Computational Biophysics
Software
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.
DL-SCAN
The software, user manual, and sample data can be found
Related paper: Bhattarai A, Meyer J, Petersilie L, Shah S I, Leu L, Rose C R, Ullah G. A Deep Learning-Based
Segmentation of Cells and Analysis (DL-SCAN),
PunctaSpecks
The software, user manual, and sample data can be found
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,
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,
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,
Other open source codes
Adeoye T, Shah S I, Demuro A, Rabson D A, and Ullah G. Upregulated Ca2+ release from
the endoplasmic reticulum leads to impaired presynaptic function in Alzheimer鈥檚 disease,
Code and instructions for this paper can be found
H眉bel N, Mahshid S Hosseini-Zare, Ziburkus J, and Ullah G. The role of glutamate in
neuronal ion homeostasis: a case study of spreading depolarization,
Code reproducing key results is archieved with the paper in
H眉bel N and Ullah G. Astrocytes swell more than neurons during prolonged depolarizations in anions-dependent manner,
H眉bel N, Andrew DR, and Ullah G. Large extracellular space leads to neuronal susceptibility to ischemic injury in Na+/K+ pumps-dependent manner,
Ullah G, Demuro A, Parker I, and Pearson JE. Analyzing and modeling the kinetics of amyloid beta pores associated with Alzheimer鈥檚 disease pathology,
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,
Code for this paper can be found
Wei Y, Ullah G, Schiff SJ, Unification of neuronal spikes, seizures, and spreading depression,
Bruno W, Ullah G, Mak DOD, and Pearson JE. Automated maximum likelihood separation of signal from baseline in noisy quantal data, .
Ullah G, Bruno W, and Pearson JE. Simplification of reversible Markov chains by removal
of states with low equilibrium occupancy,
Code for this paper can be found
Ullah G and Schiff SJ. Assimilating seizure dynamics,
Code for this paper can be found
Ullah G and Schiff SJ. Tracking and control of neuronal Hodgkin-Huxley dynamics,
Code for this paper can be found
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.
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.