Home / Content / STATPHYSBIO / Publications+Code

Pressé Lab Publications/Code

Code Availability

Code for our projects are accessible on our lab Github.

In Review

(*Corresponding author)

2023

2022

Our code as well as the data used to generate publication figures are available here.

Our code is available for download.

Our code is available for download, as well as the data used to generate publication figures.

Our code is available for download on Zenodo along with the data sets used to generate publication figures.

See Nature Computational Science news & views article by Jean Baptiste Masson about our work.

Our code is available for download along with the data sets used to generate publication figures..

2021

          See ASU News for a news story covering our work by James Klemaszewski.

          Our code is now available for download including all the files to regenerate the publication figures

           and analyzed experimental data sets.

         Our code is now available for download including all the files to regenerate the publication figures

          and analyzed data sets.

        Our code is now available for download including all the files to regenerate the publication figures

          and analyzed experimental data sets.

2020

          Our code is now available for download.

          Our code is now available for download.

           Our  code is now available for download.

           See  ASU Now for a news story about our work.

          Our code is now available for download.

2019

        Our Confocal analysis code assuming a single diffusive species and Multi-diffusive species confocal analysis code are now available for download.

       See   Springer Nature

       See  Phys.org

       See  Science Daily

       See  Nanowerk      

       See   7th Space Family Portal

       See   Photonics.com   

            Our analysis code is now available for download.

            Our code is now available for download.

           Our  SI available for download.

          Our FRET analysis code is now available for download.

2018 

           Our XL-ICON analysis code is now available for download.

2017

           See Biophysical Journal Research Highlight.
           See Welt.
           See Zeit.
           See Bild.
           See Science Direct.
           See Spiegel.
           See SciShow with 270k+ views.

           Our ICON analysis code is now available for download.

           Our iHMM analysis code is now available for download.

2016

           Our Photobleaching analysis code is now available for download with documentation. Also available

           on Github .

2015

 See Comment on "Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions" by R.Golestanian -- arXiv response to criticism of our work (cited therein).
Our Python analysis code is now available for download with documentation.
An APS Story is written about our work.
Our Mathematica analysis code is now available for download.

 

2014

2013

See Tsallis' rebuttal on the arXiv to our PRL. Our PRL plainly shows that Tsallis' model inference prescription imposes structure in models that are not justified from the data. The rebuttal simply asserts that our starting axioms (due to Shore & Johnson) are not applicable to out-of-equilibrium systems (where it is qualitatively argued that the Tsallis entropy applies). Actually, this is a logical error. The axioms of Shore & Johnson have no notion of equilibrium. The PRL and rebuttal stand on their own. We will probably not publish a reply unless Tsallis' rebuttal manages to get published in a refereed journal (unlikely). We add that Tsallis entropy is not a small deal. The original paper by Tsallis has been cited about 5000 times and Tsallis (who lives in Brazil) is the single most cited author in South America. We are focused on developing new, and in many ways stronger, ideas which we hope will help focus the community's attention on principled inference methods that work.

"Extracting conformational memory from single-molecule kinetic data"
Steve Pressé*, Julian Lee, Ken A. Dill, J. Phys. Chem. B, (2013).

2012 and earlier

See CV for even earlier Ph.D. and postdoc work...