CellOrganizer for Singularity¶
About CellOrganizer for Singularity¶
Singularity enables users to have full control of their environment. Singularity containers can be used to package entire scientific workflows, software and libraries, and even data.
CellOrganizer for Singularity is an image with compiled binaries from CellOrganizer functions
img2slml, the top-level function to train generative models of cells, and
slml2img, the top-level function to generate simulated instances from a trained generative model.
slml2info, the top-level function to generate a report from information extracted from a single generative model.
slml2report, the top-level function to generate a report from comparing generative models.
slml2slml, the top-level function to combine models into a single model file.
Installing CellOrganizer for Singularity¶
About Singularity¶
Singularity performs operating-system-level virtualization. To learn about Singularity and how to use it, click here
Setup¶
The following instructions describe
How to install Singularity, the virtualization engine that will run the container
How to download the latest Cellorganizer image
How to start a shell container from the Singularity image
How to run some of the demos included in the container
Source Code¶
The source code to build the Singularity image can be found at here.
For convenience, the Singularity image can be found at CellOrganizer.
Installing Singularity¶
Before downloading the image, you need to install Singularity. Installing Singularity is beyond the scope of this document.
To follow the official instructions to install Singularity, click here.
Download the repository and build the image using Singularity
Open terminal and enter the commands:
git clone https://github.com/icaoberg/singularity-cellorganizer
cd singularity-cellorganizer
bash ./script.sh .
Download the most recent image using Singularity command line (Recommended)
Open terminal and enter the command:
singularity pull shub://murphygroup/singularity-cellorganizer
Pulling the image from Singularity Hub should produce output similar to
Once the download is complete, you can confirm the image was downloaded by listing the singularity images of the repository:
ls murphygroup-singularity-cellorganizer-master-latest.simg
Demos¶
There are several demos included within the CellOrganizer software bundle. These demos are intended to illustrate CellOrganizer’s functionality, and should be used to familiarize the user with the input/output format of various top-level functions such as img2slml and slml2img. Certains demos have been deprecated and will be removed in future versions of CellOrganizer.
Demo |
Training |
Synthesis |
Other |
Deprecated |
|---|---|---|---|---|
demo2D00 |
True |
|||
demo2D01 |
True |
|||
demo2D02 |
True |
|||
demo2D03 |
True |
X |
||
demo2D04 |
True |
|||
demo2D05 |
True |
|||
demo2D06 |
True |
|||
demo2D07 |
True |
|||
demo2D08 |
True |
|||
demo2D09 |
True |
|||
demo3D00 |
True |
|||
demo3D01 |
True |
|||
demo3D04 |
True |
|||
demo3D05 |
True |
|||
demo3D06 |
True |
X |
||
demo3D07 |
True |
|||
demo3D08 |
True |
|||
demo3D09 |
True |
|||
demo3D10 |
True |
|||
demo3D11 |
True |
|||
demo3D12 |
True |
|||
demo3D15 |
True |
|||
demo3D17 |
True |
|||
demo3D19 |
(True) |
Report |
||
demo3D20 |
(True) |
Plot |
||
demo3D25 |
True |
|||
demo3D29 |
(True) |
Info |
||
demo3D34 |
True |
|||
demo3D35 |
(True) |
Info |
||
demo3D42 |
True |
|||
demo3D44 |
True |
|||
demo3D47 |
Model |
|||
demo3D48 |
True |
|||
demo3D50 |
True |
|||
demo3D51 |
(True) |
Plot |
||
demo3D52 |
True |
|||
demo3D53 |
True |
|||
demo3D55 |
(True) |
Plot |
Running CellOrganizer for Singularity¶
List all applications in the cellorganizer-singularity image¶
To list the CellOrganizer functions included in the image, open Terminal and enter the command:
singularity apps singularity-cellorganizer/murphygroup-singularity-cellorganizer-master-latest.simg
This will display these functions
img2slml
slml2img
slml2info
slml2report
slml2slml
Run a demo that invokes img2slml¶
An example of a demo that trains a generative model from a series of .tif image files is demo2D01. To run this demo, change your current directory to ~/singularity-cellorganizer/demos/2D/demo2D01 by entering:
cd demos/2D/demo2D01
You should find the shell script demo2D01.sh. To run the demo enter the command:
singularity run -a img2slml ../../../murphygroup-singularity-cellorganizer-master-latest.simg demo2D01.sh
The ‘-a’ flag allows us to specify the function binary that we will use in the script. This demo will save a folder param containing .mat files as well as a .mat file lamp2.mat to the same directory (~/singularity-cellorganizer/demos/2D/demo2D01). These .mat files contain information characterizing the trained generative model.
Running the demo in the container should produce results similar to
Run a demo that invokes slml2img¶
An example of a demo that produces simulated images from a trained generative model is demo2D02. To run this demo, change your current directory to /home/singularity-cellorganizer/demos/2D/demo2D02 by entering from your home directory:
cd demos/2D/demo2D02
You should find the shell script demo2D02.sh. To run the demo, enter the command:
singularity run -a slml2img ../../../murphygroup-singularity-cellorganizer-master-latest.simg demo2D02.sh
This demo will save a folder img containing these simulated images to the same directory.
Run custom script that invokes img2slml¶
An example running custom function parameters for img2slml stored within a .txt file. Within this directory (i.e. /path/to/input.txt), you can run the command:
singularity run -a img2slml ~/singularity-cellorganizer/murphygroup-singularity-cellorganizer-master-latest.simg img2slml input.txt