Computational Biophysics
@ USF Physics




The following three software were developed for processing and analyzing data produced by fluorescence microscopy and electrophysiology. These programs are open source, easy to use, and provide extensive information about data from these experimental techniques. Users are welcome to use these software and customize the open source codes provided for their own research. We request that our papers be cited in case the the user finds these algorithms useful.

PunctaSpecks

The software, user manual, and sample data can be found Here
Related paper: Shah S I, Ong H L, Demuro A, and Ullah G. PunctaSpecks: A Tool for Automated Detection, Tracking, and Analysis of Multiple Types of Fluorescently Labeled Biomolecules, Cell Calcium (2020) 102224.

CellSpecks

The software, code, and user manual are archieved with the paper in the Supporting Material on the Biophysical Journal website.
Related paper:Shah S I, Smith M, Swaminathan D, Parker I, Ullah G, Demuro A. CellSpecks: A Software for Automated Detection and Analysis of Calcium Channels in Live Cells, Biophysical Journal (2018) 115(11) 2141-2151.

TraceSpecks

The software, code, and user manual are archieved with the paper in the Supporting Material on the Biophysical Journal website.
Related paper:Shah S I, Demuro A, Mak DOD, Parker I, Pearson JE, and Ullah G. TraceSpecks: a software for automated idealization of noisy patch-clamp and imaging data, Biophysical Journal, (2018) 115(1) 9-21.





Other open source codes


Hübel N, Mahshid S Hosseini-Zare, Ziburkus J, and Ullah G. The role of glutamate in neuronal ion homeostasis: a case study of spreading depolarization, PLoS Computational Biology (2017) 13(10): e1005804
Code reproducing key results is archieved with the paper in Supporting Information Text 2.

Hübel N and Ullah G. Astrocytes swell more than neurons during prolonged depolarizations in anions-dependent manner, PLoS One, (2016) 11(3):e0147060
Code for this paper can be found Here

Hübel N, Andrew DR, and Ullah G. Large extracellular space leads to neuronal susceptibility to ischemic injury in Na+/K+ pumps-dependent manner, Journal of Computational Neuroscience, (2016) 40(2) 177-192
Code for this paper can be found Here

Ullah G, Demuro A, Parker I, and Pearson JE. Analyzing and modeling the kinetics of amyloid beta pores associated with Alzheimer’s disease pathology, PLoS ONE 10(9) (2015) e0137357.
Code for this paper can be found Here

Ullah G, Wei Y, Dahlem MA, Wechselberger M, Schiff SJ. The role of cell volume in the dynamics of seizure, spreading depression, and anoxic depolarization, PLoS Computational Biology, 11(8) (2015) e1004414.
Code for this paper can be found here

Wei Y, Ullah G, Schiff SJ, Unification of neuronal spikes, seizures, and spreading depression, Journal of Neuroscience, 34(35) (2014) 11733.
Code for this paper can be found here

Bruno W, Ullah G, Mak DOD, and Pearson JE. Automated maximum likelihood separation of signal from baseline in noisy quantal data, Biophysical Journal, 105 (2013) 68..
Code for this paper can be found here

Ullah G, Bruno W, and Pearson JE. Simplification of reversible Markov chains by removal of states with low equilibrium occupancy, Journal of Theoretical Biology, 311 (2012) 117.
Code for this paper can be found Here

Ullah G and Schiff SJ. Assimilating seizure dynamics, PLoS Computational Biology, 6 (2010), e1000776.
Code for this paper can be found Here

Ullah G and Schiff SJ. Tracking and control of neuronal Hodgkin-Huxley dynamics, Physical Review E, 79, 040901(R) (2009).
Code for this paper can be found Here

Ullah G, Cressman JR, Barreto E, and Schiff SJ. The influence of sodium and potassium dynamics on excitability, seizures, and the stability of persistent states: II. Network and glial dynamics, Journal of Computational Neuroscience, 26 (2009) 171.
Code for this paper can be found here

Cressman JR, Ullah G, Ziburkus J, Schiff SJ, and Barreto E. The influence of sodium and potassium dynamics on excitability, seizures, and the stability of persistent states: I. Single neuron dynamics, Journal of Computational Neuroscience, 26 (2009) 159.
Code for this paper can be found here