{ "info": { "author": "Arvind Balijepalli", "author_email": "arvind.balijepalli@nist.gov", "bugtrack_url": null, "classifiers": [], "description": ".. image:: https://travis-ci.org/usnistgov/mosaic.svg?branch=devel-1.0\n :target: https://travis-ci.org/usnistgov/mosaic\n.. image:: https://badge.fury.io/gh/usnistgov%2Fmosaic.svg\n :target: https://badge.fury.io/gh/usnistgov%2Fmosaic\n \nMOSAIC: A modular single-molecule analysis interface\n=================================\n\n\nMOSAIC 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.\n\nNanometer-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.\n\n**If you use MOSAIC in your work, please cite:** `Analytical Chemistry 2016, (88) pp. 11900\u201311907 `_ and `ACS Nano 2014, (8) pp. 1547\u20131553. `_\n\n\nInstallation\n=================================\n\nPlease refer to the `Installation `_ section of the MOSAIC documentation for details on installation.\n\n\nGetting Help\n=================================\n\nFor questions and help, please join our `mailing list `_. \n\nTo subscribe:\n\n\tEmail `mosaic-request@nist.gov `_ with subject 'subscribe'\n\nTo unsubscribe:\n\n\tEmail `mosaic-request@nist.gov `_ with subject 'unsubscribe'\n\nOnce subscribed, you can send messages by emailing `mosaic@nist.gov `_.\n\n\nReporting Problems\n=================================\n\nReport problems using our `issue tracker `_ on Github.\n\n\nChange Log\n=================================\n\n**v1.3.5**\n\n- Saves raw events in database. Resolves #93.\n\n**v1.3.4**\n\n- Fixed a bug in the default settings that prevented the analysis from starting in some instances.\n\n**v1.3.3**\n\n- Added support for Chimera data files.\n- Resolves issues #92 and #95. \n\n**v1.3.2**\n\n- Fixed event partiioning bugs.\n- [GUI] UI tweaks.\n\n**v1.3.1**\n\n- Bug fix release.\n \n**v1.3**\n\n- Added a new MOSAIC examples repository that contains plotting scripts and Jupyter notebooks (https://github.com/usnistgov/mosaic-examples)\n\n- Updated Bessel fiter implementation to allow causal and non-causal filters.\n- Added the CUSUM+ algorithm (see pull requests #34, #43, #45, and #46)\n- Added the ability to read arbitrary binary files.\n- Renamed StepResponseAnalysis to ADEPT 2-state.\n- Renamed multiStateAnalysis to ADEPT.\n- CUSUM+ is now used to generate initial guesses for ADEPT\n- Streamlined unit test framework. Added new tests for CUSUM+.\n- Updated MOSAIC dependencies to include newer package versions and pandas. Run 'python setup.py mosaic_deps' to update.\n- Added a new metadata column (mdStateResTime) that saves the residence time of each state to the database. This affects ADEPT and CUSUM+.\n- Processing time per event is now saved to the database.\n- Added support for warning status codes that begin with 'w'. These codes preserve metadata in the SQLite output and are used to flag events that need closer inspection.\n- Removed mosaicgui from PyPi. 'pip install mosaic-nist' only installs command line modules. \n- Top level ConvertTrajIO supports binary and ASCII files.\n- Added Travis continous integration support.\n- [GUI] Added a binary update service for Windows and OS X.\n- [GUI] Added a table that displays fit parameters in the event viewer window.\n- [GUI] Added more descriptive fit errors.\n- [GUI] Added CUSUM+ support to MOSAIC GUI.\n- [GUI] Export SQLITE database to CSV (#56).\n- [GUI] Support for warning codes in fit event viewer.\n- [GUI] Performance optimizations.\n- [GUI] Fit window in MOSAIC GUI displays idealized pulses overlays.\n- [GUI] Added additional analysis statistics.\n\n- [Addons] Added CUSUM+ support to Mathematica addon (PlotEvents in MosaicUtils.m)\n- [Addons] Mathematica queries are *optionally* handled through an external Python script to improve performance.\n- [Addons] Added an option to limit PlotEvents in Mathematica addon to N events.\n\n- Known Issues: See #8, #10, #40, #63 and #69.\n\n**v1.2**\n\n- Added support for arbitrary binary file formats (#33)\n- [GUI] Included binary file support.\n- Documentation updates and bug fixes.\n- *Known Issues:* See #8 and #10.\n\n**v1.1**\n\n- [Addons] IGOR support.\n- PyPi package automatically installs MOSAIC dependencies.\n- Miscellaneous bug fixes.\n- *Known Issues:* See #8 and #10.\n\n**v1.0**\n\n- Fixed a bug in multistate code that constrained the RC constant resulting in systematic fitting errors (pull request #25).\n- Updated multistate to include a separate RC constant for each state, to be consistent with functional form in Balijepalli et al., ACS Nano 2014.\n- Misc bug fixes in tsvTrajIO parsing.\n- The number of states is saved to the MDIO DB for multistate analysis (issue #26).\n- Created a new package on PyPI (mosaic-nist) to allow installation with setuptools.\n- [GUI] Updated help link to point to Sphinx documentation on Github.\n- *Known Issues:* See #8 and #10 \n\n**v1.0b3.2**\n\n- [GUI] Misc bug fixes\n- [Addons] Added code to import MOSAIC output into Matlab (pull requests #18 and #20)\n- [Addons] Updated Mathematica addons to automatically decode multi-state data.\n- Resolves issues #16 and #22\n\n**v1.0b3.1**\n\n- [GUI] Added multiState support to mosaicgui.\n- Analysis information such as alogirthms used, data type, etc. are now stored within a MDIO database.\n- [GUI] Autocomplete in mosaicgui only suggests database columns that are valid when used in a query.\n- Reorganized Mathematica addon code.\n\n\n**v1.0b3**\n\n- Fixed a bug that prevented events longer than ~700 data points from being correctly analyzed.\n- Fixed a problem that prevented event data from being correctly padded before analysis.\n- Resolves #2. TrajIO settings are now read in from the settings file.\n- [GUI] Resolves #3. Threshold entry box in GUI becomes nonresponsive when meanOpenCurr is negative.\n- [GUI] Resolves #4. Analysis fails when using wavletDenioseFilter from GUI.\n- [GUI] Histogram in BlockDepthViewer window can be saved to a CSV file from the File Menu.\n- Analysis log is saved to the MDIO database.\n- [GUI] ConsoleLogViwer displays the analysis log saved in the MDIO database.\n- [GUI] Added a new dialog that displays an experimental feature warning wavelet-based denoising is selected.\n- Updated error codes reported in database to be more descriptive of the failure.\n- Improved and expanded unit testing framework.\n- Moved installation and testing to setuptools.\n\n\n**v1.0b2**\n\n- [GUI] Fixed threshold update error from 1.0b1.\n- Considerably improved automatic open channel state detection.\n- The default settings string is now included within the source code.\n- Implemented new top-level class ConvertToCSV that allows conversion of data read by any TrajIO object to comma separated files.\n- Updated build system and unit testing framework.\n- [GUI] Misc UI updates.\n\n\n**v1.0b1**\n\n- [GUI] Added a menu option to save a settings file prior to starting the analysis.\n- [GUI] Current threshold is now defined by an ionic current. The trajectory viewer displays the deviation of the threshold from the mean current.\n- 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.\n- When an analysis file is loaded, widgets in the main window remain enabled. This allows starting a new analysis run with the current settings.\n- [GUI] Implemented an analysis log viewer that displays the event processing log.\n- [GUI] Initial commit of wavelets based peak detection in blockdepthview.\n- [GUI] Added all points histogram to trajectory viewer. \n- *Known Issues:* Selecting automatic baseline detection can sometimes cause the threshold in the trajectory viewer to change. 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