# ACE Configurator for ELISpot
ACE facilitates (1) generation of ELISpot configurations (peptide-pool assignments)
using a deep learning approach to cluster similar peptides and (2) deconvolution
of pool spot counts for identification of immunogenic peptides.
[](https://github.com/pirl-unc/ace/actions/workflows/main.yml)
[](https://opensource.org/licenses/Apache-2.0)
## 01. Installation
### 01-1. Standalone Graphical User Interface (Recommended)
Please note that the ACE GUI software will take a long time to load (~30 seconds :coffee:).
We also recommend that you have [Google Chrome](https://www.google.com/chrome/) installed on your machine.
| Operating System | Link | Version |
|------------------|----------------------------------------------------------------------------------------------------------|-------------------|
| Mac | [Download](https://github.com/pirl-unc/ace/releases/download/v0.1.1.0/ace-elispot-0.1.1.0-mac.zip) | v0.1.1.0 (latest) |
| Windows 10 | [Download](https://github.com/pirl-unc/ace/releases/download/v0.1.1.0/ace-elispot-0.1.1.0-windows10.zip) | v0.1.1.0 (latest) |
For Windows versions, first unzip the file and look for an application file called `ACE` inside the unzipped foler.
Previous versions of ACE are available [here](https://github.com/pirl-unc/ace/releases).
### 01-2. Python Package
ACE is available on [PyPI](https://pypi.org/project/ace-elispot/)
```
pip install ace-elispot
```
You can also download a specific version of ACE from [here](https://github.com/pirl-unc/ace/releases).<br/>
Subsequently install the ACE package using pip:
```
pip install ace-elispot-<version>.tar.gz
```
#### Dependencies
* python3 (>= 3.10)
* pandas (>=1.5.2)
* numpy (>=1.23.1)
* ortools (9.3.10497)
* torch
* transformers (==4.30.2)
* scikit-learn
* openpyxl
* golfy (>=2.5.0)
* levenshtein
## 02. Usage
ACE is available as a command-line interface after you install the python package:
```
usage: ace [-h] [--version] {generate,deconvolve,verify} ...
ACE Configurator for ELISpot.
positional arguments:
{generate,deconvolve,verify}
ACE sub-commands.
generate Generates an ELISpot experiment configuration.
deconvolve Deconvolve hit peptide IDs given read-outs from an ELISpot experiment.
verify Verifies whether an ELISpot assignment satisfies all ACE constraints.
options:
-h, --help show this help message and exit
-v, --version show program version number and exit
```
Read the full documentation on the python package at https://pirl-unc.github.io/ace/
## 03. Citation
If you use ACE in a publication, please cite our
[preprint](https://www.biorxiv.org/content/10.1101/2023.09.02.554864v1) describing ACE.
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"description": "# ACE Configurator for ELISpot\n\nACE facilitates (1) generation of ELISpot configurations (peptide-pool assignments) \nusing a deep learning approach to cluster similar peptides and (2) deconvolution \nof pool spot counts for identification of immunogenic peptides.\n\n[](https://github.com/pirl-unc/ace/actions/workflows/main.yml)\n[](https://opensource.org/licenses/Apache-2.0)\n\n## 01. Installation\n\n### 01-1. Standalone Graphical User Interface (Recommended)\n\nPlease note that the ACE GUI software will take a long time to load (~30 seconds :coffee:). \nWe also recommend that you have [Google Chrome](https://www.google.com/chrome/) installed on your machine.\n\n| Operating System | Link | Version |\n|------------------|----------------------------------------------------------------------------------------------------------|-------------------|\n| Mac | [Download](https://github.com/pirl-unc/ace/releases/download/v0.1.1.0/ace-elispot-0.1.1.0-mac.zip) | v0.1.1.0 (latest) | \n| Windows 10 | [Download](https://github.com/pirl-unc/ace/releases/download/v0.1.1.0/ace-elispot-0.1.1.0-windows10.zip) | v0.1.1.0 (latest) |\n\nFor Windows versions, first unzip the file and look for an application file called `ACE` inside the unzipped foler.\nPrevious versions of ACE are available [here](https://github.com/pirl-unc/ace/releases).\n\n### 01-2. Python Package \n\nACE is available on [PyPI](https://pypi.org/project/ace-elispot/)\n\n```\npip install ace-elispot\n```\n\nYou can also download a specific version of ACE from [here](https://github.com/pirl-unc/ace/releases).<br/>\nSubsequently install the ACE package using pip:\n\n```\npip install ace-elispot-<version>.tar.gz\n```\n\n#### Dependencies\n\n* python3 (>= 3.10)\n* pandas (>=1.5.2)\n* numpy (>=1.23.1)\n* ortools (9.3.10497)\n* torch\n* transformers (==4.30.2)\n* scikit-learn\n* openpyxl\n* golfy (>=2.5.0) \n* levenshtein\n\n## 02. Usage\n\nACE is available as a command-line interface after you install the python package:\n\n```\nusage: ace [-h] [--version] {generate,deconvolve,verify} ...\n\nACE Configurator for ELISpot.\n\npositional arguments:\n {generate,deconvolve,verify}\n ACE sub-commands.\n generate Generates an ELISpot experiment configuration.\n deconvolve Deconvolve hit peptide IDs given read-outs from an ELISpot experiment.\n verify Verifies whether an ELISpot assignment satisfies all ACE constraints.\n\noptions:\n -h, --help show this help message and exit\n -v, --version show program version number and exit\n```\n\nRead the full documentation on the python package at https://pirl-unc.github.io/ace/\n\n## 03. Citation\n\nIf you use ACE in a publication, please cite our \n[preprint](https://www.biorxiv.org/content/10.1101/2023.09.02.554864v1) describing ACE.\n",
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