Metadata-Version: 2.1
Name: RLNEK
Version: 1.0.1
Summary: RLNEK is so cool
Home-page: https://github.com/zrollins/RLNEK
Author: Allison Chan & Zachary Rollins
Author-email: awlchan@ucdavis.edu
License: GNU
Description: Corresponding Manuscript:
        "Receptor-Ligand Non-Equilibrium Kinetics (RLNEK) 1.0: An Integrated Trackmate Laminar Flow Chamber Analysis"
        
        Trackmate Dependencies:
        >=ImageJ 2.3.0/1.53f51
        >=Java 1.8.0_301 [64-bit]
        >=Trackmate v7.4.0
        
        RLNEK Dependencies:
        >= Python 3.7
        >= pandas 1.3.5
        >= numpy 1.22.0
        >= scipy 1.7.3
        >= matplotlib 3.5.1
        
        RLNEK Modules:
        Module 0A - convert flow rate to applied tether/tensile force
        Module 0B - determine non-specific bond lifetime
        Module 0C - determine if coating concentration/site density range meets single-molecule criteria
        Module 1 - determine Nb/NT & koff @ various flow rates, coating concentrations
        NT Optimization - optimize NT values for given flow rate across various site densities (precursor to Module 2)
        Module 2 - determine Nb/NT, koff, k+, & kin @ various flow rates, site densities
        
        Tips:
        1. Please read manuscript and corresponding User Guide to understand experimental parameters and data necessary to perform calculations.
        2. In previous versions of Trackmate, the files are outputted in different formats. Ensure that Trackmate "tracks" and "spots" files are formatted correctly (e.g., in the "spots" file, particleIDS are listed in numerical order of trackIDs & numerical order of frames). Use provided test files as a reference.
        3. All modules can handle replicates for a given condition. Please see test folders for implementation.
        4. Collect Receptor-Ligand Non-Equilibrium Kinetics.
        
        Appendix:
        Nb = number of cells/spheres bound
        NT = total number of cells/spheres to cross field of view
        Nb/NT = capture efficiency
        koff = force-dependent dissociation rate (1/ bond lifetime)
        k+ = effective on rate of cell/spheres (includes diffusive & kinetic timescales)
        kin = intrinsic on rate of receptor-ligand pair (assumed constant)
        ***Extension of variable names/descriptions: "appendix.pdf"***
        
        Digitized Data:
        Data that was digitized from previous manuscripts and used in this RLNEK manuscript is provided in the "Digitized_Data" folder. 
        
        Copyright Notice:
        Copyright 2021-2022 Allison Chan, Zachary A Rollins, Venktesh S. Shirure, Steven C. George, and The Regents of the University of California
        
        License Notice:
        This file is part of RLNEK.
        
        RLNEK is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
        
        RLNEK is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
        
        You should have received a copy of the GNU General Public License along with RLNEK. If not, see <https://www.gnu.org/licenses/>.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
