Open Source C 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

This software accompanies the textbook "Quantum Wells, Wires and Dots" (4th Edition), Paul Harrison and Alex Valavanis, Wiley, Chichester (2015). It is adapted (by the same authors) from code that was originally supplied on a CD with the first edition of the book [1] and is now made available under the GPL3 license. In brief, we encourage everyone to use the software in your studies and research, to study and modify the source-code and to share it widely. However, you are not permitted to include any of our code in a closed-source project.

Genomecomb is a package for the analysis of complete genome data. It can be used to compare, annotate and especially filter the results of complete genome sequencing.

AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA was developed by Ton Rullmann and Jurgen Doreleijers in the NMR Spectroscopy Department, Utrecht.

ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat.

Clustering project. It allows you to hot plug agent (treating tasks) to a known controller (dispatching tasks on agents according filters). Tasks are submitted by the client. No need to install extra stuff on computers treating tasks, just the agent.

MBDyn_sim_suite is a collection of free pre&post-processing tools and simulation models for the open-source multi-body analysis software MBDyn forming a general purpose simulation environment for structural dynamics with an emphasis on wind turbines.

SIPeS - Site Identification from Paired-end Sequencing

The Anteater moves to a new site, available under tranalyzer.com. This tool generates extended netflow-like flow/packet statistics from large pcap files or ethernet interfaces. It is intended to serve as a tool for IT troubleshooting, encrypted traffic mining, AI preprocessing and forensic analysis. A packet based "tshark mode" for detailed header and content inspection is improved for troubleshooting and security purposes. Flow based and packet based content inspection and extraction, better reporting, geo and organisation labeling, forensics support and encapsulation support such as ethip, teredo, anything in anything, SCTP, etc are new features of the 0.8.14. Checkout the tutorials: https://www.tranalyzer.com/tutorials