Attached in this repository are the code and data used in my doctoral thesis Assembling an Integrated Pipeline to Construct Patient-Specific Cancer Models1. Specifically, you will find:
Phenotype control example files:
- ck_example.txt -- text file for Contol Kernel example expressions
- edge_control_example.txt -- text file for edge control, can save as an M2 file
- FVS_example.py -- python file to run Feedback Vertex Set control
- node_control_example.txt -- text file for node control, can save as an M2 file
- SM_example.txt -- text file of Boolean rules for Stable Motif example
- SM_example.py -- python file to run Stable Motifs
- thesis_examples.m -- cumulative MATLAB file of examples
- thesisTC1.txt -- time-course data for EQL example
How-To files that detail how to find controls and simulate:
- Guide for Controls
- How-To Simulate
Necessary MATLAB functions and files
- MATLAB Toolbox
For files specific to the pancreatic cancer chapters, see https://github.com/drplaugher/PCC_Mutations. Some code/files have been adapted from previously published versions, and I have tried to make such notes within the relevent files.
NOTICE: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Footnotes
-
An Integrated Computational Pipeline to Construct Patient-Specific Cancer Models (2022). Daniel Plaugher, Theses and Dissertations--Mathematics. 93. https://uknowledge.uky.edu/math_etds/93 ↩