Publication code - Zenodo

All codes to regenerate data/ML experiments for the following paper:

---

Using mechanistic models and machine learning to design single-color multiplexed Nascent Chain Tracking experiments

---

William S. Raymond¹, Sadaf Ghaffari², Luis U. Aguilera³, Eric M. Ron¹, Tatsuya Morisaki⁴, Zachary R. Fox^1,5, Michael P. May¹, and Timothy J. Stasevich^4,6, Brian Munsky^1,3,*

1. School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
2. Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
3. Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA
4. Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
5. Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
6. Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
   

For questions about the codes, please contact: wsraymon@rams.colostate.edu, Luis.aguilera@colostate.edu and brian.munsky@colostate.edu

---

Several large movie files are omitted that are used to make Figure 9 and Figure 3, these can be provided upon request.

• multiplexing_7_1.tif
• P300_KDM5B_base_experiment/base_experiment0.tif
• P300_KDM5B_base_experiment/base_experiment1.tif
• P300_KDM5B_base_experiment/base_experiment2.tif

Publication code

All codes to regenerate data/ML experiments for the following paper:

---

Using mechanistic models and machine learning to design single-color multiplexed Nascent Chain Tracking experiments

---

William S. Raymond¹, Sadaf Ghaffari², Luis U. Aguilera³, Eric M. Ron¹, Tatsuya Morisaki⁴, Zachary R. Fox^1,5, Michael P. May¹, and Timothy J. Stasevich^4,6, Brian Munsky^1,3,*

1. School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
2. Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
3. Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA
4. Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
5. Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
6. Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
   

For questions about the codes, please contact: wsraymon@rams.colostate.edu, Luis.aguilera@colostate.edu and brian.munsky@colostate.edu

---

Several large movie files are omitted that are used to make Figure 9 and Figure 3, these can be provided upon request.

• multiplexing_7_1.tif
• P300_KDM5B_base_experiment/base_experiment0.tif
• P300_KDM5B_base_experiment/base_experiment1.tif
• P300_KDM5B_base_experiment/base_experiment2.tif