sacdallago / mecu

TPCA data analysis tool

MECU

Protein, Protein-Protein and Complex Webpage

Getting Started

1. docker-compose up -d (to just run the app)

Prerequisites

• npm: 6.4.1
• node: v8.11.3
• psql: 10.3

Installing

Check Prerequisites

1. pull the repo
2. npm install
3. npm run start

Example private/config.js

Consists of the configuration options to get the app running.

Default config.js if private/config.js does not exist:

module.exports = {
    "database" : {
        "username": process.env.databaseuser,
        "password": process.env.databasepassword,
        "port": process.env.databaseport || `5432`,
        "uri": process.env.databaseuri || `localhost`,
        "collection": process.env.databasecollection || `mecu`,
        "logging": process.env.databaselogging || false
    },
    "passport" : {
        "google" : {
            "clientId": process.env.googleclientid,
            "clientSecret": process.env.googleclientsecret
        }
    },
    "application" : {
        "hostname" : process.env.applicationhostname,
        "protocol": process.env.applicationprotocol,
        "port": process.env.applicationport || `3000`
    },
    "analytics" : {
        "google" : {
            "trackingId": process.env.googletrackingid
        }
    },
    "sessionSecret" : process.env.sessionsecret
};

Overwrite these environment-parameters when starting the docker container.

Deployment

TODO

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

• Christian Dallago - Initial work
• Klaus Niedermair - Continues work

See also the list of contributors who participated in this project.

License

TODO

Acknowledgments

• Hat tip to anyone whose code was used
• Inspiration
• etc

Additional

UML Diagram

Upload Experiment format:

Current

.txt file accepted format (!! table is only for better visualization !!):

Header	Accession	Description	GeneName	Peptides	PSMs	AAs	MW.kDA	pI	QuantifyingPSMs	T37	T40	T43	T46	T49	T52	T55	T58	T61	T64
Example Line	A0A023T672	RNA-binding protein 8A OS=Mus musculus GN=RBM8 PE=1 SV=1	RBM8	10	32	174	19.877	5.72	11	1.000	0.958	0.976	0.922	8.100	0.830	0.612	0.386	0.284	0.256

Lines are one dataset (tab spaced). Header line is included in the file.