Metadata-Version: 1.0
Name: mosaic-nist
Version: 1.0
Summary: A Modular Single-Molecule Analysis Interface.
Home-page: http://pypi.python.org/pypi/mosaic-nist/
Author: Arvind Balijepalli
Author-email: arvind.balijepalli@nist.gov
License: LICENSE.txt
Description: MOSAIC: A modular single-molecule analysis interface
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        MOSAIC is a single molecule analysis toolbox that automatically decodes multi-state nanopore data. By modeling the nanopore system with an equivalent circuit, MOSAIC leverages the transient response of a molecule entering the channel to quantify pore-molecule interactions. In contrast to existing techniques such as ionic current thresholding or Viterbi decoding, this technique allows the estimation of short-lived transient events that are otherwise not analyzed.
        
        Nanometer-scale pores have demonstrated potential use in biotechnology applications, including DNA sequencing, single-molecule force spectroscopy, and single-molecule mass spectrometry. The data modeling and analysis methods implemented in MOSAIC allow for dramatic improvements in the quantification of molecular interactions with the channel in each of these applications.
        
        **If you use MOSAIC in your work, please cite:**
        
        A. Balijepalli, J., Ettedgui, A. T. Cornio, J. W. F. Robertson K. P. Cheung, J. J. Kasianowicz & C. Vaz, "`Quantifying Short-Lived Events in Multistate Ionic Current Measurements. <http://pubs.acs.org/doi/abs/10.1021/nn405761y>`_" *ACS Nano* 2014, **8**, 1547–1553.
        
        
        
        Change Log
        =================================
        
        **v1.0**
        
        - Fixed a bug in multistate code that constrained the RC constant resulting in systematic fitting errors (pull request #25).
        - Updated multistate to include a separate RC constant for each state, to be consistent with functional form in Balijepalli et al., ACS Nano 2014.
        - Misc bug fixes in tsvTrajIO parsing.
        - The number of states is saved to the MDIO DB for multistate analysis (issue #26).
        - Created a new package on PyPI (mosaic-nist) to allow installation with setuptools.
        - [GUI] Updated help link to point to Sphinx documentation on Github.
        
        **v1.0b3.2**
        
        - [GUI] Misc bug fixes
        - [Addons] Added code to import MOSAIC output into Matlab (pull requests #18 and #20)
        - [Addons] Updated Mathematica addons to automatically decode multi-state data.
        - Resolves issues #16 and #22
        
        **v1.0b3.1**
        
        - [GUI] Added multiState support to mosaicgui.
        - Analysis information such as alogirthms used, data type, etc. are now stored within a MDIO database.
        - [GUI] Autocomplete in mosaicgui only suggests database columns that are valid when used in a query.
        - Reorganized Mathematica addon code.
        
        
        **v1.0b3**
        
        - Fixed a bug that prevented events longer than ~700 data points from being correctly analyzed.
        - Fixed a problem that prevented event data from being correctly padded before analysis.
        - Resolves #2. TrajIO settings are now read in from the settings file.
        - [GUI] Resolves #3. Threshold entry box in GUI becomes nonresponsive when meanOpenCurr is negative.
        - [GUI] Resolves #4. Analysis fails when using wavletDenioseFilter from GUI.
        - [GUI] Histogram in BlockDepthViewer window can be saved to a CSV file from the File Menu.
        - Analysis log is saved to the MDIO database.
        - [GUI] ConsoleLogViwer displays the analysis log saved in the MDIO database.
        - [GUI] Added a new dialog that displays an experimental feature warning wavelet-based denoising is selected.
        - Updated error codes reported in database to be more descriptive of the failure.
        - Improved and expanded unit testing framework.
        - Moved installation and testing to setuptools.
        
        
        **v1.0b2**
        
        - [GUI] Fixed threshold update error from 1.0b1.
        - Considerably improved automatic open channel state detection.
        - The default settings string is now included within the source code.
        - Implemented new top-level class ConvertToCSV that allows conversion of data read by any TrajIO object to comma separated files.
        - Updated build system and unit testing framework.
        - [GUI] Misc UI updates.
        
        
        **v1.0b1**
        
        - [GUI] Added a menu option to save a settings file prior to starting the analysis.
        - [GUI] Current threshold is now defined by an ionic current. The trajectory viewer displays the deviation of the threshold from the mean current.
        - Analysis settings are saved within the analysissettings table of the sqlite database. When an analysis database is loaded into the GUI, settings are parsed from within the database.
        - When an analysis file is loaded, widgets in the main window remain enabled. This allows starting a new analysis run with the current settings.
        - [GUI] Implemented an analysis log viewer that displays the event processing log.
        - [GUI] Initial commit of wavelets based peak detection in blockdepthview.
        - [GUI] Added all points histogram to trajectory viewer. 
        - *Known Issues:* Selecting automatic baseline detection can sometimes cause the threshold in the trajectory viewer to change. Moving the slider will cause the settings and trajectory windows to synchronize.
        
Platform: UNKNOWN
