays, Sequenom MassArray and Bioanalyzer. GNomEx is a web application with a Flash client user interface and a Java backend that runs on Apache Tomcat. MySQL is used for the database, although any modern RDBMS can be used.

OpenAstrology is Java based Object-orientated implementation of Astrology. OpenAstrology will provide a platfrom to plug-in in the knowledge of Astrology and the derived solution will be the best real time Astrology solution

Elements is a free, open-source, cross-platform software tool for creating and editing custom weather files for building energy modeling. The goal of the project is to develop a comprehensive, integrated application suitable for handling all of the common tasks associated with weather files.

lilpM32 is a MIPS-like processor designed in Logisim, assembler program and documentation for them. Complete assembler and fully functional instruction set with I/O and subroutines features allow to write full-blown complicated programs.

BizGEO is an open source platform developed to provide a simple interface for geographical data collection and data storage. BizGEO is integrated with a standard open source map server (GeoServer) to form an integrated GIS data collection suite. BizGEO is made up of three main components; BizGEOServer which is a facility for managing data by organising them in projects; BizGEOApp, a mobile app which is being used by the field users to collect data through set of defined forms, and GeoServer which manages and publishes the data using open standards.

ConquestWebView is a web based dicom viewer for the conquest dicom server application available from http://www.xs4all.nl/~ingenium/dicom.html. The project is written in PHP and Flex. Note that the system converts DICOM images to JPG before display.

EyeMap is a visualization and analysis tool for text reading eye movement data. It can process Unicode, proportion/non-proportion and spaced/unspaced reading materials, which supports various languages and experiment methods.

FlexGIS allows end-users to perform basic geospatial analysis in a Flash frontend, without having to be familiar with standard GIS tools. Users can combine layers on-the-fly, to create advanced data visualizations. Note: Source code has been moved to GitHub (so people can submit pull requests if they've modified code and want to share). https://github.com/rvaidya/FlexGIS

MGFp is open parser implementation for the Mascot Generic Format (MGF). It uses bison/flex to define a formal grammar and provides the necessary C++ adapter classes. The software is provided under a BSD license. Development on SF.net has ceased. You can find the project at http://kirchnerlab.github.com/libmgf/

A strong, yet minimalistic Math-oriented Programming Language (MML) providing an easy-to-use console and a command-line script interpreter, targetted towards fast calculations for extremely big numbers, and bundled with a number of math libraries.

MooGraph is an utility to produce interactive dynamical graphs from statistical data. Deliberately inspired to GapMinder, it represents the evolution of multivariate data in time by means of coloured bubbles of variable sizes on an (x,y) plot.

In randomised controlled trials, interventions may have several components. This simple program will enable you to depict any randomised trial graphically It will standardise the construction process and ensure every step is covered. For more information

Abandoned version of qbc. DOES NOT WORK properly

Fully functional scientific calculator with natural input

Semantics Visualizations enable understanding complex matters in an easy way. The research group “Semantics Visualization” is working on processing, enriching, and visualizing any kind of semantic data to provide visually discoverable information. Thereby processes of knowledge acquisition, human information retrieval, and decision making are supported by a variety of interactive visual representations. The developed visualizations do not only allow to investigate the masses amount of various semantic formats on Web, e.g. Linked- Data or Social Networks, they also enable the interactive illustration of structured data. With SemaVis we developed a technology that provides various perspectives on the semantics of information. By combining different visualization techniques users and enterprises are able to perceive various data and information characteristics. SemaVis enables a facilitate human access to the “Internet of Data”.

VarPlan is a web application to visualize and manage variants as tree like graph view. The approach is to keep the overview on hundreds of variants with their meta informations.

The Virtual Commons (http://commons.asu.edu) is an open software initiative devoted to computational experiments on collective action and resource governance and funded by Arizona State University's Center for Behavior, Institutions, and the Environment (http://cbie.asu.edu). NOTE: we've moved our development to GitHub at https://github.com/virtualcommons - please look for the latest versions there.

VisualSense was developed to serve as an analysis tool for textual and numerical data extracted from image analysis of artwork from different cultures and influences. It can be used for any kind of data respecting the format (specified in the README)

WiiGesture is a library to add gestural interaction in web-applications that are based on Adobe Flash/Flex/Air. Therefore it uses the WiiFlash service (http://wiiflash.bytearray.org/?page_id=50) to retrieve the sensor data and an internal algorithm based on template matching recognizes performed gestures in real-time. For easier gesture training, a so called WiiGesture-Learning desktop tool was developed that automatically generates gesture templates by performing gestures with at least one repetition. The result is an XML file that can be exported and included in the WiiGesture-API so that trained gestures are known to the API. For research purposes also an analysis tool was developed to compare gestures from different participants/users. We used it to identify intuitive gestures from users for certain commands. The entire work was part of my diploma thesis I wrote in 2008 at Fraunhofer IGD. The gesture recognition API was included in a number of example scenarios.

This project is in its initial stage of development. It was created as part of the iQUEST project that's funded by NSF to create online resources for middle school science classrooms.

Application to optimize DNA sequences coding protein to put in in the different organizm (f.e. human protein in E.Coli). It proposes the optimal cutting places to connect many shorter fragments into bigger one using ligaze.

A set of command-line utilities for annotating and manipulating DNA sequences in FASTA format. Generate restriction fragments, ORF's, translations, reverse complement, etc. . - and tie it all together with Unix pipes for complete virtual cloning.

talc is a terminal calculator designed with very large number support and a simple grammar. It is designed to be both scriptable and interactive.

It's a RIA project with Flex,Spring,Hibernate Integration,for improve the user experience.