The software contained is licensed to you under the GNU General Public License Version 3. It basically enables you to do whatever you want with the software if you do not re-distribute it to others in any form. It also enables you to re-distribute to others, without further consent of the original authors; however, several obligations need to be fulfilled as explained in the license.
Often there exist several misconceptions about free software and its licenses among researchers. Therefore we would like to clarify:
- If you do not share the source code or your modified version of it with others, there is no limitation on your use of this software. There is no obligation put on you whatsoever.
- it is perfectly fine to incorporate any results obtained with the software in your publications. We would appreciate if you would give the appropriate citation.
It is also fine to combine the software with any other pieces you have from whatever source. Just make sure to not distribute the resulting sources or binaries to others (or see the next point).
If you want to share the software with others, or publish it, you need to follow some easy rules as outlined in the license. A typical scenario is to put the source code online alongside your paper. You are allowed to publish the software as long as it is done under the same, or a compatible free software license. All you need to do is preserve the original copyright notices, give reference to the original software, state what changes you made and provide the source code to the receiving party. See the license itself for the details.
You retain the copyright on any change you make to the software. Free software does not mean you have to give back, or give up ownership of your own work. However, contributing back to the project is in the interest of you and your fellow researchers in the field.