Package qubx
source code
QUB Express - an interactive simulator of ion channel
current
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Source zip
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git repository:
http://lambda.med.buffalo.edu/qub-express.git
Prerequisites:
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Python >= 2.5
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pygtk, pycairo
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numpy, scipy
Compiled libraries:
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qubfast -- simulation and other heavy math; wrapped
in qubx.fast.
To run:
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Compile the libraries and place them where they will be found. (In
Windows: the folder containing qubx\; in Unix: /usr/lib or
$LD_LIBRARY_PATH)
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cd qub-express (the folder containing qubx\)
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(unix only:) export QUBX_PATH=.
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python -m qubx.express
The main entry point is in qubx.express. Class qubx.express.App creates the main window, of class qubx.express.Cube.
Copyright 2008-2014 Research Foundation State University of New York
This file is part of QUB Express.
QUB Express 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.
QUB Express 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,
named LICENSE.txt, in the QUB Express program directory. If not, see
<http://www.gnu.org/licenses/>.
- qubx.GTK: General-purpose UI components.
- qubx.accept: Functions for parsing strings into various data types, ranging from
string (a no-op) to a system of differential equations.
- qubx.acquirefile
- qubx.chop: Build selection lists.
- qubx.crash_rep: Crash detection and reporting
- qubx.cube: Components for the top level of the QUB Express or Fitness.
- qubx.dataGTK: Specialized scope for qub data.
- qubx.data_abf: Reads Axon binary data using ABFFIO.dll, if available.
- qubx.data_acquire: Reads .acquire data files.
- qubx.data_fit: Curve fitting tool acting on data window.
- qubx.data_gpatch: Reads .gpatch data files.
- qubx.data_ibw
- qubx.data_panel: Components for the top level of the QUB Express or Fitness.
- qubx.data_pulse: Reads Pulse and Patchmaster files.
- qubx.data_tacidl: Reads idealized data from TacFit table of transitions, saved with
extension .tacidl.
- qubx.data_types: Data file structure and i/o.
- qubx.date: Date/time conversion between module datetime, Delphi, and
"HH:MM:SS".
- qubx.express: Top level of the application QUB Express.
- qubx.extract: Panel to chop, process and save extracts of data.
- qubx.faces: Container widgets.
- qubx.fast: Interface to the qubfast library.
- qubx.fit: Curve Fitting.
- qubx.fit_robot: Background thread to operate qubx.fit.
- qubx.fit_robots: Background thread to operate qubx.fit.
- qubx.fit_space: Widget to display and control qubx.fit_robot.
- qubx.fitness: Top level of the application QUB Express.
- qubx.global_namespace: Container for global namespace, used by qubx.pyenv.env; import and
define names in qub-express/global_names.py
- qubx.hill: Auto-fit of Hill equation.
- qubx.hist: Histograms panel with amplitude histogram.
- qubx.http_post
- qubx.ideal: Interface to the qubidl module (in the qubfast library) for
efficiently handling sequences of dwells.
- qubx.ideal_tools: Panel to modify idealized data.
- qubx.idealize: Provides a visual panel (qubx.faces.Face) to idealize single-molecule data.
- qubx.kalman: Kalman filter panel for Data.
- qubx.list_average: Panel with live average of selections in active List.
- qubx.list_figure: Panel which generates high-quality figures of the selections in
active List.
- qubx.maths: Mathematical utilities.
- qubx.model: Hidden Markov model and math.
- qubx.modelGTK: Panel which shows an open qub model.
- qubx.model_charts: Model visualizations and matrices.
- qubx.model_constraints: System of linear constraints for constrained optimization.
- qubx.model_link: "Modeling Tools" menu: "Link to this model
online"
- qubx.modeling_utils: QubX.Modeling.Utils panel; hosts a registry of generic
model/data-based optimizers, and sub-panels which can use them.
- qubx.models_panel: Components for the top level of the QUB Express.
- qubx.notebook: Base classes and registry for notebook figure export.
- qubx.notebookGTK: GUI components to control notebook export of figures.
- qubx.notebook_qtiplot: Notebook plugin to send figures to QtiPlot
- qubx.notebook_scidavis: plugin to send figures to SciDAVis
- qubx.optimize: Globally available pluggable optimizer framework.
- qubx.optimizeGTK: GUI configuration for globally available pluggable optimizers.
- qubx.pyenv: Support for user scripting, including
- qubx.pyenvGTK: GUI support for user scripting.
- qubx.remote_ctl: Gives outside processes access to the Python interpreter.
- qubx.scope: 2d data display with oscilloscope-inspired controls.
- qubx.script_seq: GUI support for user scripting.
- qubx.select_charts: Charts and stats
- qubx.settings: Preferences and presets management.
- qubx.settingsGTK: pygtk GUI for qubx.settings.
- qubx.simulate: Panel to control and orchestrate simulation and protocols.
- qubx.simulation_protocol: Simulation protocol waveforms, same as
QuB/PythonScripts/AcquisitionProtocol.
- qubx.singleInstance: Passes command-line args from duplicate processes to the primary
one.
- qubx.sock: Network base classes.
- qubx.sorted_collection: Sequence sorted by a key function.
- qubx.spectrum
- qubx.splash_main: Components for the top level of the QUB Express or Fitness.
- qubx.stimulus: Panel to idealize stimulus signal(s).
- qubx.table: Classes to represent tabular information.
- qubx.tableGTK: GTK components for qubx.table.
- qubx.table_panel: Components for the top level of the QUB Express or Fitness.
- qubx.table_tree: Storage and retrieval of qubx.table info into qubx.tree format.
- qubx.task: Thread management and multiprocessing.
- qubx.tifffile: Read and write image data from and to TIFF files.
- qubx.toolspace: Widget with switchable mouse controllers (Tools) and transparent
overlays and layers.
- qubx.tree: Classes for reading and writing all QuB binary files.
- qubx.treeGTK: pygtk support for qubtree: clipboard and visual editing.
- qubx.tree_native: Wrapper for qubtree shared library (gui mainly uses numpy variant
from qubx.tree); this is the 'native' flavor, unless you have the
obsolete _qubtree extension library.
- qubx.trials: Components for the managing and visualizing qubx.trialset.TrialSets.
- qubx.trialset: A trialset is a qubx.table.SimpleTable with one stored model per
row.
- qubx.ulp_diff
- qubx.undo: Unlimited undo/redo.
- qubx.util_panels: Components for the top level of the QUB Express or Fitness.
- qubx.util_types: General-purpose types and utilities.
- qubx.vcheck_client: Check over network for updates, invoked by qubx.cube.Cube (main
window aka QubX) shortly after startup, and daily thereafter.
- qubx.workflow: GUI support for user scripting.
- qubx.xmlt: XML tools; so far just conversion between object attributes and
xml.
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