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relax 3.3.8 GPL (GNU General Public License)

An Open Source software designed for the study of molecular dynamics on Linux OSes

Aestimo 1.0 GPL v3

An Open Source 1-dimensional self-consistent Schrödinger-Poisson solver for Linux

Aseba 1.3.3 LGPL (GNU Lesser General Public License)

An Open Source, event-based robot framework for efficiently and easily programming robots

graph-tool 2.2.35 GPL (GNU General Public License)

An Open Source module designed to help users with statistical analysis of graphs

BOINC 7.2.42 GPL (GNU General Public License)

An Open Source software to donate computing power to scientific research projects

Yade 1.12.0 GPL (GNU General Public License)

This is Yet Another Dynamic Engine designed especially for discrete numerical models

Where is M13? 2.3 Freeware

A free and multi-platform app that isplays deep sky objects within and around the Galaxy

VisTrails 2.1.4 GPL (GNU General Public License)

An Open Source and cross-platform scientific workflow management system written in Qt

Avogadro2 0.7.2 BSD License

An Open Source advanced molecular visualizer and editor used in chemistry and bioinformatics

F-Engrave 1.44 GPL v3

An Open Source text to g-code software that runs on Linux, Mac and Windows platforms