FindSim package on PyPi

.travis.yml

@@ -13,4 +13,6 @@ before_script:
 
 script:
     - cp ./.travis/matplotlibrc .
-    - ./test.sh
+    - python -m pip install .
+    - python -m pip install pymoose --pre --upgrade # till we relase 3.2.0
+    - ./test.sh 

MANIFEST.in

@@ -0,0 +1 @@
+recursive-include . *.xml

README.md

@@ -14,99 +14,185 @@ provides a score that reports how closely the two match.
 # LICENSE
 This file and the files in this repository are licensed under GPL v3 or later.
 
-# Version
+# Install 
 
-Latest release is 1.1.0, which can be downloadable at  
-	https://github.com/BhallaLab/FindSim/archive/v1.1.0.zip  
-	https://github.com/BhallaLab/FindSim/archive/v1.1.0.tar.gz
+One can get `FindSim` using `python-pip`.
+
+To install last stable release (__NOTE__ This uses moose version 3.1.4 (outdated
+with this release))
+
+     $ pip install FindSim 
+
+Or, to install the nightly built,
+
+     $ pip install FinSim --pre   # recommended 
+
+Alternatively, you can download the source code and install it yourself.
+
+1. Install MOOSE which can be found here https://moose.ncbs.res.in/readthedocs/install/install.html  
+2. Install FindSim
+
+```
+git clone https://github.com/BhallaLab/FindSim
+cd FindSim
+python setup.py install  
+```
+
+After successful installation, two commands are available at your disposal
+`findsim` and `findsim_parallel`. To see the help message, pass `-h` option to
+either of these commands. For example, `findsim -h` will show you following
+message.
+
+```
+usage: findsim [-h] [-m MODEL] [-d DUMP_SUBSET] [-p PARAM_FILE] [-t] [-hp]
+               [-hs] [-o] [-s SCALE_PARAM SCALE_PARAM SCALE_PARAM]
+               [-settle_time SETTLE_TIME]
+               script
+
+FindSim argument parser This program loads a kinetic model, and runs it with
+the specified stimuli. The output is then compared with expected output
+specified in the same file, to generate a model score.
+
+positional arguments:
+  script                Required: filename of experiment spec, in tsv format.
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -m MODEL, --model MODEL
+                        Optional: model filename, .g or .xml
+  -d DUMP_SUBSET, --dump_subset DUMP_SUBSET
+                        Optional: dump selected subset of model into named
+                        file
+  -p PARAM_FILE, --param_file PARAM_FILE
+                        Optional: Generate file of tweakable params belonging
+                        to selected subset of model
+  -t, --tabulate_output
+                        Flag: Print table of plot values. Default is NOT to
+                        print table
+  -hp, --hide_plot      Hide plot output of simulation along with expected
+                        values. Default is to show plot.
+  -hs, --hide_subplots  Hide subplot output of simulation. By default the
+                        graphs include dotted lines to indicate individual
+                        quantities (e.g., states of a molecule) that are being
+                        summed to give a total response. This flag turns off
+                        just those dotted lines, while leaving the main plot
+                        intact.
+  -o, --optimize_elec   Optimize electrical computation. By default the
+                        electrical computation runs for the entire duration of
+                        the simulation. With this flag the system turns off
+                        the electrical engine except during the times when
+                        electrical stimuli are being given. This can be *much*
+                        faster.
+  -s SCALE_PARAM SCALE_PARAM SCALE_PARAM, --scale_param SCALE_PARAM SCALE_PARAM SCALE_PARAM
+                        Scale specified object.field by ratio.
+  -settle_time SETTLE_TIME, --settle_time SETTLE_TIME
+                        Run model for specified settle time and return dict of
+                        {path,conc}.
+
+```
 
+Command `findsim_parellel` is a helper utility: it runs multiple simulations
+using `findsim` in parellel.
 
-# Install 
-	To run FindSim script one needs to  
-		- Install MOOSE which can be found here  
-			https://moose.ncbs.res.in/readthedocs/install/install.html  
-		- Install FindSim:  
-			Clone the entire repository using  
-  				>git clone https://github.com/BhallaLab/FindSim 
-			or, clone specific branch such as "stable" using:
-				>git clone -b <branch-name> https://github.com/BhallaLab/FindSim
-
-=============================================================================
-# File organization:
-	FindSim/             				: project directory  
-	FindSim/stable					: Stable branch. Stable version of `develop` branch  
-	FindSim/Curated					: Folder contains FindSim worksheets to which the model is well fit.
-	FindSim/models					: Model files 
-	FindSim/findSim.py				: Main findSim script  
-	FindSim/runAllParallel.py			: Batch/parallel wrapper script.  
-	FindSim/FindSim-Exptworksheet.xlsx		: Template worksheet with inline help and units, for Microsoft Excel.  
-	FindSim/FindSim-Exptworksheet.ods		: Template worksheet with inline help and units, for Libre Office.  
-	FindSim/FindSim-Schema.xml 			: Schema for tsv files for worksheet.  
-	FindSim/README.md				: This file  
-
-=============================================================================
-# Quick start: 
-A. Run one of the example experiments on the default model, generating a graph to compare model to experiment:  
-	To run the script, run the command in python and `synSynth7.g` is the latest model that is tested out the worksheets.  
-  	>python findSim.py Curated/FindSim-Jain2009-Fig2B.tsv --model synSynth7.g  
-  				or  
-  	>python findSim.py Curated/FindSim-Jain2009-Fig2B.tsv  
-
-B. Batch run:  
-	-runAllParallel.py script runs the findSim program on all tsv files in the specified directory, computes their scores, and prints out basic stats of the scores. It can do this in parallel using Python's multiprocessing library.  
+# Quick start
+
+To run one of the example experiments on the default model (`synSynth7.g`) and generate a graph 
+to compare model to experiment.  
+
+```
+findsim Curated/FindSim-Jain2009-Fig2B.tsv  
+```
+
+You can also pass the model explicitly, 
+
+```
+findsim Curated/FindSim-Jain2009-Fig2B.tsv --model models/synSynth7.g  
+```
+
+
+## Batch run
+
+To findSim program on all tsv files in the specified directory, computes their
+scores, and prints out basic stats of the scores, you should use
+`findsim_parallel` command.
 
-	>python runAllParallel.py Curated -n 8  (run of the entire set of `Curated` experiments on 8 cores)  
-						or  
-	>python runAllParallel.py Directory (of tsv files) -n (Number of processes to spawn) --model (synSynth7.g)  
+```
+findsim_parellel Curated -n 8 
+```
+
+It will run the entire set of `Curated` experiments in parallel using 8
+independant processes (it will be effectively if your computer has at least 8
+cores). The value of `-n` should not be more than `N+1` where `N` is the number
+of processors on your system (use system utility `nproc` to see this number).
 
-C. Syntax help:  
-	>python findSim.py -h  
-	>python runAllParallel.py -h  
+More detailed invocation of this command looks like the following:
 
+```
+findsim_parallel path/to/tsv/files -n 6 --model synSynth7.g
+```
 
-=============================================================================
+# Repository organization
 
-Generating Figures for   
-"FindSim: a Framework for Integrating Neuronal Data and Signaling Models."  
-by  
-Nisha A. Viswan, G.V. HarshaRani, Melanie I. Stefan, Upinder S. Bhalla
-Front Neuroinform. 2018 Jun 26;12:38. doi: 10.3389/fninf.2018.00038. eCollection 2018.
+    FindSim/             		: project directory  
+    FindSim/stable			: Stable branch. Stable version of `develop` branch  
+    FindSim/Curated	   		: Folder contains FindSim worksheets to which the model is well fit.
+    FindSim/models			: Model files 
+    FindSim/findSim.py			: Main findSim script  
+    FindSim/runAllParallel.py		: Batch/parallel wrapper script.  
+    FindSim/FindSim-Exptworksheet.xlsx	: Template worksheet with inline help and units, for Microsoft Excel.  
+    FindSim/FindSim-Exptworksheet.ods	: Template worksheet with inline help and units, for Libre Office.  
+    FindSim/FindSim-Schema.xml 		: Schema for tsv files for worksheet.  
+    FindSim/README.md			: This file  
 
-All these are run using the development branch "stable"  
-Please change into the branch to run these.  
+# Extra
+
+Generating Figures for  __FindSim: a Framework for Integrating Neuronal Data
+and Signaling Models by  Nisha A. Viswan, G.V. HarshaRani, Melanie I. Stefan,
+Upinder S. Bhalla Front Neuroinform. 2018 Jun 26;12:38. doi:
+10.3389/fninf.2018.00038. eCollection 2018.__
+
+All these are run using the branch `release.1.1.0`. Please change into the
+branch to run these.
 
 Figure 6: bottom  
-python findSim.py Curated/FindSim-Jain2009_Fig4F.tsv --model models/synSynth7.g  
+    python findSim.py Curated/FindSim-Jain2009_Fig4F.tsv --model models/synSynth7.g  
 
 Figure 7B:  
-python findSim.py Curated/FindSim-Bhalla1999_fig2B.tsv --model models/synSynth7.g  
-python findSim.py Curated/FindSim-Gu2004_Fig3.tsv --model models/synSynth7.g  
+    python findSim.py Curated/FindSim-Bhalla1999_fig2B.tsv --model models/synSynth7.g  
+    python findSim.py Curated/FindSim-Gu2004_Fig3.tsv --model models/synSynth7.g  
 
 Figure 7C:  
-python findSim.py Curated/FindSim-Ji2010_fig1C_ERK_acute.tsv --model models/synSynth7.g  
+    python findSim.py Curated/FindSim-Ji2010_fig1C_ERK_acute.tsv --model models/synSynth7.g  
 
 Figure 7D:  
-python findSim.py Curated/FindSim-Bhalla1999_fig4C.tsv --model models/synSynth7.g  
+    python findSim.py Curated/FindSim-Bhalla1999_fig4C.tsv --model models/synSynth7.g  
+
 
-=============================================================================
 # Other resources
-Project is hosted at https://github.com/BhallaLab/FindSim
 
-The web template for experiment worksheet can be found here https://www.ncbs.res.in/faculty/bhalla-findsim/worksheet  
+- The web template for experiment worksheet can be found here
+https://www.ncbs.res.in/faculty/bhalla-findsim/worksheet  
+
+- The MOOSE site: http://moose.ncbs.res.in. MOOSE documentation:
+  http://moose.ncbs.res.in/readthedocs/install/index_install.html
 
-The MOOSE site: http://moose.ncbs.res.in  
+- Two papers were used as the initial basis for the models, and which in turn
+  refer to a large number of experimental studies for their data:
 
-MOOSE documentation: http://moose.ncbs.res.in/readthedocs/install/index_install.html  
+    1. Bhalla US., Iyengar R. Emergent properties of networks of biological signaling pathways. Science. 1999 Jan 15;283(5400):381-7.  
+    2. Jain P, and Bhalla, U.S. Signaling logic of activity-triggered dendritic protein synthesis: an mTOR gate but not a feedback switch. PLoS Comput Biol. 2009 Feb;5(2):e1000287. Epub 2009 Feb 13  
 
-Two papers were used as the initial basis for the models, and which in turn
-refer to a large number of experimental studies for their data:  
-	- Bhalla US., Iyengar R. Emergent properties of networks of biological signaling pathways. Science. 1999 Jan 15;283(5400):381-7.  
-	- Jain P, and Bhalla, U.S. Signaling logic of activity-triggered dendritic protein synthesis: an mTOR gate but not a feedback switch. PLoS Comput Biol. 2009 Feb;5(2):e1000287. Epub 2009 Feb 13  
+- Two more papers were used for some of the experiments
 
-Two further papers were used for some of the experiments:  
-	- Gu J, et al. Beta1,4-N-Acetylglucosaminyltransferase III down-regulates neurite outgrowth induced by costimulation of epidermal growth factor and integrins through the Ras/ERK signaling pathway in PC12 cells. Glycobiology. 2004 Feb;14(2):177-86. Epub 2003 Oct 23  
-	- Ji Y, et al. Acute and gradual increases in BDNF concentration elicit distinct signaling and functions in neurons. Nat Neurosci. 2010 Mar;13(3):302-9. doi: 10.1038/nn.2505. Epub 2010 Feb 21.  
+    1. Gu J, et al. Beta1,4-N-Acetylglucosaminyltransferase III down-regulates
+       neurite outgrowth induced by costimulation of epidermal growth factor and
+       integrins through the Ras/ERK signaling pathway in PC12 cells.
+       Glycobiology. 2004 Feb;14(2):177-86. Epub 2003 Oct 23
+    2. Ji Y, et al. Acute and gradual increases in BDNF concentration elicit
+       distinct signaling and functions in neurons. Nat Neurosci. 2010
+       Mar;13(3):302-9. doi: 10.1038/nn.2505. Epub 2010 Feb 21.
 
-DOQCS database, from which models were derived: http://doqcs.ncbs.res.in  
-	Sivakumaran S. et al. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.
-Bioinformatics. 2003. 19(3):408–415
+- DOQCS database, from which models were derived: http://doqcs.ncbs.res.in
+  __Sivakumaran S. et al. The Database of Quantitative Cellular Signaling:
+  management and analysis of chemical kinetic models of signaling networks.
+  Bioinformatics. 2003. 19(3):408–415__

TestTSV/fepsp.tsv

@@ -0,0 +1,80 @@
+Experiment metadata		
+transcriber	Upi	
+organization	NCBS	
+emailId	[email protected]	
+exptSource	None
+citationId	None
+authors	None
+journal	None. This is a purely fictional _experiment_ for the purposes of testing findSim
+
+
+Experiment context		
+exptType	TimeSeries	
+species	rat	
+cell-types	hippocampal CA1 pyramidal neuron	
+temperature (Celsius)	30	
+Include	all	
+details		
+notes	HFS, LTP	
+
+Stimuli		
+compartment	dend	
+timeUnits	sec	
+quantityUnits	Hz	
+entities	synInput	
+field	rate	
+Data		
+Time	Value	
+0	0	
+10	100
+11	0	
+
+Stimuli		
+compartment	dend	
+timeUnits	sec	
+quantityUnits	ratio	
+entities	synapse	
+field	weight	
+Data		
+Time	Value	
+0	1	
+10	1	
+11	0.4	
+
+
+Readouts		
+timeUnits	sec	
+quantityUnits	mV	
+useXlog	FALSE	
+useYlog	FALSE	
+ratioReferenceTime	1	
+ratioReferenceEntity	soma	
+entities	soma	
+field	fEPSP_peak	
+useNormalization	False	
+Data		
+Time	Value	stderr
+6	0.15	0
+8	0.15	0
+15	0.4	0
+16	0.45	0
+17	0.5	0
+18	0.55	0
+20	0.6	0
+
+Model mapping		
+modelSource	internal	
+fileName	models/plastic8.py	
+citationId		
+citation		
+authors		
+modelSubset	all	
+modelLookup	soma:elec/soma,synInput:elec/head0/glu/sh/synapse/synInput,synapse:elec/head0/glu/sh/synapse	
+scoringFormula	abs((expt-sim)/(datarange+1e-9))	
+solver	none	
+notes		
+# Monitor response with a low stimulus amplitude/weight with initial 
+# test pulses 4 and 8 sec. Then give a 100Hz synaptic input at t = 10-11s.
+# Then monitor response at 15, 20 s.
+
+

__main__.py

@@ -0,0 +1,23 @@
+"""__main__.py: 
+
+Entry point for this package.
+"""
+
+__author__           = "Dilawar Singh"
+__copyright__        = "Copyright 2017-, Dilawar Singh"
+__version__          = "1.0.0"
+__maintainer__       = "Dilawar Singh"
+__email__            = "[email protected]"
+__status__           = "Development"
+
+
+def run():
+    from FindSim import findSim
+    findSim.main()
+
+def run_parallel():
+    from FindSim import runAllParallel
+    runAllParallel.main()
+
+if __name__ == '__main__':
+    run()