:chart: SIMON is powerful, flexible, open-source and easy to use machine learning knowledge discovery platform :computer:
PANDORA
is a comprehensive suite of advanced analytical tools designed to support a wide range of biomedical research applications.
PANDORA
uses advanced machine learning techniques, including clustering, t-SNE, PCA, UMAP, and interpretable machine learning models to enhance biomedical discovery. It supports multiclass outcomes, facilitating predictive modeling, biomarker discovery, and omics data analysis for systems biology.
PANDORA
can be installed using Docker, a pre-built version of the platform can be pulled from DockerHub. In order to run PANDORA
, users will first need to install Docker.
version 17.05
or later is required)Windows Power Shell
=> Click Start, type PowerShell, and then click Windows PowerSheldocker run --rm --detach --name genular --tty --interactive --env IS_DOCKER='true' --env TZ=Europe/London --oom-kill-disable --volume genular_frontend_latest:/var/www/genular/pandora --volume genular_backend_latest:/var/www/genular/pandora-backend --volume genular_data_latest:/mnt/usrdata --publish 3010:3010 --publish 3011:3011 --publish 3012:3012 --publish 3013:3013 genular/pandora:latest
PANDORA
will be downloaded and started, and it can be accessed via a web browser at http://localhost:3010
To ensure a clean re-installation of PANDORA, follow these steps to remove the existing Docker container, images, and volumes associated with PANDORA. This process will remove all data and settings related to the previous PANDORA installation.
Identify the names or IDs of your PANDORA container(s), volume(s), and image(s).
Use these commands to list entities:
docker ps
(for running) or docker ps -a
(for all)docker images
docker volume ls
(Or use Docker GUI)
## Stop and delete any old PANDORA Container
docker stop <ContainerName>
## Delete
docker rm <ContainerName>
## Check for any images and remove them if necessary
docker images
## Check for any volumes
docker volume ls
## Remove them as-well
docker volume rm genular_frontend_latest genular_backend_latest genular_data_latest
## Now you can proceed with clean installation
Contributions are very much welcome!
If you need any help, please use community forums.
fixes-xxx-issue
or add-xxx-feature
where xxx
is a short description of the changes or feature you are adding.PANDORA
master
branch. We’ll do a quick review and give you feedback.If you’d like to start a conversation feel free to e-mail us.
I would also like to hear from you if you find this project useful and helpful!
#genular
on freenode.net
(or use the web client).If you discover a security vulnerability within PANDORA
, please e-mail us. All security vulnerabilities will be promptly addressed. You are also welcome to open PR request.
Resource | Link |
---|---|
File an issue | https://github.com/genular/pandora/issues |
Blog | https://genular.org/blog/ |
https://twitter.com/genular |
For more information please check LICENCE
file.
PANDORA
can be used for research purposes, you should cite
the aforementioned papers in any resulting publication.
Adriana Tomic, Ivan Tomic, Yael Rosenberg-Hasson, Cornelia L. Dekker, Holden T. Maecker, Mark M. Davis.
SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses
http://www.jimmunol.org/content/early/2019/06/13/jimmunol.1900033.abstract
doi: 10.4049/jimmunol.1900033
Adriana Tomic, Ivan Tomic, Levi Waldron, Ludwig Geistlinger, Max Kuhn, Rachel L. Spreng, Lindsay C. Dahora, Kelly E. Seaton, Georgia Tomaras, Jennifer Hill, Niharika A. Duggal, Ross D. Pollock, Norman R. Lazarus, Stephen D.R. Harridge, Janet M. Lord, Purvesh Khatri, Andrew J. Pollard, Mark M. Davis.
SIMON: Open-Source Knowledge Discovery Platform
https://www.cell.com/patterns/fulltext/S2666-3899(20)30242-7
doi:10.1016/j.patter.2020.100178